nausicaä
power of diversity comes from the limits of what we can know and thus what we can do. when circumstances move beyond what we can personally readily deal with, there is the need for collective diversity of experience and ability.
history is written by the victors: the effect of the push of the past on the fossil record
graham e. budd, richard p. mann 2018
doi.org/10.1111/evo.13593
The diversity of life through time shows some striking patterns. For example, the animals appear in the fossil record about 550 million years ago, in an enormous burst of diversification called the “Cambrian Explosion.” Many groups of organisms appear to originate like this, but later on in their evolutionary history, their rates of diversification and morphological change seem to slow down. These sorts of patterns can be seen both in the fossil record, and also in reconstructions of past diversity by looking at the relationships between living organisms, and they have given rise to a great deal of debate.
Do organisms have more evolutionary flexibility when they first evolve? Or do ecosystems get “filled up” as more species evolve, giving fewer opportunities for further diversification later on? In their new paper, Graham Budd and Richard Mann make the provocative argument that these patterns may be largely illusory, and that we would still expect to see them even if rates of evolutionary change stay the same on average through time.
Biologists and palaeontologists use statistical models called “birth-death models” to model how random events of speciation and extinction give rise to patterns of diversity. Just as one can roll a dice five times and get five sixes or none, the outcomes of these random models are very variable. These statistical fluctuations are particularly important at the origin of a group, when there are only a few species. It turns out that the only groups that survive this early period are those that happen to diversify quickly — all the others go extinct. As is it exactly those groups that go on to be the large successful groups we see living today, and that fill most of the fossil record, it follows that they are likely to show this rapid pattern of diversification at their origin — but only because they are a biased subset of all groups. Later in their history, when such groups are diverse, statistical fluctuations have much less effect, and therefore their rate of evolution appears to slows down to the background average.
As a result, the patterns we discover by analyzing such groups are not general features of evolution as a whole, but rather represent a remarkable bias that emerges by only studying groups we already know were successful. This bias, called “the push of the past,” has indeed been known about theoretically for about 25 years, but it has been almost completely ignored, probably because it was assumed to be negligible in size. However, Budd and Mann show that the effect is very large, and can in fact account for much of the variation we see in past diversity, especially when we combine it with the effects of the great “mass extinctions” such as the one that killed off the dinosaurs some 66 million years ago. Because the resulting patterns are an inevitable feature of the sorts of groups available for us to study, Budd and Mann argue, it follows that we cannot perceive any particular cause of them: they simply arise from statistical fluctuation.
The push of the past is an example of a much more general type of pattern called “survivorship bias” which can be seen in many other areas of life, for example in business start-ups and finance and the study of history. In all these cases, failure to recognize the bias can lead to highly misleading conclusions. Budd and Mann argue that the history of life itself is not immune to such effects, and that many traditional explanations for why diversity changes through time may need to be reconsidered
abstract Survivorship biases can generate remarkable apparent rate heterogeneities through time in otherwise homogeneous birth‐death models of phylogenies. They are a potential explanation for many striking patterns seen in the fossil record and molecular phylogenies. One such bias is the “push of the past”: clades that survived a substantial length of time are likely to have experienced a high rate of early diversification. This creates the illusion of a secular rate slow‐down through time that is, rather, a reversion to the mean. An extra effect increasing early rates of lineage generation is also seen in large clades. These biases are important but relatively neglected influences on many aspects of diversification patterns in the fossil record and elsewhere, such as diversification spikes after mass extinctions and at the origins of clades; they also influence rates of fossilization, changes in rates of phenotypic evolution and even molecular clocks. These inevitable features of surviving and/or large clades should thus not be generalized to the diversification process as a whole without additional study of small and extinct clades, and raise questions about many of the traditional explanations of the patterns seen in the fossil record.
selection for diversity
paradoxical survival: examining the parrondo effect across biology
kang hao cheong et al. 2019
doi.org/10.1002/bies.201900027
identified key connections between numerous seemingly disjointed works, culminating in an emergent pattern of nested recurrent mechanics that appear to span the entire biological gamut, from the smallest of spatial and temporal scales to the largest. The authors explained that the pivotal role the paradox plays in the shaping of living systems has become increasingly apparent, which points strongly towards its potential identity as a universal principle underlying biological diversity and persistence.
"Developments in Parrondo's paradox to date have revealed a potential unifying fundamental characteristic of life itself, more valuable to our understanding of nature than its individual components," said co-author Jin Ming Koh.
The picture that the authors paint of biological reality is a striking one. Their work suggests that the biosphere might be supported by countless layers of Parrondo?paradoxical effects, each ingesting inevitably losing strategies and producing enhanced outcomes at a slightly larger temporal or spatial scale for the layer above, in what may be visualized as a fractal?like recurrent pattern. Such an imagery offers a fresh perspective on our view of nature and of ourselves.
The trio is now attempting to analyze the detailed structure of these mechanisms, which might span from hugely macroscopic spatial scales of entire ecosystems to the molecular inner workings of cells, and from the million?year timescales of evolution to sub-microsecond genetic and molecular processes. "Every cell, organism and species, and species assemblage and ecosystem, is necessarily mortal, yet the biosphere persists," said Assistant Professor Cheong.
abstract Parrondo's paradox, in which losing strategies can be combined to produce winning outcomes, has received much attention in mathematics and the physical sciences; a plethora of exciting applications has also been found in biology at an astounding pace. In this review paper, the authors examine a large range of recent developments of Parrondo's paradox in biology, across ecology and evolution, genetics, social and behavioral systems, cellular processes, and disease. Intriguing connections between numerous works are identified and analyzed, culminating in an emergent pattern of nested recurrent mechanics that appear to span the entire biological gamut, from the smallest of spatial and temporal scales to the largest—from the subcellular to the complete biosphere. In analyzing the macro perspective, the pivotal role that the paradox plays in the shaping of biological life becomes apparent, and its identity as a potential universal principle underlying biological diversity and persistence is uncovered.
coevolution maintains diversity in the stochastic ‘kill the winner’ model
chi xue and nigel goldenfeld 2017
doi.org/10.1103/physrevlett.119.268101
When many species are competing for the same finite resource, a theory called competitive exclusion suggests one species will outperform the others and drive them to extinction, limiting biodiversity. But this isn’t what we observe in nature. Theoretical models of population dynamics have not presented a fully satisfactory explanation for what has come to be known as the diversity paradox.
Now researchers at the Carl R. Woese Institute for Genomic Biology at the University of Illinois at Urbana-Champaign have shed new light on this fundamental question in ecology, by improving a popular proposed scenario for diversity known as “Kill the Winner.” Chi Xue and Nigel Goldenfeld, supported by the NASA Astrobiology Institute for Universal Biology, which Goldenfeld directs, approached the diversity paradox from the perspective of non-equilibrium statistical mechanics.
Goldenfeld and Xue developed a stochastic model that accounts for multiple factors observed in ecosystems, including competition among species and simultaneous predation on the competing species. Using bacteria and their host-specific viruses as an example, the researchers showed that as the bacteria evolve defenses against the virus, the virus population also evolves to combat the bacteria. This “arms race” leads to a diverse population of both and to boom-bust cycles when a particular species dominates the ecosystem then collapses — the so-called “Kill the Winner” phenomenon. This coevolutionary arms race is sufficient to yield a possible solution to the diversity paradox.
Goldenfeld and Xue looked at a classic example of the diversity paradox from marine biology, the paradox of the plankton. In observed marine ecosystems, many plankton species and bacterial strains coexist and have high diversity.
Goldenfeld explains, “There any many tentative hypotheses to solve the paradox. The one we are interested in is the ‘Kill the Winner’ (KtW) hypothesis. In a nutshell, it says that the problem with the diversity paradox is the assumption of a steady state. A real ecosystem is never in a steady state, but undergoes population fluctuations due to the interplay between predators and prey.
“Take for example competing strains of bacteria, each of which is prey to a host-specific virus. In this scenario, as soon as a particular bacterial species starts to dominate in the ecosystem, the virus (or bacterial phage) that preys preferentially on that host will have plenty of targets, and so will proliferate, culling the host-bacteria population. After this viral attack, another bacterial species may emerge as the most abundant for a time, until its population is likewise diminished by its bacterial phage. This host-specific predation maintains the coexistence of competing species by preventing a winner from emerging, so that in a sense, species go through boom-bust cycles of abundance.”
“Moreover,” Xue adds, “in a system where plankton compete with bacteria for a resource, a protozoan group that hunts down all bacterial strains non-selectively suppresses the population of the entire bacterial community and thus leaves space for plankton species to survive. The KtW idea works on two layers here: the coexistence of bacteria and plankton as the first layer, and the coexistence of bacterial strains as the second. It’s a very appealing theory and has become one of the most influential ideas in marine ecology.”
However, the original formulation of KtW required a widely-used technical simplification. Xue points out, “The original KtW model did not account for spatial variations or any fluctuation effects, and was formulated in terms of continuous biomass concentrations and deterministic ordinary differential equations. The significance of this is that it incorrectly accounts for what happens when viruses attack bacteria, for example. In this formulation, the population of bacteria in a region of space can get smaller and smaller during viral predation, but never reaches zero. In a sense, the theory allows the number of bacteria to be a fraction, when in reality it must be an integer like zero, one, two, etc. So the theory under-estimates what happens during viral attack, and in particular cannot capture extinction.”
To go beyond the simplified model, Xue and Goldenfeld developed a stochastic model of bacteria-virus interactions that could describe population fluctuations, in order to see whether the KtW scenario really emerged from calculations more detailed than those undertaken previously.
Their model described the outcome of the bacteria-virus encounters using a method similar to that used in statistical thermodynamics to describe colliding atoms in a gas. Just as one can compute the properties of gases — such as sound waves and thermal effects — from understanding the atomic collisions, Xue and Goldenfeld used statistical mechanics methods to compute the behavior of populations from understanding bacteria-virus encounters.
Goldenfeld explained that the KtW scenario was not put into their calculations by hand. Their goal was to model the bacteria-virus interactions at an individual level to see if KtW emerged. However, from their simulations, Xue and
Goldenfeld were surprised to find that the species in their model didn’t even co-exist let alone exhibit KtW dynamics — they were driven to extinction!
Xue noted, “The breakdown of the original KtW model in the presence of stochasticity was a surprise to us. Stochasticity represents something closer to the randomness of nature. We hadn’t expected this very reasonable model to fail.” The researchers realized that there is another way in which ecosystems are not in a steady state, separate from the population fluctuations that they had attempted to model.
Real ecosystems are also evolving. Indeed, when they also included coevolution into their model, the model recapitulated the biodiversity observed in nature.
Goldenfeld describes, “In the case of the ecosystem in our marine biology example, there is coevolution of each bacteria strain and its host-specific virus as they compete in what can be described as an arms race. As the bacteria find ways to evade the attack of viruses, the viruses evolve to counter the new defenses. In this coevolving KtW model, the arms race is driven by mutations that arise in both bacterial and viral strains.”
Xue adds, this idea has support from genomics. “Researchers, especially in marine microbial ecology, have found that different bacterial strains show strong variation in regions of their genomes that are believed to be associated with phage resistance. This observation links the diversity of bacterial genomes to the virus predation and agreed with our coevolving KtW framework.”
“And the extinction issue can now be avoided,” Xue continues. “When a strain goes extinct, it, or something close to it, can still reemerge later as a mutant from another strain. This co-evolutionary mechanism acts in addition to spatial heterogeneity, which also helps diversity: if a particular strain becomes extinct in a particular region of space, it is possible that it can be re-seeded by the migration or diffusion of that strain from somewhere else. Thus, at long time scales, the diversity of the system is maintained.”
Goldenfeld says it was satisfying to see how the use of stochastic modeling enabled the team to include the already well-known coevolutionary arms race within a simple model, from which emerged Kill-the-Winner dynamics.
“The KtW model is a profoundly important idea,” he asserts, “but it needs to be supplemented by additional factors such as co-evolution and spatial variation. Our work demonstrates the breakdown of the simplest but most widely used version of the theory and presents a way to restore its explanatory power. It’s exciting that our theoretical model not only captured the diversity that we were trying to explain, but also is consistent with a seemingly disconnected strand of data from the field of genomics, thus providing a satisfying narrative that works from the level of ecosystems down to the genome itself.”
Goldenfeld and Xue plan to pursue this line of inquiry further. They speculate that diversity is generally related to how far away an ecosystem is from equilibrium. Future work will attempt to quantify the relationship between diversity and the distance from equilibrium.
The results of this theoretical study are in principle testable in experiments:
“I am most excited about the possibility that the coevolving KtW model can be tested by conducting experiments with coevolving bacteria and phages,” Xue comments. “The short reproduction time and high mutation frequency make microbial systems a good candidate to test models in which evolutionary and ecological dynamics happen at the same time scale.”
The researchers’ interest in this problem arose from a seemingly different area of science. Goldenfeld explains that this work has implications for open questions in astrobiology and for detecting life on extraterrestrial worlds.
“The diversity of ecosystems, especially microbial ones, is a key factor in understanding the likelihood that life can gain enough of a toehold in a planetary environment not only to survive, but also to be detectable. With the groundbreaking discovery by the Cassini mission of global oceans of liquid water on Europa (moon of Jupiter) and Enceladus (moon of Saturn), marine microbial ecology is poised to become an even more active component of astrobiology. Understanding the fundamental mechanisms driving biodiversity — a pervasive feature of terrestrial ecosystems — will help us predict the observability of non-terrestrial life on worlds that will be within reach of our probes in the coming decades.”
abstract The “kill the winner” hypothesis is an attempt to address the problem of diversity in biology. It argues that host-specific predators control the population of each prey, preventing a winner from emerging and thus maintaining the coexistence of all species in the system. We develop a stochastic model for the kill the winner paradigm and show that the stable coexistence state of the deterministic kill the winner model is destroyed by demographic stochasticity, through a cascade of extinction events. We formulate an individual-level stochastic model in which predator-prey coevolution promotes the high diversity of the ecosystem by generating a persistent population flux of species.
social genes are selection hotspots in kin groups of a soil microbe
sébastien wielgoss et al. 2019
doi.org/10.1126/science.aar4416
The microbe Myxococcus xanthus is particularly cooperative. Found in soils all over the world, it has been used by scientists as a model organism to study microbial development and cooperation. The cells of this predatory bacterium form cooperative groups that swarm together and hunt other microorganisms within the soil. In order to move as a group, they secrete lubricating substances and cast out appendages that attach to the surrounding surface and other cells, moving them forward as they retract these appendages. When food becomes scarce, thousands of these bacteria aggregate into a fruiting body and form resting spores, allowing them to withstand hunger and drought.
Closely related, yet very different
Researchers previously had theoretical reasons to expect that cooperative groups of microbes in nature might generally be socially homogeneous, as this would prevent conflict between cells from undermining cooperation. Genetically distinct individuals from different groups have been shown to often avoid, obstruct, and even combat each other. "Our knowledge about the genetic composition within cooperative groups of these social bacteria in nature used to be very limited," says Sébastien Wielgoss, a lecturer in the research group of Professor Gregory Velicer, Institute for Integrative Biology, ETH Zurich.
With their colleagues, Wielgoss and Velicer have more closely examined the genetic relationships between members of the same M. xanthus fruiting body group in the soil. They used one of the largest collections of M. xanthus strains worldwide, kept by Velicer in his laboratory freezers.
In a study recently published in Science, the researchers used genetic analyses to show that while cooperative groups of the soil bacterium M. xanthus do consist of closely related cells, the number of genetic types and varieties of social behaviour found within individual fruiting-body groups are unexpectedly high. The researchers inferred that these collections of diversified cell lines can remain intact for hundreds of generations.
Selection on social genes
For their study, the researchers investigated groups of cells that descended recently from a common ancestor. Mutation formed various socially different, but closely related, cell lines within these groups, with lines differing in how fast they swarm or how many spores they produce within a fruiting body.
Some forms of diversity pose a threat to group productivity. For example, individual bacteria can exhibit "cheating" behaviour: they contribute little to the group while exploiting its other members and lowering group function. "However, behavioural studies with these same groups have not found such socially disruptive cheating," Wielgoss said. In contrast, while the majority of groups are highly genetically and socially diverse, the observed diversity does not appear to undermine cooperative functions at the group level.
The researchers attribute this high diversity of behavioural patterns to evolutionary selection that focuses on a small number of "social" genes that control the social habits of the bacteria. Mutations in these "selection hotspots" favoured by natural selection cause a variety of behavioural changes, yielding a diverse society of cells with varying levels of spore production and swarming speed. The researchers speculate that distinct lines in the same group likely also differ in their cooperative hunting abilities, although this was not tested in this study.
Wielgoss explained that natural selection may favour some combinations of diversified cell lines over other combinations or even over homogeneous groups: "Cell groups with a large behavioural repertoire may respond to environmental changes more effectively. They may often be more evolutionarily successful than homogeneous groups of cells that all behave in the same way. 'Cultural diversity' appears to be rather frequent among bacterial social groups."
Understanding cell cooperation
Microorganisms are omnipresent. They fulfil important functions in our everyday lives: as helpers in our intestinal flora, as pathogens or as agents in food production. Many combine into cooperative groups of cells in nature, too. The researchers believe that these new insights into the genetic and behavioural properties of cooperative soil bacteria may help us to understand cooperation within other types of bacteria as well, including the important pathogen Pseudomonas aeruginosa that infects immuno-compromised patients and causes serious long-term infections.
abstract The composition of cooperative systems, including animal societies, organismal bodies, and microbial groups, reflects their past and shapes their future evolution. However, genomic diversity within many multiunit systems remains uncharacterized, limiting our ability to understand and compare their evolutionary character. We have analyzed genomic and social-phenotype variation among 120 natural isolates of the cooperative bacterium Myxococcus xanthus derived from six multicellular fruiting bodies. Each fruiting body was composed of multiple lineages radiating from a unique recent ancestor. Genomic evolution was concentrated in selection hotspots associated with evolutionary change in social phenotypes. Synonymous mutations indicated that kin lineages within the same fruiting body often first diverged from a common ancestor more than 100 generations ago. Thus, selection appears to promote endemic diversification of kin lineages that remain together over long histories of local interaction, thereby potentiating social coevolution.
adaptation of a chytrid parasite to its cyanobacterial host is hampered by host intraspecific diversity
ramsy agha et al. 2018
doi.org/10.3389/fmicb.2018.00921
experimental evidence of frequency-dependent selection on group behaviour
jonathan n. pruitt et al. 2019
doi.org/10.1038/s41559-019-0852-z
African social spider Stegodyphus dumicola (S. dumicola). While colonies of S. dumicola do not compete with one another face to face, a single plant may be home to several colonies, resulting in increased competition for flying prey.
Pruitt and his team travelled to two sites in southern Africa and created 'neighourhoods' or clusters of competing spider colonies with very different foraging strategies: some colonies were dominated by docile hunting societies while others were dominated by aggressive societies.
After comparing the aggressive and docile societies, researchers learned that whichever strategy was in the minority performed the best.
When aggressive societies dominated the landscape, they overexploited resources fueling an even greater need for prey to maintain their aggressive societal engines. In these conditions, docile societies flourished because they can subsist on less and outlasted their aggressive rivals.
When docile societies dominated, researchers were surprised to discover there was no relationship between resource intake and reproductive success, suggesting they operate well even with extremely low resources.
"The key here is there is a trade-off between the ability to domineer and monopolize resources from rivals and the ability to live off of little," says Pruitt. "No single strategy ever completely annihilates the opposing strategy, which is why we see various kinds of societal traits maintained through evolutionary time."
abstract Evolutionary ecologists often seek to identify the mechanisms maintaining intraspecific variation. In social animals, whole groups can exhibit between-group differences in their collective traits. We examined whether negative frequency-dependent selection (that is, a rare-type advantage) could help to maintain between-group variation. We engineered neighbourhoods of social spider colonies bearing bold or shy foraging phenotypes and monitored their fecundity in situ. We found that bold colonies enjoyed a rare-type advantage that is lost as the frequency of bold colonies in a neighbourhood increases. The success of shy colonies was not frequency dependent. These dynamics seem to be driven by a foraging advantage of bold colonies that is lost in bold neighbourhoods because prey become scarce, and shy colonies perform better than bold colonies under low-resource conditions. Thus, to understand selection on collective traits, it is insufficient to examine groups in isolation. The phenotypic environment in which groups reside and compete must also be considered.
sharper eyes see shyer lizards: collaboration with indigenous peoples can alter the outcomes of conservation research
georgia ward‐fear et al. 2019
doi.org/10.1111/conl.12643
Dr Georgia Ward-Fear, a conservation biologist and herpetologist (amphibians and reptiles), said this was the first published study to measure the scientific contribution that Indigenous peoples bring to a research project, beyond the moral or ethical value.
"This is of major importance for Indigenous peoples around the world," Dr Ward-Fear said. "Traditional owners often don't have a voice in science. This is a case study for Indigenous groups globally to hold up and say 'we deserve a voice' and 'we deserve input into research'."
James 'Birdy' Birch, a leading ranger from the Balanggarra Aboriginal Corporation in the Kimberley said: "The university-educated scientists have research tools, data and methods that work for them. But we have every-day lived experience. We have knowledge of the land and the animals passed down over thousands of years. If we put these skills together, it paints a clearer picture."
Working with traditional owners of the land
Dr Ward-Fear, from the School of Life and Environmental Sciences, and her team have been working in the Kimberley, a remote area of northern Western Australian. Her conservation work involves protecting large goannas from the devastating impacts of invasive, poisonous cane toads.
Over 18 months, teams made up of a Western scientist and an Indigenous ranger would set out at daybreak to find and capture the goannas -- which can grow up to 1.7 metres in length and weigh more than six kilograms. They fitted the lizards with radio transmitters and then released them and trained them to avoid eating the large toads. They did this by approaching the animal in the field, and feeding the goanna a small toad, large enough to make them sick but not kill them. This put the lizards off eating the toads once the invasion arrived.
The aversion training, developed with Emeritus Professor Rick Shine, has been hugely successful and is now being rolled out on a large scale via the Cane Toad Coalition, a consortium of scientists, government authorities, conservation groups and the Australian Research Council.
But Dr Ward-Fear said the success of the initial project would not have been possible without the input of the Balanggarra Rangers, who are traditional owners of the land.
"Working with Indigenous rangers, you get to see their unique skillsets. Once we showed that the trial worked, I was curious to see whether this contributed to the success of the study in a way we could quantify," Dr Ward-Fear said.
"Even though we worked in teams and had the same opportunity to spot the lizards, there were significant differences in the animals that the rangers spotted," Dr Ward-Fear said. "The rangers have amazing observation skills and ability to see animals in a landscape. They could see the shape of a goanna when they were not moving, were in the shade or dappled light or from much further away. The Western scientists tended to see animals that were closer, out in the open or moving."
Published today in Conservation Letters, the study found the Indigenous rangers were able to find and collect a subset of large varanid lizards (goannas) that Western scientists were unable to spot. Importantly, these lizards displayed different behavioural profiles throughout the study: they were more 'shy' than the bolder lizards foraging in broad daylight; and they also learned the aversion technique better than the braver lizards.
"These ranger-spotted animals responded better to the conservation technique and they actually drove the significant result of the study," Dr Ward-Fear said. "If we hadn't worked with rangers and we hadn't collected that subsample of animals then our results wouldn't have been significant."
Local knowledge
James 'Birdy' Birch is the head ranger with the Balanggarra Rangers. He said the rangers had unique skills to offer the scientists.
"We had access to country for a start," Mr Birch said. "We knew where the goannas were and we caught over 100 of them. We just had a keen eye. We could see them miles away.
"My rangers all grew up on this country hunting for goanna with their parents. It is knowledge passed down for thousands of years."
Mr Birch believes science can benefit from combining the two "ways of looking."
"You've got the Western way of looking with all the tools and the data, and you've got the Indigenous way of looking at things. Together, Western science and Indigenous knowledge, they complement each other. We've got our skills and you guys have got your skills, we can put them together and find out so much, we were amazed by the results."
Dr Ward-Fear said the scientific community already knows it is ethical to work with the traditional owners of the land. "But now we know there is ethical and scientific value in working together in meaningful collaborations," she said.
abstract Our ecological studies on large varanid lizards in a remote region of tropical Australia reveal a direct benefit to collaboration with local indigenous people. Although they worked together, in pairs, western scientists and indigenous rangers found lizards with different behavioral phenotypes (“personalities”). The resultant broader sampling of the lizard population enabled us to detect positive effects of a conservation management intervention. Those effects would not have been evident from the subset of animals collected by western scientists, and hence, involvement by researchers from both cultures critically affected our conclusions and paved the way for large‐scale deployment of a novel conservation initiative in Northern Australia.
adaptive individual variation in phenological responses to perceived predation levels
robin n. abbey-lee, niels j. dingemanse 2019
doi.org/10.1038/s41467-019-09138-5
Bold great tits lay their eggs earlier when under threat, the shy ones put it off. Such personality differences help maintain the biological variation essential for the survival of populations, as Ludwig-Maximilians-Universitaet (LMU) in Munich biologists have now shown.
Bird populations can adapt to environmental change, as revealed by their flexible choice of the optimal time for rearing their chicks. Thus high temperatures induce them to begin nest building and egg-laying early in the year. In colder years, they tend to postpone the whole business until later. Natural selection favors such behavioral adaptability -- provided that the required variation is available, i.e. genetic variants are present that confer 'phenotypic plasticity' on local populations. A study of great tits (Parus major), carried out by LMU behavioral biologist Niels Dingemanse and his doctoral student Robin Abbey-Lee, has now shown that this adaptability is in part attributable to differences in character and 'personality' between individuals. Their findings appear in the online journal Nature Communications.
In addition to ambient temperatures, the level of predation has an influence on the timing of nesting behavior, as fledglings are particularly vulnerable to attacks by birds of prey. The European sparrowhawk (Accipiter nisus) is a major predator of great tits. Sparrowhawks brood at a time when the new generation of tits is at the fledgling stage, which ensures that there will be plenty of food available for their young families. Conversely, great tits react to the hawks' presence by deferring breeding, in order to reduce the risk to their own offspring. As soon as they hear the call of the hunting sparrowhawk, they become markedly more alert and sing less often. "In previous studies, however, we found that not all birds display this reaction to the same degree," says Dingemanse. "Different individuals exhibit different personalities, and some are more explorative, daring and more aggressive than others."
Abbey-Lee and Dingemanse have now investigated whether these differences in character contribute to variation in the timing of breeding at the population level. During the breeding season -- from April to June -- the researchers exposed birds in a total of 12 tit populations to either the recorded call of the sparrowhawk or the song of the harmless blackbird.
The results showed, under these two conditions, character differences indeed had an impact on the timing of the breeding season. The more daring birds eagerly explore their local environment and normally breed late. But when confronted with an imminent threat -- implied by the apparent presence of actively hunting sparrowhawks -- they began breeding earlier than usual. The less valiant pairs behaved in exactly the opposite way. In the end, the two personality types achieved essentially equal levels of breeding success. The study's authors conclude from this that variation in character and personality does contribute to phenotypic plasticity in the timing of breeding periods in the population as a whole. "In this way, populations can also become more resilient in the face of anthropogenic alterations of their environments, such as climate change," Dingemanse points out.
abstract The adaptive evolution of timing of breeding (a component of phenology) in response to environmental change requires individual variation in phenotypic plasticity for selection to act upon. A major question is what processes generate this variation. Here we apply multi-year manipulations of perceived predation levels (PPL) in an avian predator-prey system, identifying phenotypic plasticity in phenology as a key component of alternative behavioral strategies with equal fitness payoffs. We show that under low-PPL, faster (versus slower) exploring birds breed late (versus early); the pattern is reversed under high-PPL, with breeding synchrony decreasing in conjunction. Timing of breeding affects reproductive success, yet behavioral types have equal fitness. The existence of alternative behavioral strategies thus explains variation in phenology and plasticity in reproductive behavior, which has implications for evolution in response to anthropogenic change.
transmissible cancer and the evolution of sex
frédéric thomas et al. 2019
doi.org/10.1371/journal.pbio.3000275
One of the greatest enigmas of evolutionary biology is that while sex is the dominant mode of reproduction among multicellular organisms, asexual reproduction appears much more efficient and less costly. However, in a study publishing on June 6 in the open-access journal PLOS Biology, researchers suggest that sexual reproduction is favored by selection because, unlike asexual reproduction, it not only provides important evolutionary advantages in constantly changing environments, but also prevents the invasion of transmissible cancer, or "cheater" cells.
Multicellular organisms are societies of cooperating clonal cells that emerged and evolved one billion years ago. A key point in the evolution of multicellular organisms was therefore the ability to prevent cheater cells from overexploiting the cooperative system; this evolutionary constraint favoured the emergence of the many known mechanisms that suppress cancer, notably the immune system. Whatever the efficiency of these mechanisms, a prerequisite of all these defences is the ability to recognize cheater cells from normal ones.
Not only did first multicellular organisms have to deal with their own cheater cells, they also had to evolve adaptations to prevent them being colonized by foreign malignant cells (i.e. infectious ones). Because asexual reproduction leads to identical ("clonal") organisms, this mode of reproduction is risky due to the possibility of being invaded by clonal infectious cell lineages (i.e. transmissible cancers). Conversely, sexual reproduction decreases the compatibility of contagious cancer cells with their hosts, limiting individual infection risk, as well as the risks of transmission between parent and offspring. Sexual reproduction also generates genetic variation that facilitates the detection of foreign cells, the first and critical step of immune protection.
Although relatively rare, transmissible cancers do exist (e.g. Tasmanian devils, dogs, bivalves), and increasing evidence suggests that most, if not all, malignant cells are potentially transmissible provided a suitable transmission route is offered. Given the ubiquity of cancer in multicellular organisms, in combination with the plethora of potential transmission routes, sexual reproduction may have been favoured as a less risky, more profitable option to produce viable offspring despite its associated costs.
The authors claim that to their knowledge, the proposed role of transmissible cheater cells as initiator and driver force underlying the evolution of sexual reproduction is a novel explanation, that will contribute to a paradigm shift in our understanding of evolution.
abstract The origin and subsequent maintenance of sex and recombination are among the most elusive and controversial problems in evolutionary biology. Here, we propose a novel hypothesis, suggesting that sexual reproduction not only evolved to reduce the negative effects of the accumulation of deleterious mutations and processes associated with pathogen and/or parasite resistance but also to prevent invasion by transmissible selfish neoplastic cheater cells, henceforth referred to as transmissible cancer cells. Sexual reproduction permits systematic change of the multicellular organism’s genotype and hence an enhanced detection of transmissible cancer cells by immune system. Given the omnipresence of oncogenic processes in multicellular organisms, together with the fact that transmissible cancer cells can have dramatic effects on their host fitness, our scenario suggests that the benefits of sex and concomitant recombination will be large and permanent, explaining why sexual reproduction is, despite its costs, the dominant mode of reproduction among eukaryotes.
cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks
jia zheng et al. 2019
doi.org/10.1126/science.aax1837
Genetic variation -- that is, accumulated mutations in the DNA -- is the fuel for all evolutionary change: the more genetic variation, the faster evolution works and the more possibilities for novel adaptive solutions.
But one kind of genetic variation -- hidden, or "cryptic," variation -- doesn't alter the appearance or behavior of an organism in its usual environment.
"It's an underappreciated kind of genetic variation," says corresponding author Andreas Wagner, an evolutionary biologist at the University of Zurich and external professor at the Santa Fe Institute, "and it plays an important role in evolution."
Previous work has shown that cryptic variation in natural populations promotes rapid evolutionary adaptation. But the underlying molecular mechanisms were unclear.
To explore those mechanisms, Wagner's team worked with populations of the gut bacterium E. coli that carried a plasmid with a gene for a yellow fluorescent protein (YFP). The team designed a two-stage experiment. In stage 1, they used mutagenic PCR to increase variation in the YFP gene. Simultaneously, they selected for a narrow range of yellow fluorescence. Any bacteria not sufficiently yellow were excluded, a process called 'stabilizing selection.' In this way, they built up deep stores of cryptic genetic variation without altering the yellow color of the YFP protein.
During stage 2, the team changed the selection rules and began selecting for E. coli that fluoresced in the green part of the spectrum ('directional selection'). They also introduced control populations of E. coli that lacked enhanced cryptic variation in YFP. The E. coli cell lines with stores of cryptic variation evolved green fluorescent protein (from YFP genes) that were both greener and genetically more diverse than any produced by the control E. coli lineages.
In the experiment, says co-author Joshua Payne (ETH Zurich), cryptic variation did more than drive evolutionary adaptation faster. Cell lines with deep reserves of cryptic variation evolved greener YFP proteins, forms of the protein that were inaccessible to regular bacteria, and they evolved by multiple unique routes not available to regular E. coli.
Current laboratory directed evolution often leads to the same evolutionary outcomes each time. The new work shows how amassing cryptic variation can open doors to otherwise inaccessible regions of protein sequence space, says first author Jia Zheng, a postdoctoral researcher at the University of Zurich.
In the wild, cryptic variation helps fish adapt to life in caves. In the lab, cryptic variation might help a biomolecule bind a new receptor. "Our work can help develop new directed evolution strategies to find innovative biomolecules for biotechnological and medical applications," says Zheng.
Like a fat savings account, cryptic variation is a store of variation that becomes available in an emergency to fuel rapid evolutionary change critical to the survival of a lineage
abstract Cryptic genetic variation can facilitate adaptation in evolving populations. To elucidate the underlying genetic mechanisms, we used directed evolution in Escherichia coli to accumulate variation in populations of yellow fluorescent proteins and then evolved these proteins toward the new phenotype of green fluorescence. Populations with cryptic variation evolved adaptive genotypes with greater diversity and higher fitness than populations without cryptic variation, which converged on similar genotypes. Populations with cryptic variation accumulated neutral or deleterious mutations that break the constraints on the order in which adaptive mutations arise. In doing so, cryptic variation opens paths to adaptive genotypes, creates historical contingency, and reduces the predictability of evolution by allowing different replicate populations to climb different adaptive peaks and explore otherwise-inaccessible regions of an adaptive landscape.
flowering phenology shifts in response to biodiversity loss
amelia a. wolf et al. 2017
doi.org/10.1073/pnas.1608357114
Advanced spring flowering has been described as a fingerprint of climate change—a public, visible display of the detrimental effects of global warming. However, warming experiments fail to account for the full magnitude of observed changes in phenology, suggesting that other factors may play important roles. We show that peak flowering time shifts earlier for most species when we experimentally reduce plant diversity. Additionally, peak flowering times of plant species are more evenly distributed across the season in high-diversity plots. Overall, these results demonstrate the importance of biotic interactions in influencing flowering times and indicate that advancing phenology, one of the most well-described and well-publicized phenomena linking global warming to plant communities, may result equally from biodiversity declines.
Observational studies and experimental evidence agree that rising global temperatures have altered plant phenology—the timing of life events, such as flowering, germination, and leaf-out. Other large-scale global environmental changes, such as nitrogen deposition and altered precipitation regimes, have also been linked to changes in flowering times. Despite our increased understanding of how abiotic factors influence plant phenology, we know very little about how biotic interactions can affect flowering times, a significant knowledge gap given ongoing human-caused alteration of biodiversity and plant community structure at the global scale. We experimentally manipulated plant diversity in a California serpentine grassland and found that many plant species flowered earlier in response to reductions in diversity, with peak flowering date advancing an average of 0.6 days per species lost. These changes in phenology were mediated by the effects of plant diversity on soil surface temperature, available soil N, and soil moisture. Peak flowering dates were also more dispersed among species in high-diversity plots than expected based on monocultures. Our findings illustrate that shifts in plant species composition and diversity can alter the timing and distribution of flowering events, and that these changes to phenology are similar in magnitude to effects induced by climate change. Declining diversity could thus contribute to or exacerbate phenological changes attributed to rising global temperatures.
functional reduction in pollination through herbivore-induced pollinator limitation and its potential in mutualist communities
paul glaum, andré kessler 2017
doi.org/10.1038/s41467-017-02072-4
the lung is a site of platelet biogenesis and a reservoir for haematopoietic progenitors
emma lefrançais et al. 2017
doi.org/10.1038/nature21706
distinct modes of cell competition shape mammalian tissue morphogenesis
stephanie j. ellis et al. 2019
doi.org/10.1038/s41586-019-1199-y
skin cells in mice engage in two forms of competition, one taking place during early embryonic development and the other occurring just before birth. The researchers believe that this cutthroat cellular conflict is crucial to the cultivation of healthy skin.
The winner takes it all
In the wings of developing fruit flies, cells that divide slowly -- so-called "losers" -- die when they come into contact with more rapidly dividing "winners." Though this process has been extensively studied, scientists remained unsure about what purpose it might serve, and whether cell competition is limited to the insect world.
Taking up these questions, researchers in the laboratory of Elaine Fuchs, the Rebecca C. Lancefield Professor, began searching for evidence of competition among epithelial cells of developing mice. They created a population of losers by manipulating genes that slow the pace of cell growth and labeled these cells with green fluorescence. They then labeled winners with red fluorescence, allowing the team to monitor survival in the two populations.
Loser cells, the researchers found, died at a disproportionate rate compared to winners.
"We saw that the losers were proliferating slower, but in order to really call it competition we had to show that they were being actively eliminated by the winners," says postdoctoral fellow Stephanie Ellis. "So we made movies to track interactions between the cells."
The recordings revealed that losers cells surrounded by winners were much more likely to die than those that hung out with other losers -- an indication that the two groups were indeed competing.
Healthy competition
Next, the scientists asked whether the cellular antagonism they observed in developing skin persists later in development. Mammalian skin starts out as a single layer and acquires additional layers over the course of development, ultimately forming a sturdy, stratified barrier that protects the inside of the body from the outside world.
In their first set of experiments, the researchers observed cell death only in the early monolayer tissue. This finding, however, did not convince Ellis that competition was completely absent in more mature skin.
"I thought, perhaps multilayer tissues use a different method to get rid of loser cells," she says. "And that's exactly what we saw."
The researchers found that, though loser cells in stratified tissues don't die, they do get roughed up a bit: they are shoved to the surface of skin, where they are eventually shed from the body. And again, the researchers found that the losers were more likely to be ejected in this fashion when they came into contact with winners.
The scientists also showed that when competition is disrupted, skin develops more slowly and forms a less effective barrier. This is the first study to demonstrate that competition is vital to healthy tissue development -- a finding that, Ellis says, could have clinical implications.
"If you have a barrier disorder -- a wound healing defect, for example -- then promoting better competition could lead to faster restoration of barrier function and faster healing," she says.
"Our research is also consistent with cancer studies showing that healthy cells often eliminate cells with oncogenic mutations, and prevent them from developing into cancers," adds Fuchs. "In this case, healthy cells start out as the winners. Eventually, however, a more fit cancer cell emerges that is endowed with weapons to better compete with normal tissue cells -- giving the cancer cell winner status."
Fuchs' team is currently exploring how healthy stem cells lose their competitive advantage, with the hope that cell competition could be harnessed to develop therapeutic tactics for killing off cancer cells.
abstract Cell competition—the sensing and elimination of less fit ‘loser’ cells by neighbouring ‘winner’ cells—was first described in Drosophila. Although cell competition has been proposed as a selection mechanism to optimize tissue and organ development, its evolutionary generality remains unclear. Here, by using live imaging, lineage tracing, single-cell transcriptomics and genetics, we identify two cell competition mechanisms that sequentially shape and maintain the architecture of stratified tissue during skin development in mice. In the single-layered epithelium of the early embryonic epidermis, winner progenitors kill and subsequently clear neighbouring loser cells by engulfment. Later, as the tissue begins to stratify, the basal layer instead expels losers through upward flux of differentiating progeny. This cell competition switch is physiologically relevant: when it is perturbed, so too is barrier formation. Our findings show that cell competition is a selective force that optimizes vertebrate tissue function, and illuminate how a tissue dynamically adjusts cell competition strategies to preserve fitness as its architectural complexity increases during morphogenesis.
a systematic review of ecological attributes that confer resilience to climate change in environmental restoration
britta l. timpane-padgham et al. 2017
doi.org/10.1371/journal.pone.0173812
contrasting responses of functional diversity to major losses in taxonomic diversity
stewart m. edie et al. 2017
doi.org/10.1073/pnas.1717636115
Global biodiversity consists not only of the sum of taxonomic units such as species, but also of their ecological or functional variety. These two components of biodiversity might be expected to rise or fall in tandem, but we find they are capable of strikingly independent behavior. In three major declines in taxonomic diversity—spatially from equator to poles today and temporally in the Permian–Triassic and Cretaceous–Paleogene extinctions—only the first one shows a concomitant drop in the number of functional groups, whereas virtually all functional categories survived the extinction events. We present a conceptual framework for understanding this contrast, and we suggest that the differing behavior of these two biodiversity components will be important in anticipating the impacts of impending losses in today’s biota.
Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian–Triassic and Cretaceous–Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss.
uplift-driven diversification in the hengduan mountains, a temperate biodiversity hotspot
yaowu xinga, richard h. ree 2017
doi.org/10.1073/pnas.1616063114
Why do so many species occur in mountains? A popular but little-tested hypothesis is that tectonic uplift creates environmental conditions (new habitats, dispersal barriers, etc.) that increase the rate at which resident species divide and evolve to form new ones. In China’s Hengduan Mountains region, a biodiversity hotspot uplifted over the last 8 million years, this rate does in fact show a significant increase during that time, relative to the rate for adjacent older mountains, and to the rate of species immigration. The Hengduan Mountains flora is thus made up disproportionately of species that evolved within the region during its uplift, supporting the original hypothesis and helping to explain the prevalence of mountains as global biodiversity hotspots.
A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification—that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We tested this hypothesis in the context of the Qinghai–Tibetan Plateau (QTP) and adjoining mountain ranges, using the phylogenetic and geographic histories of multiple groups of plants to infer the tempo (rate) and mode (colonization versus in situ diversification) of biotic assembly through time and across regions. We focused on the Hengduan Mountains region, which in comparison with the QTP and Himalayas was uplifted more recently (since the late Miocene) and is smaller in area and richer in species. Time-calibrated phylogenetic analyses show that about 8 million y ago the rate of in situ diversification increased in the Hengduan Mountains, significantly exceeding that in the geologically older QTP and Himalayas. By contrast, in the QTP and Himalayas during the same period the rate of in situ diversification remained relatively flat, with colonization dominating lineage accumulation. The Hengduan Mountains flora was thus assembled disproportionately by recent in situ diversification, temporally congruent with independent estimates of orogeny. This study shows quantitative evidence for uplift-driven diversification in this region, and more generally, tests the hypothesis by comparing the rate and mode of biotic assembly jointly across time and space. It thus complements the more prevalent method of examining endemic radiations individually and could be used as a template to augment such studies in other biodiversity hotspots.
polygamy slows down population divergence in shorebirds
josephine d'urban jackson et al. 2017
doi.org/10.1111/evo.13212
zorba, spock, or voldemort?
matthew sweet 2017
ribbonfarm.com/2017/04/11/zorba-spock-or-voldemort/
To be rational is to make the seemingly right decision, for the seemingly right reason, at the seemingly right time.

Of course, the real question is, how do you know when you’ve found the “right” decision, reason and time? One way to go about discovering it, according to the evangelists of rationality, is to flatten the curve of human experience.
In Antifragile, Nassim Taleb makes a point about complex systems. He says that to thrive they need variety and novelty. For a complex system, randomness is a necessity.
This applies to the human body, a gloriously complex system. Muscles need a range of stimulation that varies in frequency, intensity and duration to be at their most strong and supple. Joints need to be moved through multiple planes under a variety of loads to retain their stability and mobility. The cardiovascular systems needs to be challenged and tested to be at its most effective. All this needs to be done, but not in an organised way. The human body needs random variety, not regimented variety.
diversity in information and how to process it
the type of intuition sonya is seeking seems to be the kind i have, but it comes with unexpected costs: taking everything in that you can means you do not have conscious access to everything, because it exceeds our conscious ability
sanity on the weird timeline
sonya mann 2017
ribbonfarm.com/2017/03/14/maintaining-sanity-weird-timeline/
“While journalists and other experts maintain that truth is basically facts added up, the reality is that all of us, to very different degrees, uncover our own facts and assimilate them to our pre-existing beliefs about what’s true and false, right and wrong,” Nathan Jurgensen wrote. “Even when people see the same information, it means radically different things to them.”
If the world looks weird to you and me today, that is not a matter for rueful laughter, it is a sign that we are probably badly wrong about lots of things.
And being totally wrong about how the world works is a threat to survival.
I never used to obsess about this, but it’s a tautology that you can’t see your own blind spots.
Adam Elkus put it simply: “The price of being able to not be overwhelmed by the world is to have a filter, a cartoon-like image of reality that we can use in our day-to-day lives.” Systems engineer Mathias Lafeldt wrote, “One reason we tend to look for a single, simple cause of an outcome is because the failure is too complex to keep it in our head. Thus we oversimplify without really understanding the failure’s nature and then blame particular, local forces or events for outcomes.”
What I need is intuition that relies on experience rather than belief. Intuition that is optimized for being a functional human being, one who has a variety of healthy engagement modes at her disposal, rather than intuition that is optimized for yielding intellectually consistent results.
Maybe flexibility and the ability to move fast are more useful than being right. Earlier I said, “I’d rather be uncertain than wrong, but I’d rather be right than uncertain.” Maybe being right isn’t just not everything — it’s not a thing at all. Although I’ve long accepted that truth is subjective on an academic level, it’s hard for me to let the idea go deep.
Is it okay for day-to-day normality to feel strange? Is it adaptive or safe to process the world that way? The answer I’ve come to is both yes and no. If reflecting on the absurdity is where the processing ends, then no, it isn’t adaptive or safe. But navigating meta-rationally with sensitive fingertips is adaptive, and epistemically safe, although not necessarily comfortable.
Truth is not objective; every paradigm is true through a particular lens. Certainty becomes irrelevant, because certainty requires a commitment to one viewpoint, which you refuse to grant. Incidentally, I find that this helps a lot in terms of maintaining emotional equanimity.
diversity goes beyond the ends or means dichotomy, the dichotomy described by sonya
arguing about how the world should burn
sonya mann 2017
ribbonfarm.com/2017/05/16/arguing-about-how-the-world-should-burn/
Some constraint on one’s options is acceptable to most of us. We’re social creatures; we need companionship. Cooperating and specializing is also good for productivity, and therefore survival. When you decide to have governance, to codify the norms of your community, you’ve already decided to limit people’s freedom. Your next decision is what constraints you’re going to impose. What will you punish and what will you tax? What will you encourage and subsidize?
Content and process are two dueling answers to this question, championed by fighters who mostly don’t understand the cause they’ve been marshalled to defend. Those who espouse the content approach want to push people out when they don’t buy into the norms and beliefs of the majority. Those who espouse the process approach want to compel everyone to obey the same rules. Neither side will ever be satisfied as long as the other exists.
weaponized sacredness
sarah perry 2015
ribbonfarm.com/2015/05/07/weaponized-sacredness/
resistance to malaria through structural variation of red blood cell invasion receptors
ellen m leffler et al. 2017
doi.org/10.1126/science.aam6393
pharmacogenomics of gpcr drug targets
alexander s. hauser et al. 2017
doi.org/10.1016/j.cell.2017.11.033
•GPCRs targeted by FDA-approved drugs show genetic variation in the human population
•Genetic variation occurs in functional sites and may result in altered drug response
•We present an online resource of GPCR genetic variants for pharmacogenomics research
•Understanding variation in drug targets may help alleviate economic healthcare burden
Natural genetic variation in the human genome is a cause of individual differences in responses to medications and is an underappreciated burden on public health. Although 108 G-protein-coupled receptors (GPCRs) are the targets of 475 (∼34%) Food and Drug Administration (FDA)-approved drugs and account for a global sales volume of over 180 billion US dollars annually, the prevalence of genetic variation among GPCRs targeted by drugs is unknown. By analyzing data from 68,496 individuals, we find that GPCRs targeted by drugs show genetic variation within functional regions such as drug- and effector-binding sites in the human population. We experimentally show that certain variants of μ-opioid and Cholecystokinin-A receptors could lead to altered or adverse drug response. By analyzing UK National Health Service drug prescription and sales data, we suggest that characterizing GPCR variants could increase prescription precision, improving patients’ quality of life, and relieve the economic and societal burden due to variable drug responsiveness.
time
disease spread in age structured populations with maternal age effects
jessica clark, jennie s. garbutt, luke mcnally, tom j. little 2017
doi.org/10.1111/ele.12745
evolutionary dynamics of incubation periods
bertrand ottino-loffler et al. 2017
doi.org/10.7554/elife.30212.001
When one child goes to school with a throat infection, many of his or her classmates will often start to come down with a sore throat after two or three days. A few of the children will get sick sooner, the very next day, while others may take about a week. As such, there is a distribution of incubation periods – the time from exposure to illness – across the children in the class.
When plotted on a graph, the distribution of incubation periods is not the normal bell curve. Rather the curve looks lopsided, with a long tail on the right. Plotting the logarithms of the incubation periods, however, rather than the incubation periods themselves, does give a normal distribution. As such, statisticians refer to this kind of curve as a “lognormal distribution”. Remarkably, many other, completely unrelated, diseases – like typhoid fever or bladder cancer – also have approximately lognormal distributions of incubation periods. This raised the question: why do such different diseases show such a similar curve?
Working with a simple mathematical model in which chance plays a key role, Ottino-Löffler et al. calculate how long it takes for a bacterial infection or cancer cell to take over a network of healthy cells. The model explains why a lognormal-like distribution of incubation periods, modeled as takeover times, is so ubiquitous. It emerges from the random dynamics of the incubation process itself, as the disease-causing microbe or mutant cancer cell competes with the cells of the host.
Intuitively, this new analysis builds on insights from the “coupon collector’s problem”: a classical problem in mathematics that describes the situation where a person collects items like baseball cards, stamps, or cartoon monsters in a videogame. If a random item arrives every day, and the collector’s luck is bad, they may have to wait a long time to collect those last few items. Similarly, in the model of Ottino-Löffler et al., the takeover time is dominated by dramatic slowdowns near the start or end of the infection process. These effects lead to an approximately lognormal distribution, with long waits, as seen in so many diseases.
Ottino-Löffler et al. do not anticipate that their findings will have direct benefits for medicine or public health. Instead, they believe their results could help to advance basic research in the fields of epidemiology, evolutionary biology and cancer research. The findings might also make an impact outside biology. The term “contagion” has now become a familiar metaphor for the spread of everything from computer viruses to bank failures. This model sheds light on how long it takes for a contagion to take over a network, for a variety of idealized networks and spreading processes.
abstract The incubation period for typhoid, polio, measles, leukemia and many other diseases follows a right-skewed, approximately lognormal distribution. Although this pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here, we propose an explanation based on evolutionary dynamics on graphs. For simple models of a mutant or pathogen invading a network-structured population of healthy cells, we show that skewed distributions of incubation periods emerge for a wide range of assumptions about invader fitness, competition dynamics, and network structure. The skewness stems from stochastic mechanisms associated with two classic problems in probability theory: the coupon collector and the random walk. Unlike previous explanations that rely crucially on heterogeneity, our results hold even for homogeneous populations. Thus, we predict that two equally healthy individuals subjected to equal doses of equally pathogenic agents may, by chance alone, show remarkably different time courses of disease.
age-related differences in the structural and effective connectivity of cognitive control: a combined fmri and dti study of mental arithmetic
thomas hinault et al. 2019
doi.org/10.1016/j.neurobiolaging.2019.06.013
"Your task performance can be impaired not just because you can't remember, but because you can't suppress other memories that are irrelevant," said senior author Susan Courtney, a cognitive neuroscientist at Johns Hopkins. "Some 'memory problems' aren't a matter of memory specifically, but a matter of retrieving the correct information at the right time to solve the problem at hand."
The findings were just posted in Neurobiology of Aging.
The researchers had 34 young adults (18 to 30) and 34 older adults (65-85) perform a mental arithmetic task while their brain activity was measured through functional magnetic resonance imaging, or fMRI. Other images were also collected to measure the integrity of the connections between brain areas called white matter tracts.
The task compared the participants' ability to inhibit irrelevant information automatically retrieved from long term memory. They were asked to indicate whether a proposed solution to an addition or multiplication problem was correct or not -- for instance 8x4=12 or 8+4=32. These examples would create interference as participants considered the right answer because although they should answer "incorrect," the proposed solution seems correct at first glance, based on long-term memories of basic math. This interference did not exist when participants were asked to answer clearly false equations like 8x4=22. Making the task even more complicated, the subjects were sometimes asked to switch to multiplication after they saw the addition symbol and vice versa.
Older people were a fraction of a second slower at answering the questions than younger participants, particularly when there was interference, but the more dramatic difference showed up in the brain scans. Older individuals who had more difficulty with interference also had more frontal brain activation than young adults.
The brain imaging demonstrated that in some aging participants, fibers connecting the front and back of the brain appear to have been damaged over the years. However other older individuals had fibers similar to much younger subjects. The greater the integrity of these fibers, the better the participant's task performance, said lead author Thomas Hinault, a postdoctoral fellow at Johns Hopkins.
"Everyone we studied had good functioning memory, but still we saw differences," Hinault said. "There are so many disruptions in the world and being able to suppress them is crucial for daily life."
The researchers were surprised to find that during parts of the task that were the trickiest, where participants had to switch between multiplication and addition and were asked to add after they saw a multiplication command or vice versa, the people with the strongest brain fiber connections counterintuitively performed even better. Something about deliberately exercising the mind in this fashion made the most agile minds even more so.
"If you have good connections between brain networks, that will help," Courtney said. "If not, you have interference."
abstract •We studied aging effects on the facilitation of inhibition after rule updating.
•Diffusion tensor imaging and functional magnetic resonance imaging were used to assess functional and structural connectivity.
•Reduced facilitation and larger frontal activation were observed in older adults.
•Preservation of frontoparietal connectivity was associated with performance.
•Connectivity changes contribute to the interindividual variability during aging.
Cognitive changes with aging are highly variable across individuals. This study investigated whether cognitive control performance might depend on preservation of structural and effective connectivity in older individuals. Specifically, we tested inhibition following working memory (WM) updating and maintenance. We analyzed diffusion tensor imaging and functional magnetic resonance imaging data in thirty-four young adults and thirty-four older adults, who performed an arithmetic verification task during functional magnetic resonance imaging. Results revealed larger arithmetic interference in older adults relative to young adults after WM updating, whereas both groups showed similar interference after WM maintenance. In both groups, arithmetic interference was associated with larger activations and stronger effective connectivity among bilateral anterior cingulate, bilateral inferior frontal gyrus, and left angular gyrus, with larger activations of frontal regions in older adults than in younger adults. In older adults, preservation of frontoparietal structural microstructure, especially involving the inferior frontaloccipital fasciculus, was associated with reduced interference, and stronger task-related effective connectivity. These results highlight how both structural and functional changes in the cognitive control network contribute to individual variability in performance during aging.
predators
loss of consumers constrains phenotypic evolution in the resulting food web
matthew a. barbour et al. 2020
doi.org/10.1002/evl3.170
What effect does extinction of species have on the evolution of surviving species? Evolutionary biologists have investigated this question by conducting a field experiment with a leaf galling fly and its predatory enemies. They found that losing its natural enemies could make it more difficult for the prey to adapt to future environments.
According to many experts, the Earth is at the beginning of its sixth mass extinction, which is already having dire consequences for the functioning of natural ecosystems. What remains unclear is how these extinctions will alter the future ability of remaining species to adapt.
Researchers from the University of Zurich have now pursued this question with a field experiment in California. They investigated how the traits of a tiny fly changed when a group of its natural enemies was removed. From their observations, they drew conclusions about changes in the genetic diversity of the flies.
Specific elimination of parasitoids
The fly Iteomyia salicisverruca lives on willow leaves in tooth-shaped growths called galls, which it induces in its larval stage. The natural enemies of this fly include several species of parasitic wasps. These wasps lay their eggs inside the fly larva within the gall, where they then develop into parasitic predators known as parasitoids. Before the adult wasp leaves the gall, it devours its host, the fly.
Some species of these parasitoids attack before the gall is formed, while others parasitize fly larvae later in their development and pierce through the gall. The researchers specifically eliminated the latter group of natural enemies by attaching fine-meshed nets over leaves with galls before they were attacked.
After three months, the biologists collected about 600 galls and checked if the fly larvae had survived. They also measured three traits that influence a fly's survival from parasitoid attack: the size of the gall; the number of flies within a gall; and the fly's preference to create galls on particular genetic varieties of willow trees. Using these data they then created "fitness landscapes" using computer models, which visualize the adaptability of a species.
Fewer enemies, less variability
It turned out that different combinations of these three traits helped flies survive ? when all of the fly's natural enemies were present. "So there are several equally good solutions that ensure the survival of the fly," says Matt Barbour, the study's lead author. In contrast, after some natural enemies were removed, only one specific combination of traits helped flies survive. "This suggests that the extinction of natural enemies constrains fly evolution toward only one optimal solution." Genetic variations that lead to a different development of the traits could thus be permanently lost in the flies' genome.
This loss of diversity might be of consequence: "The diversity of potential solutions for survival acts to preserve genetic variability in the gall's traits," says Barbour. And since genetic variation provides the raw material for evolution, the findings suggest that the extinction of this fly's natural enemies may make it more difficult for it to adapt to a changing environment.
"Thinking about the big picture, our study hints at a potential insidious side effect of extinctions," says Barbour. "The extinction of natural enemies may compromise the ability of remaining species to adapt and persist in an uncertain and changing world." If this is true, this would put many ecosystems at even greater risk than we currently realize.
abstract The loss of biodiversity is altering the structure of ecological networks; however, we are currently in a poor position to predict how these altered communities will affect the evolution of remaining populations. Theory on fitness landscapes provides a framework for predicting how selection alters the evolutionary trajectory and adaptive potential of populations, but often treats the network of interacting populations as a “black box.” Here, we integrate ecological networks and fitness landscapes to examine how changes in food‐web structure shape phenotypic evolution. We conducted a field experiment that removed a guild of larval parasitoids that imposed direct and indirect selection pressures on an insect herbivore. We then measured herbivore survival as a function of three key phenotypic traits to estimate directional, quadratic, and correlational selection gradients in each treatment. We used these selection gradients to characterize the slope and curvature of the fitness landscape to understand the direct and indirect effects of consumer loss on phenotypic evolution. We found that the number of traits under directional selection increased with the removal of larval parasitoids, indicating evolution was more constrained toward a specific combination of traits. Similarly, we found that the removal of larval parasitoids altered the curvature of the fitness landscape in such a way that tended to decrease the evolvability of the traits we measured in the next generation. Our results suggest that the loss of trophic interactions can impose greater constraints on phenotypic evolution. This indicates that the simplification of ecological communities may constrain the adaptive potential of remaining populations to future environmental change.
the community ecology of herbivore regulation in an agroecosystem: lessons from complex systems
john vandermeer et al. 2019
doi.org/10.1093/biosci/biz127
“Although the take-home message of Huffaker’s experiment is that environmental heterogeneity can stabilize an inherently unstable system, what is less frequently discussed is Huffaker’s observations of the resulting spatial distribution of the mites.”
“The same equations that Turing used for chemistry, we can use in ecology,” said John Vandermeer, a professor in the U-M Department of Ecology and Evolutionary Biology and first author of a study in the December issue of BioScience. “Those equations say you should get spots of predators and spots of prey in a system, and we’ve proven you do.”
The finding, he says, helps shed light on the complex agroecological system of coffee farms and how the “control from above” (focused on pests) model is also more complicated than a predator-prey relationship. The system includes a complex community of predators, parasites and diseases that interact with each other in complicated ways that eventually generate a self-organized system that exerts effective control over the herbivore.
“This is an important finding because it shows how organisms in nature are embedded within a complex web of interactions and, therefore, the simplistic pest management approach of ‘one pest, one natural enemy’ may not be the most appropriate one for pest management,” said co-author Ivette Perfecto, the George W. Pack Professor of Ecology, Natural Resources and Environment at U-M’s School for the Environment and Sustainability.
“Rather, a complex systems approach that accounts for nonlinearities and networks of interactions is what is needed.”
Turing pattern
Turing explained the creation of nonrandom patterns in chemistry by observing chemical reactions and how they are destabilized. A chemical reaction is stabilized by the balance of an activation and repression process. Then there’s diffusion: a drop of ink in water eventually diffuses and can’t be separated from the water. But, Turing observed, if the repression force diffused at a greater rate than the activation force, a nonrandom pattern would develop.
“Turing figured that if you took this reaction process, you can put together two forces that are stabilizing themselves and you put them together and that destabilizes the whole system, forming patterns,” Vandermeer said. “Something very similar happens in ecological systems: the predator is eating the prey and the prey’s population goes down, and then the predators’ population goes down, that’s a regulating thing. When you have diffusion — in biology we call it migration — the predator moves in space and the prey moves, too.”
Vandermeer and Perfecto looked at data they collected in an organic coffee farm in Chiapas, Mexico, mapping the distribution of shade trees containing nests of Azteca sericeasur ants. While there are between 7,000 to 11,000 shade trees in the plot depending on the year, only about 700 have Aztecas on them. Each nest has anywhere between 10 to 20 queens.
Phorid flies find these clusters, parasitizing the ants by planting an egg on the ant’s head. Larvae will develop until the ant’s head falls off and a new fly emerges, repeating the cycle. As the local population of ant nests builds up, spatial clusters are formed and become larger, and so does the population of phorid flies, which will in turn act as a repressor in the system, resulting in the patchy distributions of ants similar to the leopard’s patches.
“Turing was talking about his chemicals and we’re talking about ants and flies,” Vandermeer said. “We predicted that our ants and our flies should form these little clusters and we found that they do.”
The complexity of farming coffee
In their study, the researchers explored the complex relationships between predators, prey and their environment, including the green coffee scale, a relatively benign coffee pest that rarely reaches pest status; the Azya orbigera, a predatory beetle that feasts on the scale; and the Azteca ant, which protects the scale from the beetle.
Under protection from the ants, the scales effectively have a refuge from the beetle predators and they increase dramatically in numbers. With such high local population density, a fungal disease takes over and the scale insects decline rapidly. Thus the combination of a predator, a refuge in the clusters of ant nests and a fungal disease keeps the scale insects under control.
And then there’s the coffee rust, which has decimated coffee farms across Latin America but remains fairly controlled in Puerto Rico. The rust is spread by spores in the wind, but the same fungus that causes the disease in the scale insects, is also an antagonist of the rust, complicating the situation considerably.
The researchers warn about the temptation of providing simple answers to farmers seeking solutions to perceived problems in their farms — for example, by getting rid of the shade trees that house the ants.
“If we get rid of the shade trees, then the ants would go away. If the ants go away, there’s no place to have a refuge for the scale insects to escape the predator. So the beetle would eat all of the scale insects and then itself die of starvation,” Vandermeer said. “And when the next season arrives, the scale insects would come back without any predators to stop them. So if you get rid of the shade trees you get rid of the control.”
The same can be said when it comes to rust, he says. Coffee rust spreads by spores that are taken by the wind and a canopy of shade trees above the coffee acts as a windbreak.
“So if you take the shade trees out of the system, you get the wind in the system, and with the wind brings the spores,” Vandermeer said. “Since it’s a complex system, it requires a more holistic approach to understand and manage, and there’s more potential for surprise.”
abstract Whether an ecological community is controlled from above or below remains a popular framework that continues generating interesting research questions and takes on especially important meaning in agroecosystems. We describe the regulation from above of three coffee herbivores, a leaf herbivore (the green coffee scale, Coccus viridis), a seed predator (the coffee berry borer, Hypothenemus hampei), and a plant pathogen (the coffee rust disease, caused by Hemelia vastatrix) by various natural enemies, emphasizing the remarkable complexity involved. We emphasize the intersection of this classical question of ecology with the burgeoning field of complex systems, including references to chaos, critical transitions, hysteresis, basin or boundary collision, and spatial self-organization, all aimed at the applied question of pest control in the coffee agroecosystem.
top predators determine how biodiversity is partitioned across time and space
benjamin van allen et al. 2017
doi.org/10.1111/ele.12798
cascading predator effects in a fijian coral reef ecosystem
douglas b. rasher et al. 2017
doi.org/10.1038/s41598-017-15679-w
cascading impacts of large-carnivore extirpation in an african ecosystem
justine atkins et al. 2019
doi.org/10.1126/science.aau3561
"Large carnivores play a critical, and disproportionate, role in their ecosystems, and their populations are declining worldwide," said Justine Atkins, a graduate student in ecology and evolutionary biology at Princeton. "However, there is real reason to be hopeful in many of these systems," she said. She and a team of colleagues found evidence that reintroducing key carnivores in a large-mammal ecosystem could undo the damage caused by their removal. Their work appears in the March 8 issue of the journal Science.
The researchers were working in Gorongosa National Park, where the Mozambican civil war took a tremendous toll on wildlife populations. Most herbivore species have been recovering, but several major large carnivores -- leopards, hyenas and African wild dogs -- were eliminated from the park.
"That's a tragic thing, but what it does is enable us to study how behavior and ecology changes when the predators are removed," said Robert Pringle, an associate professor of ecology and evolutionary biology and the senior author on the paper. "It's not quite an experiment, but it's almost like one. We found that one of the common antelope species, bushbuck, which typically is a very shy, secretive forest-dweller, has expanded out into the open plains. The plants in the plains are very nutritious, and the bushbuck that have colonized those areas are bigger and in better shape than their counterparts in the forest. And the presence of bushbuck in this new habitat has negative effects on the plants that bushbuck eat."
All herbivores have to weigh the nutritional benefits of foraging in a certain area against the risk that they might get killed and eaten in the process. If the risk is too high, they will avoid an area, even if it is nutritionally rich. In this way, high-risk areas for herbivores become safe spaces for palatable plants. The link between herbivores' fear of carnivores and the benefits for vegetation is what ecologists call a "trophic cascade," the term for the impact that meat-eating predators can have on plants.
"Historically, the diverse group of predators in Gorongosa were effectively keeping herbivores confined to areas with lower predation risk," said Pringle. "The elimination of predators broke the rules that ordinarily govern where herbivores go and what they eat, and that has effects all the way through the food chain."
The project began in 2015, when Pringle and other members of the research team observed that some bushbuck, a usually shy species of antelope native to the region, had stopped hiding in woodlands and begun frequenting the open, largely treeless grasslands on the Gorongosa floodplain. A detailed study of Gorongosa prior to the Mozambican civil war, which lasted from 1977 to 1992, had reported that bushbuck did not occur in these treeless areas. The researchers hypothesized that the elimination of the leopards, wild dogs and hyenas had created a "landscape of fearlessness," where the formerly timid antelopes now browsed freely -- to the detriment of the local vegetation.
They spent years designing and executing a study that looked at every link in the hypothesized chain of effects between the absent predators and the plants of the Gorongosa plains. Using GPS collars and aerial censuses from 2002 to 2016, they tracked the animals' movements and locations. They sequenced the plant DNA in bushbuck scat to determine exactly what the animals ate in different areas, and they quantified the nutritional quality of the plants in each habitat. They also measured the size, fat and muscle of captured bushbuck, while they were putting on the GPS collars, and found that eating the more protein-rich diet available on the floodplains contributed to bigger, stronger bushbuck.
"The two most important pieces of the study were two experiments that Justine performed in the field in 2016 and 2017," said Pringle. "One was to use the sounds and scents of large carnivores to simulate risk -- the idea was to try to scare the bushbuck into thinking that predators were present and see how that affected their behavior."
Atkins played recorded leopard calls and placed artificial carnivore scat and urine so that bushbuck would hear and smell signs that their predators had returned. As predicted, bushbuck in the open plains responded to the predator cues by moving to more wooded areas that offered more hiding places. By using these cues, Atkins was able to conclude that the fear of predation, not any killing by actual predators, caused the change in bushbuck behaviors.
"The other thing that Justine did, which was really innovative, was to use the results of our diet analysis to identify a plant that was only really eaten by bushbuck and not by other large herbivores," said Pringle. "Then, with that knowledge, she built cages around the plants to prevent bushbuck from eating them, which enabled her to isolate the effects of bushbuck on the growth of the plant."
She found that the plants protected from bushbuck grew rapidly, which suggests that they may rebound strongly when predators are reintroduced to the park and the bushbuck retreat to woody areas.
By combining information from a diverse range of measurements with controlled field experiments, Atkins and her colleagues successfully documented each link in the hypothesized trophic cascade.
"The research team used a series of well-designed experiments," said Laura Prugh, an associate professor of quantitative wildlife sciences at the University of Washington, who was not involved in this research. "It is rare to have so many components of food web interactions quantified, and their research nicely sets the stage for predicting how the ecosystem will respond when carnivores are reintroduced."
Working in Gorongosa provided an unprecedented "natural experiment" to study the effects of local predator extinction on an ecosystem of large mammals, said Corina Tarnita, an associate professor of ecology and evolutionary biology who is Atkins' adviser and co-author.
"It enables us to explore profound theoretical concepts and questions that have previously been accessible primarily in much smaller and more controlled systems," she said. "In most complex systems, the issue of scaling presents a non-trivial challenge: Just because something is true at small scales doesn't necessarily make it true at larger scales. So being able to test the extent to which fundamental ecological principles scale up is invaluable."
"Our work really underscores the importance of top carnivores, which are declining globally," said Ryan Long, an assistant professor of fish and wildlife sciences at the University of Idaho, who was a co-author on the project. "Carnivores influence ecosystems in complex ways that go beyond just killing and eating other animals, but it can be really challenging to get experimental evidence of those kinds of effects in large-mammal systems. Our study provides a really compelling combination of observational and experimental support for the notion that large herbivores modify their behavior in response to the fear of predators, and that those changes in behavior affect both their own condition and the plant communities they rely on for food."
"This careful study suggests that the interplay between predators, prey and the plants they eat is more flexible than previously thought," said Michelle Elekonich, a program director at the National Science Foundation, which provided funding for this research. "By showing that human-induced disruptions to these complex interactions can be reversed, the authors have provided invaluable information to guide restoration efforts in ecosystems negatively affected by human activity."Since the study ended, ecologists in Gorongosa have continued their restoration efforts with the support of the Greg Carr Foundation. The vanguard, a pack of African wild dogs, were reintroduced in mid-2018.
"The first pack of African wild dogs introduced are well settled in, hunt very successfully, and mostly prey on bushbuck -- especially those on the open floodplain," said Paola Bouley, associate director of conservation at Gorongosa National Park. "They just hammer the bushbuck drifting out in the open."
This research is "exciting confirmation we are on the right track in Gorongosa, focusing strongly on top predator recovery to bring an entire ecosystem back in to balance," Bouley said. "We're observing one of the grandest ecological restoration stories on the planet as it unfolds."
abstract The world’s largest carnivores are declining and now occupy mere fractions of their historical ranges. Theory predicts that when apex predators disappear, large herbivores should become less fearful, occupy new habitats, and modify those habitats by eating new food plants. Yet experimental support for this prediction has been difficult to obtain in large-mammal systems. Following the extirpation of leopards and African wild dogs from Mozambique’s Gorongosa National Park, forest-dwelling antelopes (bushbuck, Tragelaphus sylvaticus) expanded into treeless floodplains, where they consumed novel diets and suppressed a common food plant (waterwort, Bergia mossambicensis). By experimentally simulating predation risk, we demonstrate that this behavior was reversible. Thus, whereas anthropogenic predator extinction disrupted a trophic cascade by enabling rapid differentiation of prey behavior, carnivore restoration may just as rapidly reestablish that cascade.
can marine reserves restore lost ecosystem functioning? a global synthesis
brian s. cheng et al. 2019
doi.org/10.1002/ecy.2617
“modern levels of predation in the coastal oceans may currently only be a fraction of the baseline prior to human exploitation.”
at less effective reserves, the odds that a predator consumed prey species was 1-to-1, just an even chance, the researchers note. In contrast, at highly effective reserves, the odds of a prey species being preyed upon skyrockets to 49-to-1. "You would not want to be a prey species in these reserves," Cheng notes.
He likens the creation of a marine protected area to rebuilding a village, which means bringing back many different types of workers to do varied jobs: teachers, police officers, firefighters, shopkeepers and carpenters, for example. Without teachers, students would have no school, he points out, and having no firefighters would be dangerous.
"We are trying to rebuild many, many communities like this in the ocean," Cheng says. "We have historically removed many of the fish and other species that have important jobs as predators and herbivores, just like the teachers and firefighters. Imagine trying to rebuild these communities without paying attention to this. Our research points out that these rebuilt ocean communities are not all the same, and we need to pay attention to the different kinds of jobs each species does in order to rebuild in an effective and sustainable way."
Results of this work highlight an important gap in scientific knowledge about marine reserves, Cheng says. "Past efforts have mainly focused on quantifying the abundance and diversity of fished species inside reserves. This is a critical first step, but it doesn't give us information on how communities within reserves are altered by protected status. If you remove a species, will another take on its role or function, or not?"
abstract Marine protected areas (MPAs) have grown exponentially, emerging as a widespread tool to conserve biodiversity and enhance fisheries production. Although numerous empirical studies and global syntheses have evaluated the effects of MPAs on community structure (e.g., biodiversity), no broad assessment concerning their capacity to influence ecological processes (e.g., species interactions) exists. Here, we present meta‐analyses that compare rates of predation and herbivory on a combined 32 species across 30 MPAs spanning 85° of latitude. Our analyses synthesize the fate of 15,225 field experiment assays, and demonstrate that MPAs greatly increased predation intensity on animals but not herbivory on macroalgae or seagrass. Predation risk, quantified as the odds of prey being eaten, was largely determined by predator abundance and biomass within reserves. At MPAs with the greatest predator accumulation, the odds of predation increased to nearly 49:1, as opposed to 1:1 at MPAs where predators actually declined. Surprisingly, we also found evidence that predation risk declined with increased sea‐surface temperature. Greater predation risk within MPAs was consistent with predator and prey population abundance estimates, where predators increased 4.4‐fold within MPAs, whereas prey decreased 2.2‐fold. For herbivory, the lack of change may have been driven by functional redundancy and the inability of reserves to increase herbivore abundance relative to fished zones in our sample. Overall, this work highlights the capacity of MPAs to restore a critical ecosystem function such as predation, which mediates energy flows and community assembly within natural systems. However, our review of the literature also uncovers relatively few studies that have quantified the effects of MPAs on ecosystem function, highlighting a key gap in our understanding of how protected areas may alter ecological processes and deliver ecosystem services. From a historical perspective, these findings suggest that modern levels of predation in the coastal oceans may currently only be a fraction of the baseline prior to human exploitation.
herbivores as drivers of negative density dependence in tropical forest saplings
dale l. forrister et al. 2019
doi.org/10.1126/science.aau9460
analyzed how neighboring trees influence the growth and survival of nine coexisting species of the tree genus Inga in the Panama rainforest. They compared tree traits for resource acquisition, anti-herbivore defenses and the herbivores that live on the plants. They found that neighboring trees were basically the same in terms of acquiring resources, but had very different defenses and herbivores. Indeed, the defensive traits and shared pests impacted growth and survival, while resource acquisition traits had no effect on the plants' success. These findings indicate that anything impacting pest populations, such as climate change or habitat fragmentation, will have an impact on the health of the rainforest.
"Working in these hyper-diverse tropical rainforests makes it abundantly clear just how complex the web of interacting species really is. No species or individual lives in isolation. At all levels within the food chain species are competing with one another for precious resources and contributing a huge amount of their energy to defending themselves from the barrage of enemies they face, said Dale Forrister, doctoral candidate in the School of Biological Sciences at the University of Utah and lead author of the study. "We are excited about this study because it highlights some of the important ways these antagonistic interactions might influence tropical diversity."
This study published on March 14, 2019, in the journal Science.
It's a jungle out there
The team conducted their analysis over five years within a 50-hectare forest plot in Barro Colorado Island, Panama. The site has growth and survival data for over 423,000 trees from a previous long-term study. The researchers analyzed every individual tree sapling from the focal Inga species and calculated the similarity of their Inga neighbors' traits within a 10-meter "neighborhood." They measured four resource acquisition traits, five anti-herbivore defenses and recorded which herbivores were eating which plants.
Forrister developed a complicated model to determine how neighboring trees influence sapling growth and survival. They found that resource acquisition traits had no effect on survival, while defensive traits and herbivores had a big impact.
There are only so many ways to acquire resources. Defensive traits, however, are nearly endless. Plants and herbivores are in a constant arms race to outsmart each other. Plants develop traits to deter hungry mandibles, and herbivores adapt to deal with the leaf's defenses. The Inga genus has a quiver of anti-herbivore traits, including tiny hairs, nectar cups that attract pugnacious ant protectors, and most notably, leaves filled with poisonous compounds. Each Inga species can make hundreds or sometimes thousands of different toxins.
"People may think of a jungle like it's a giant salad bowl. It should be paradise for pests because they're surrounded by leaves. But plants have an infinite number of defense combinations -- half the weight of a young leaf is poison," said Phyllis Coley, Distinguished Professor of Biology at the University of Utah, research affiliate at the Smithsonian Tropical Research Institute and co-author of the study. "As a consequence of the diversity of defenses, each species of herbivore can only eat a few species of plants that they have adaptations for."
Closely related plants have similar defensive traits, and therefore similar pests. If a plant differs from its neighbor in terms of defenses, their herbivores aren't a threat, Coley continued. "You'll have your own herbivores, but at least you won't have all the critters in the neighborhood eating you."
Confounding chemical compounds
Plant toxins are the most important weapons for tropical plants, but testing the similarity of each species' chemicals proved problematic. Over five years, the researchers collected leaf samples in the field, dried them in a makeshift desiccator suitcase (no easy feat in 100 percent humidity) and then brought them to the U for analysis. Using high performance liquid chromatography, they separated all of the distinct compounds inside the leaves. However, only 4 percent of the Inga compounds were known to science. So, the team got creative and came up with a new metric. They used a mass spectrometer to determine the chemical structure of each compound, and established that compounds with similar structures were likely affecting herbivores in a similar way.
"Metabolomics, a relatively new field of science, offers scientist a powerful new toolbox for examining the vast amount of chemical diversity that exists out there. Chemicals play a huge role in nature, from defenses to communication they are the medium by which species interact. Being able to quantify this in a meaningful way provides a truly unique perspective," said Forrister.
But do the herbivores "care" about the traits the team was measuring and do Inga species with similar traits share herbivores? To test this, they collected caterpillars that were eating Inga leaves and sequenced their DNA to classify each as species A, species B, etc. They were unable to name the species because most of the caterpillars were new to science. They cataloged which herbivores were eating which plants, correlated the suite of compounds in the plants and inferred which plant species shared herbivore communities.
Both old-school field research and modern techniques were indispensable to this project's success.
"Despite state-of-the-art laboratory facilities, there's no substitute for spending months and months in the rainforest," said Coley. "It took us several years to collect data, and samples of leaves and herbivores. It's hot, humid and buggy, but attempting to understand the diversity of species is a biologist's dream."
The study reveals the significant role of herbivores in driving diversity in tropical ecosystems, with stark implications -- the loss of those populations could have catastrophic consequence on these important habitats.
"If climate change continues to increase the length of the dry season in the Americas, then the dynamics of the herbivore populations will change as well," said Coley. "That could have implications down the road."
abstract Ecological theory predicts that the high local diversity observed in tropical forests is maintained by negative density–dependent interactions within and between closely related plant species. By using long-term data on tree growth and survival for coexisting Inga (Fabaceae, Mimosoideae) congeners, we tested two mechanisms thought to underlie negative density dependence (NDD): competition for resources and attack by herbivores. We quantified the similarity of neighbors in terms of key ecological traits that mediate these interactions, as well as the similarity of herbivore communities. We show that phytochemical similarity and shared herbivore communities are associated with decreased growth and survival at the sapling stage, a key bottleneck in the life cycle of tropical trees. None of the traits associated with resource acquisition affect plant performance, indicating that competition between neighbors may not shape local tree diversity. These results suggest that herbivore pressure is the primary mechanism driving NDD at the sapling stage.
de novo establishment of wild-type song culture in the zebra finch
olga fehér 2009
doi.org/10.1038/nature07994
Culture is typically viewed as consisting of traits inherited epigenetically, through social learning. However, cultural diversity has species-typical constraints25, presumably of genetic origin. A celebrated, if contentious, example is whether a universal grammar constrains syntactic diversity in human languages26. Oscine songbirds exhibit song learning and provide biologically tractable models of culture: members of a species show individual variation in song27 and geographically separated groups have local song dialects28,29. Different species exhibit distinct song cultures30,31, suggestive of genetic constraints32,33. Without such constraints, innovations and copying errors should cause unbounded variation over multiple generations or geographical distance, contrary to observations33. Here we report an experiment designed to determine whether wild-type song culture might emerge over multiple generations in an isolated colony founded by isolates, and, if so, how this might happen and what type of social environment is required34. Zebra finch isolates, unexposed to singing males during development, produce song with characteristics that differ from the wild-type song found in laboratory35 or natural colonies. In tutoring lineages starting from isolate founders, we quantified alterations in song across tutoring generations in two social environments: tutor–pupil pairs in sound-isolated chambers and an isolated semi-natural colony. In both settings, juveniles imitated the isolate tutors but changed certain characteristics of the songs. These alterations accumulated over learning generations. Consequently, songs evolved towards the wild-type in three to four generations. Thus, species-typical song culture can appear de novo. Our study has parallels with language change and evolution36,37,38. In analogy to models in quantitative genetics39,40, we model song culture as a multigenerational phenotype partly encoded genetically in an isolate founding population, influenced by environmental variables and taking multiple generations to emerge.
what songbirds could teach us about constructive tweeting
ofer tchernichovski 2017
aeon.co/ideas/what-songbirds-could-teach-us-about-constructive-tweeting
female social feedback reveals non-imitative mechanisms of vocal learning in zebra finches
samantha carouso-peck, michael h. goldstein 2019
doi.org/10.1016/j.cub.2018.12.026
New research reveals that these birds don't simply learn their songs by imitating adults: They learn by watching their mothers' reactions to their immature songs.
In "Female Social Feedback Reveals Non-Imitative Mechanisms of Vocal Learning in Zebra Finches," published Jan. 31 in Current Biology, co-authors Michael Goldstein, associate professor of psychology, and doctoral candidate Samantha Carouso-Peck solve the mystery of why juvenile male zebra finches learn to sing better when females are around, even though the females don't sing.
The researchers found that the adult females guide juveniles' song development through specific interactions, similar to how human babies learn to talk. This study brings the number of species known to engage in socially guided vocal learning to four: zebra finches, humans, marmosets and cowbirds.
The researchers' clue to the zebra finch mystery came when they considered that birds see the world at several times the "critical flicker fusion rate" of humans. Simply put, birds can perceive events that happen much too fast for a human to see, and most previous research on social learning has not taken into account such rapid "bird time," in which tiny behaviors can have large social effects.
Using slowed-down video, the Cornell researchers were able to identify tiny movements, imperceptible to the human eye, made by the female zebra finches to encourage the baby songbirds. These included wing gestures and "fluff-ups," an arousal behavior in which the bird fluffs up its feathers.
"Over time, the female guides the baby's song toward her favorite version. There's nothing imitative about it," said Carouso-Peck.
The study included nine pairs of zebra finches, genetic brothers raised for the first 35 days by their respective parents. When they reached the age at which they begin to produce practice song (subsong), the siblings were split up, moved into individual soundproof containers and randomly assigned to one of two conditions: "contingent" or "yoked."
Contingent birds were monitored by Carouso-Peck, and each time they sang in a way that matched their fathers' song, she triggered a video playback of a female performing a fluff-up. The yoked bird saw the same fluff-up video at the same time as his contingent brother, but from his perspective the fluff-ups happened at random times unrelated to his song production.
After the birds' songs "crystallized" into the final version, the researchers compared them to the songs of the juveniles' fathers. They found that the birds in the contingent group learned significantly more accurate songs than their yoked brothers. Had the traditional model of song learning as pure imitation been correct, both birds would have learned the same song, because they had the same opportunity to memorize it early and practice it, according to Goldstein.
One possible reason for the zebra finch learning style, according to the researchers, is that because zebra finches use their songs to attract mates rather than defend territory, integrating female preferences into song is "a highly adaptive strategy for future reproductive success," they wrote.
"Historically we've been studying these birds in isolation. That means we've been missing out on the entire social aspect of song learning," Goldstein said.
Similarly, he said, most labs study human babies more or less in isolation.
"But what babies -- zebra finch or human -- are good at is exploiting social information in their environment," Goldstein said. "These immature behaviors are not mindless practice and noise. Their function is to motivate the adults in the room to provide information."
Zebra finches are widely used in research of vocal learning and production as well as research on Parkinson's disease, autism, stuttering and genetic disorders of speech. "Incorporating social factors into studies of zebra finch learning will strengthen the species as a model system," the paper's authors write, "as it will uncover new possibilities for drawing parallels with human speech acquisition."
abstract •Imitation, not social factors, is thought to drive zebra finch song learning
•We tested whether non-vocal visual feedback from females affects song learning
•Song learning was facilitated by contingent feedback; yoked controls did not learn
•Socially guided vocal learning is a crucial mechanism of song development
Learning of song in birds provides a powerful model for human speech development [ 1 , 2 , 3 ]. However, the degree to which songbirds and humans share social mechanisms of vocal learning is unknown. Although it has been demonstrated as a vocal learning mechanism in human infants [ 3 , 4 , 5 , 6 ], learning via active social feedback is considered rare and atypical among non-human animals 7 . We report here the first evidence that song learning in the zebra finch ( Taeniopygia guttata), the most common model species of vocal learning and development, utilizes socially guided vocal learning. We demonstrate experimentally that the songs of juvenile zebra finches are guided toward mature vocal forms by real-time visual feedback from adult females that is contingent on their early, immature vocalizations. Using a video playback paradigm, we found that juvenile birds that received non-vocal female feedback contingently on their immature song learned significantly better and more accurate song than did yoked controls that received identical but non-contingent feedback. Both contingent and non-contingent groups sang at similar rates. Thus, we have provided the first evidence suggesting that non-imitative social learning is a crucial, potentially widespread mechanism of vocal development and have established a foundational parallel between humans and our most ubiquitous animal model of vocal learning: the crucial role of social feedback to immature vocalizations in the development of communication.
crowd vocal learning induces vocal dialects in bats: playback of conspecifics shapes fundamental frequency usage by pups
yosef prat et al. 2017
doi.org/10.1371/journal.pbio.2002556
shearing in flow environment promotes evolution of social behavior in microbial populations
gurdip uppal, dervis vural 2018
doi.org/10.7554/elife.34862
has implications for diversity initiation and maintenance: both fast and slow needed
thinking, fast and slow
daniel kahneman
rate, not selectivity, determines neuronal population coding accuracy in auditory cortex
wensheng sun, dennis l. barbour
doi.org/10.1371/journal.pbio.2002459
when evolution is not a slow dance but a fast race to survive
wendy orent 2017
aeon.co/ideas/when-evolution-is-not-a-slow-dance-but-a-fast-race-to-survive
large–scale ecosystem
biodiversity effects on ecosystem functioning in a 15-year grassland experiment: patterns, mechanisms, and open questions
wolfgang w. weisser et al. 2017
doi.org/10.1016/j.baae.2017.06.002
In the past two decades, a large number of studies have investigated the relationship between biodiversity and ecosystem functioning, most of which focussed on a limited set of ecosystem variables. The Jena Experiment was set up in 2002 to investigate the effects of plant diversity on element cycling and trophic interactions, using a multi-disciplinary approach. Here, we review the results of 15 years of research in the Jena Experiment, focussing on the effects of manipulating plant species richness and plant functional richness. With more than 85,000 measures taken from the plant diversity plots, the Jena Experiment has allowed answering fundamental questions important for functional biodiversity research.
First, the question was how general the effect of plant species richness is, regarding the many different processes that take place in an ecosystem. About 45% of different types of ecosystem processes measured in the ‘main experiment’, where plant species richness ranged from 1 to 60 species, were significantly affected by plant species richness, providing strong support for the view that biodiversity is a significant driver of ecosystem functioning. Many measures were not saturating at the 60-species level, but increased linearly with the logarithm of species richness. There was, however, great variability in the strength of response among different processes. One striking pattern was that many processes, in particular belowground processes, took several years to respond to the manipulation of plant species richness, showing that biodiversity experiments have to be long-term, to distinguish trends from transitory patterns. In addition, the results from the Jena Experiment provide further evidence that diversity begets stability, for example stability against invasion of plant species, but unexpectedly some results also suggested the opposite, e.g. when plant communities experience severe perturbations or elevated resource availability. This highlights the need to revisit diversity–stability theory.
Second, we explored whether individual plant species or individual plant functional groups, or biodiversity itself is more important for ecosystem functioning, in particular biomass production. We found strong effects of individual species and plant functional groups on biomass production, yet these effects mostly occurred in addition to, but not instead of, effects of plant species richness.
Third, the Jena Experiment assessed the effect of diversity on multitrophic interactions. The diversity of most organisms responded positively to increases in plant species richness, and the effect was stronger for above- than for belowground organisms, and stronger for herbivores than for carnivores or detritivores. Thus, diversity begets diversity. In addition, the effect on organismic diversity was stronger than the effect on species abundances.
Fourth, the Jena Experiment aimed to assess the effect of diversity on N, P and C cycling and the water balance of the plots, separating between element input into the ecosystem, element turnover, element stocks, and output from the ecosystem. While inputs were generally less affected by plant species richness, measures of element stocks, turnover and output were often positively affected by plant diversity, e.g. carbon storage strongly increased with increasing plant species richness. Variables of the N cycle responded less strongly to plant species richness than variables of the C cycle.
Fifth, plant traits are often used to unravel mechanisms underlying the biodiversity–ecosystem functioning relationship. In the Jena Experiment, most investigated plant traits, both above- and belowground, were plastic and trait expression depended on plant diversity in a complex way, suggesting limitation to using database traits for linking plant traits to particular functions.
Sixth, plant diversity effects on ecosystem processes are often caused by plant diversity effects on species interactions. Analyses in the Jena Experiment including structural equation modelling suggest complex interactions that changed with diversity, e.g. soil carbon storage and greenhouse gas emission were affected by changes in the composition and activity of the belowground microbial community. Manipulation experiments, in which particular organisms, e.g. belowground invertebrates, were excluded from plots in split-plot experiments, supported the important role of the biotic component for element and water fluxes.
Seventh, the Jena Experiment aimed to put the results into the context of agricultural practices in managed grasslands. The effect of increasing plant species richness from 1 to 16 species on plant biomass was, in absolute terms, as strong as the effect of a more intensive grassland management, using fertiliser and increasing mowing frequency. Potential bioenergy production from high-diversity plots was similar to that of conventionally used energy crops. These results suggest that diverse ‘High Nature Value Grasslands’ are multifunctional and can deliver a range of ecosystem services including production-related services.
A final task was to assess the importance of potential artefacts in biodiversity–ecosystem functioning relationships, caused by the weeding of the plant community to maintain plant species composition. While the effort (in hours) needed to weed a plot was often negatively related to plant species richness, species richness still affected the majority of ecosystem variables. Weeding also did not negatively affect monoculture performance; rather, monocultures deteriorated over time for a number of biological reasons, as shown in plant-soil feedback experiments.
To summarize, the Jena Experiment has allowed for a comprehensive analysis of the functional role of biodiversity in an ecosystem. A main challenge for future biodiversity research is to increase our mechanistic understanding of why the magnitude of biodiversity effects differs among processes and contexts. It is likely that there will be no simple answer. For example, among the multitude of mechanisms suggested to underlie the positive plant species richness effect on biomass, some have received limited support in the Jena Experiment, such as vertical root niche partitioning. However, others could not be rejected in targeted analyses. Thus, from the current results in the Jena Experiment, it seems likely that the positive biodiversity effect results from several mechanisms acting simultaneously in more diverse communities, such as reduced pathogen attack, the presence of more plant growth promoting organisms, less seed limitation, and increased trait differences leading to complementarity in resource uptake. Distinguishing between different mechanisms requires careful testing of competing hypotheses. Biodiversity research has matured such that predictive approaches testing particular mechanisms are now possible.
wolfgang w. weisser et
genetic diversity affects ecological performance and stress response of marine diatom populations
sjöqvist co, kremp a 2017
doi.org/10.1038/ismej.2016.44
genotypic richness and dissimilarity opposingly affect ecosystem functioning
jousset a et al. 2017
doi.org/10.1111/j.1461-0248.2011.01613.x
jousset a et al. 2017 demonstrates a parallel of too much diversity: “increasing richness, without concomitantly increasing dissimilarity, can decrease ecosystem functioning in simple environments due to antagonistic interactions”
climate change and cultural resilience in late pre-columbian amazonia
jonas gregorio de souza et al. 2019
doi.org/10.1038/s41559-019-0924-0
impacts in the Amazon before 1492. Climatic conditions in the Amazon Basin underwent natural shifts during periods when much of the rest of the Earth also was impacted. These times are known as the Medieval Climate Anomaly, from about AD 900 to 1250, and the Little Ice Age, 1450-1850. In Amazonia, rainfall amounts and patterns changed, affecting agriculture and subsistence patterns.
Presently, climate change is affecting most parts of the world; but the difference now is that it's human-caused.
One of the biggest problems in the future may be that climate extremes will harm many countries, and that their "climate refugees" will be pushed from ancestral homes into more temperate and developed places not as badly affected by climate change. The migrations could cause great stresses in the host countries, Power said.
The surprising results of the study show that these types of crises occurred during and after the first millennium in the Amazon Basin.
"Were we getting a window into that in prehistoric Amazonia? I think so," said Power, who is also an associate professor of geography at the University of Utah. "So it's kind of a one-two punch: if the climate doesn't get you, it might be the thousands of bodies that show up that you have to feed because extreme drought forced them out of their homelands."
Climate was a dominant factor in the social and cultural changes in ancient Amazonia, he emphasized, but the study also shows "more nuanced" effects because of subsistence and cultural practices as well as population movements. In particular, those cultural groups that subsisted with diverse food resources or polycultures and agroforestry, avoided political hierarchies with an elite ruling class, and adopted a strategy of creating organic and charcoal-rich soil, called "Amazonian Dark Earth," were most resilient to extreme climate variations.
The scientists searched for indications of prehistoric climate and culture in six regions throughout the enormous Amazon Basin during the last few thousand years: the Guianas Coast, Lianos de Moxos, and the Eastern, Central, Southwestern and Southern Amazon. Up to 8-10 million people were estimated to have lived in the Greater Amazon region before European contact.
Researchers synthesized paleoecological, archaeological and paleoclimate studies by combining evidence of changes in natural vegetation and cultigens, changes in precipitation and disturbance regimes as well as changes in cultural practices and population movements.
Rainfall estimates were derived by measuring the percent of titanium in sediments deposited by runoff, as well as oxygen isotopes in cave speleothem records from across Amazonia. Botanical remains, including phytoliths (microscopic silica formations in plant tissue that are long-lasting in the soil), pollen- and other plant fossil-based evidence of cultigens, including maize, manioc, squash, peanuts and cotton was used to reconstruct subsistence strategies through time.
Another indicator of agricultural practices by some cultures was the presence or lack of Amazonian Dark Earth (ADE) produced by the accumulation of organic materials, including charcoal, into soils through time, which provides a long-term investment in soil fertility, further buffering against extreme changes in climate.
Archaeological remains that indicated social structure and presence and absence of political hierarchies were items such as pottery, elaborate architecture and earthworks, including mounds, raised fields, elite burials, canal systems as well as evidence of fortifications and defensive structures. Whether regions were burned to support agricultural production was another consideration.
Because living plants take up an isotope of carbon called C-14 that dissipates at a known rate after death, researchers compiled hundreds of radiocarbon dates from occupation sites across the Amazon basin. This helped establish the chronology of cultural change and demonstrate how people responded to pressure from climate change and migration.
Paleoecological data was synthesized from a network of sediment cores across Amazonia, from lakes, bogs and wetlands microfossil plant remains, including phytolith, pollen and charcoal records provide information about which types of plants occurred at each site and whether fire was a key process.
A tool that was important to the study is the Global Charcoal Database, which is used to explore linkages among past fire histories, climate change and the role of humans around the globe. Power helped develop the database while a post-doctoral student at the University of Edinburgh, Scotland and is part of an international team, the Global Paleofire Working Group, that continues to contribute to many interdisciplinary studies such as this one.
After synthesizing paleo data with archaeological information on cultures and agricultural practices, the team discovered that at least two different social system trajectories were in place, and that often they had different outcomes, based on flexibility.
"The flexibility, or lack thereof, of these systems explains the decline of some Amazonian societies and not others ..." the report says. Societies that collapsed were at the end of periods of growth, accumulation, restructuring and renewal. "Those societies had accumulated rigidities, and were less able to absorb unforeseen disturbances resulting in dramatic transformation."
Complex societies with social hierarchies and extensive earthworks, including raised fields, supported intensive agriculture of a limited number of crops, but eventually soil leaching and other factors left the villages vulnerable. Such settlements sometimes were able to make short-term improvements; but then, as crises grew, such as a multi-decadal drought, they became in danger of collapse.
However, while some groups underwent major reorganization, the paper says, "others were unaffected and even flourished."
The report details migrations and conflict that took place potentially in response to extreme changes in climate. It notes that the demise of mound centers in the Guianas coast around the year 1300 CE, for example, could have occurred because of a prolonged drought that the researchers documented -- or the expansion of a culture called the Koriabo "could have been responsible for conflicts leading to the ... demise, or at least accelerating a process triggered by climate change."
On the other hand, societies that depended on "polyculture agroforestry," that is, varying crops including fruit-bearing trees, "in the long term, were more resistant to climate change." These were the cultures that also tended to produced ADEs.
Still under debate is whether the formation of anthropic forests were deliberate or a result of people living in an area for centuries and disposing of nuts, seeds and waste that just happened to spread desirable plants and provide a diverse food resource. Power doesn't take a position on that, saying the combination of developing ADEs and polycultures and agroforestry were both long-term solutions to mitigating food scarcity that occurred during times of extreme climate variability, such as during the Medieval Climate Anomaly.
Diverse agriculture associated with the dark soil, with inhabitants growing corn, squash, maniocs and possibly trees, made some groups better able to withstand climate change. But these practices could not prevent conflicts with others who were flooding into their areas because of climate-induced collapse in adjacent regions.
The situation reminds Power of conditions in Ethiopia, a country from which he recently returned and is working on a similar interdisciplinary project trying to understand the rise and fall of the Aksumite Empire. Today, something like 85 percent of the population participates in agriculture production, which still relies on seasonal rainfall in many regions. Climate extremes can cause the wet season to come late some years, or even not come at all.
This causes a ripple effect, encouraging young generations to migrate, mostly to Europe, he said.
Likely, a similar thing happened with migrations in Amazonia in the period before Columbus. The newcomers were "like climate refugees," Power said, "which is an interesting corollary to today's problems."
"I believe the most important aspect of the research is showing how societies respond differently to climate change depending on several factors like the size of their population, their political organization, and their economy," said the study's lead author, Jonas Gregorio de Souza of the Universitat Pompeu Fabra, Barcelona, Spain.
"We started the research expecting that climate change would have had an impact everywhere in the Amazon, but we realized that some communities were more vulnerable than others. To summarize one of the main ideas of the paper, those pre-Columbian peoples that depended heavily on intense and specialized forms of land use ended up being less capable of adapting to climatic events."
abstract The long-term response of ancient societies to climate change has been a matter of global debate. Until recently, the lack of integrative studies using archaeological, palaeoecological and palaeoclimatological data prevented an evaluation of the relationship between climate change, distinct subsistence strategies and cultural transformations across the largest rainforest of the world, Amazonia. Here we review the most relevant cultural changes seen in the archaeological record of six different regions within Greater Amazonia during late pre-Columbian times. We compare the chronology of those cultural transitions with high-resolution regional palaeoclimate proxies, showing that, while some societies faced major reorganization during periods of climate change, others were unaffected and even flourished. We propose that societies with intensive, specialized land-use systems were vulnerable to transient climate change. In contrast, land-use systems that relied primarily on polyculture agroforestry, resulting in the formation of enriched forests and fertile Amazonian dark earth in the long term, were more resilient to climate change.
high functional diversity stimulates diversification in experimental microbial communities
alexandre jousset et al. 2016
doi.org/10.1126/sciadv.1600124
diversity spurs diversification in ecological communities
calcagno v et al. 2017
doi.org/10.1038/ncomms15810
niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly
david tilman 2004
doi.org/10.1073/pnas.0403458101
tilman 2004 holds parallels for our diversity: do certain forms take more resources (attention etc) than others, and thus act to suppress other forms? “the low invasibility of high diversity communities is predicted to result not from diversity per se, but from the uniformly low levels of resources that occur in high-diversity communities created by stochastic competitive assembly”
epigenetic contribution to diversification
heinrich bentea and ortrun mittelsten scheid 2017
doi.org/10.1073/pnas.1702748114
hybrid incompatibility caused by an epiallele
todd blevins et al. 2017
doi.org/10.1073/pnas.1700368114
rarity and persistence
geerat vermeij, richard grosberg 2017
doi.org/10.1111/ele.12872
locally rare species influence grassland ecosystem multifunctionality
soliveres et al. 2016
doi.org/10.1098/rstb.2015.0269
plant soil feedback strength in relation to large-scale plant rarity and phylogenetic relatedness
anne kempel et al. 2018
doi.org/10.1002/ecy.2145
fungal diversity regulates plant-soil feedbacks in temperate grassland
marina semchenko et al. 2018
doi.org/10.1126/sciadv.aau4578
combination cancer therapy can confer benefit via patient-to-patient variability without drug additivity or synergy
adam c. palmer, peter k. sorger 2017
doi.org/10.1016/j.cell.2017.11.009
•Anti-cancer drugs have variable efficacy within patient populations
•Drug combinations give each patient more chances that one drug could be effective
•Clinical efficacy of many combinations is accurately predicted without drug synergy
•Optimizing drug independence represents a new way to design cancer treatments
Combination cancer therapies aim to improve the probability and magnitude of therapeutic responses and reduce the likelihood of acquired resistance in an individual patient. However, drugs are tested in clinical trials on genetically diverse patient populations. We show here that patient-to-patient variability and independent drug action are sufficient to explain the superiority of many FDA-approved drug combinations in the absence of drug synergy or additivity. This is also true for combinations tested in patient-derived tumor xenografts. In a combination exhibiting independent drug action, each patient benefits solely from the drug to which his or her tumor is most sensitive, with no added benefit from other drugs. Even when drug combinations exhibit additivity or synergy in pre-clinical models, patient-to-patient variability and low cross-resistance make independent action the dominant mechanism in clinical populations. This insight represents a different way to interpret trial data and a different way to design combination therapies.
medicines ‘off-label’ to treat people with conditions that these drugs haven’t been tested on
leah shaffer 3017
mosaicscience.com/story/off-label-antidepressants-prescribed-ibd-cancer-pain
reducing urban violence
magdalena cerdá et al. 2017
doi.org/10.1097/EDE.0000000000000756
probabilistic evolution
predicting responses to contemporary environmental change using evolutionary response architectures
rachael a. bay et al. 2017
doi.org/10.1086/691233
peter ralph at uoregon
simons.berkeley.edu/sites/default/files/docs/1594/slidesralph.pdf
computing
epistemological pluralism
turkle and papert 1990
papert.org/articles/EpistemologicalPluralism.html
economy of scale: third partner strengthens a keystone ant-plant mutualism
kirsten m. prior, todd m. palmer 2018
doi.org/10.1002/ecy.2104
benefits for nurse and facilitated plants emerge when interactions are considered along the entire life-span
alicia montesinos-navarro et al. 2019
doi.org/10.1016/j.ppees.2019.125483
The first study to examine plant interactions in a hostile environment over their lifespan found that plants sheltering seedlings help the smaller plant survive and are more successful themselves, a processed in ecology called facilitation.
The study, led by Dr Rocio Pérez-Barrales at the University of Portsmouth and Dr Alicia Montesinos-Navarro at Desertification Research Center in Valencia, Spain, studied adult and seedling plants in the ‘ecological desert’ of gypsum soil in the south-east of Spain.
The findings could have significance for those managing harsh environments including coastal management.
Dr Pérez-Barrales said: “If you’re a seedling in a barren landscape — the top of a mountain or a sand dune, for example — and you’re lucky enough to end up underneath a big plant, your chances of survival are certainly better than if you landed somewhere on your own.
“What we have found which was surprising is an established large plant, called a ‘nurse’, shields a seedling, it also produces more flowers than the same plants of similar large size growing on their own.”
This win-win for adult and seedling plants in harsh environments has not previously been reported.
“Scientists have often looked at such plant relationships and found an adult or a seedling at one stage of its life, and made conclusions,” Dr Pérez-Barrales said. “But by studying these plants’ entire lifespan, from seed germination and establishment, growth of young plants, and flowering in adult plants, we have evidence that the benefits for both stack up over time.”
Dr Pérez-Barrales and her all-female team of scientists studied plant growth in southern Spain over three months during summer. The plants were growing in gypsum, a very poor soil, with little nutrients or water.
They found clear evidence the seedling and nurse were more likely to thrive when grown together, compared to either plant growing alone.
The seedling benefited from shade, more moisture and more nutrients, from the leaf litter of the ‘nurse’ plant, and probably higher bacteria and fungi in the soil, among other things. As it matured, the ‘nurse’ plant grew more flowers than similar plants nearby growing alone, greatly increasing her chances of producing seeds and propagating.
Other benefits of nurse-seedling partnerships include that more variety of plants growing together can trigger a positive cascade effects in the environment. For example, vegetation patches with nurse and facilitated plants with more flower density might be able to attract higher numbers and diversity of pollinators in an area, in turn supporting insect and soil life, and even provide a greater range of different fruit types for birds and mammals.
“The biggest winner for this system of nursing a plant is biodiversity,” Dr Pérez-Barrales said.
“The more biodiverse an area, the more we have a greater number of species of plants, insect life, bacteria, fungi, mammals and birds, the better the chances are of long-term healthy functioning of the environment and ecosystems.”
The research is likely to be of value to those who manage and protect plants in hostile and harsh environments, such as shingle and sand dunes ecosystems, both of which encircle the UK and are considered at high risk due to human intervention and climate change.
Most home gardeners and arable farmers plan to ensure their soil and conditions are the best they can be for optimum plant growth, but the findings might be of value to those who garden in inhospitable places.
Dr Pérez-Barrales suggested gardeners experiment with planting different species of different ages together to test which partnerships help plants thrive in any particular location.
abstract •Reciprocal benefits in plant-plant interactions emerge when the whole life-span is considered.
•Facilitated plants benefit at earlier developmental stages.
•Nurse plants gain a benefit when the original facilitated plants become adults.
The structure of plant communities is often influenced by facilitative interactions where ‘facilitated’ plants benefit from growing associated with ‘nurse’ plants. Facilitation has been mostly studied from the facilitated plant’s perspective, and bidirectional effects between nurse and facilitated plants have received less attention. We hypothesized that reciprocal benefits in plant-plant interactions may emerge when interactions are considered along the life-span of the plants involved. Over one spring, we selected five species with similar life-form and growth strategy, and using a full factorial design, we compared different fitness components along the plants’ life-span (seedling establishment, juvenile growth and reproductive investment in adult plants). We compared: a) plants growing in solitary stands and associated with other plants in vegetation patches; and b) plants that originally functioned as nurse plant (the largest plant of the vegetation patch) and as facilitated (not the largest plant of the vegetation patch). At an early developmental stage, facilitated plants growing in vegetation patches displayed higher seedling establishment and juvenile growth compared to solitary conspecific plants. At a later developmental stage, nurse plants in vegetation patches experienced higher reproductive investment (measured as flower production relative to plant size) compared to solitary plants, while the originally facilitated plants showed similar reproductive investment compared to their solitary pair of similar size. Facilitation is likely a complex interaction in which reciprocal benefits for both facilitated and nurse plants can be detected when interactions are considered along the plants’ life-span. Our results suggest that mutual benefits in plant-plant interactions could be important to sustain diversity in plant communities, but they appeared overlooked and deserve further attention.
young species of cupuladriid bryozoans occupied new caribbean habitats faster than old species
aaron o’dea et al. 2018
doi.org/10.1038/s41598-018-30670-9
different megafauna vary in their seed dispersal effectiveness of the megafaunal fruit platymitra macrocarpa (annonaceae)
kim r. mcconkey et al. 2018
doi.org/10.1371/journal.pone.0198960
species diversity concurrently dilutes and amplifies transmission in a zoonotic host–pathogen system through competing mechanisms
angela d. luis et al. 2018
doi.org/10.1073/pnas.1807106115
the way things are
ole nydahl
isbn 9781846940422
variation in salinity tolerance between and within anadromous subpopulations of pike (esox lucius)
johanna sunde et al. 2018
doi.org/10.1038/s41598-017-18413-8
non–genetic diversity
destabilizing mutations encode nongenetic variation that drives evolutionary innovation
katherine l. petrie et al. 2018
doi.org/10.1126/science.aar1954
alternative ecological strategies lead to avian brain size bimodality in variable habitats
trevor s. fristoe, carlos a. botero et al. 2019
doi.org/10.1038/s41467-019-11757-x
A global study comparing 2,062 birds finds that, in highly variable environments, birds tend to have either larger or smaller brains relative to their body size. Birds with smaller brains tend to use ecological strategies that are not available to big-brained counterparts. Instead of relying on grey matter to survive, these birds tend to have large bodies, eat readily available food and make lots of babies.
The new research from biologists at Washington University in St. Louis appears Aug. 23 in the journal Nature Communications.
"The fact is that there are a great many species that do quite well with small brains," said Trevor Fristoe, formerly a postdoctoral researcher at Washington University, now at the University of Konstanz in Germany.
"What's really interesting is that we don't see any middle ground here," Fristoe said. "The resident species with intermediate brain size are almost completely absent from high latitude (colder and more climatically variable) environments. The species that don't go all in on either of the extreme strategies are forced to migrate to more benign climates during the winter."
"Having a large brain is typically associated with strong energetic demands and a slower life-history," said Carlos Botero, assistant professor of biology in Arts & Sciences and co-author of the paper. "Free from these constraints, species with small brains can exhibit traits and lifestyles that are never seen in larger-brained ones.
"What we found is that alternative ecological strategies that either increase or decrease investments in brain tissue are equally capable of coping with the challenges of living in high-latitude environments," he said.
Because the brain is such a costly organ to develop and maintain, biologists have long been interested in understanding how large brain size -- in all species -- could have evolved.
One hypothesis is based around the idea that one of the main advantages of possessing a big brain is that it allows for a high degree of behavioral flexibility. With flexibility comes the ability to respond to different conditions -- such as wide swings in temperature, or changes in food availability.
The so-called cognitive buffer hypothesis is not the only possible explanation for the evolution of brain size -- but it is an important and influential one.
Relative brain size is a measure of the size of the brain as compared to the body -- think: an ostrich's brain might be much bigger than a chickadee's brain, but so is the ostrich's body. Predictably, the global distribution of relative brain size of birds follows a bell curve, with most species landing squarely in the middle, and only a handful of outliers with relatively large or relatively small brains.
Previous studies had found general trends towards larger relative brain sizes in higher latitudes, where conditions are more variable -- consistent with the cognitive buffer hypothesis. Fristoe and Botero's new study is different because it looks at the full distribution of brain sizes across environments, allowing them to test whether different sizes are over- or under-represented.
Excluding contributions from migrants -- the birds that live in polar or temperate environments only during more favorable times of the year -- the researchers found that at high latitudes, bird brain size appears to be bimodal. This morphological pattern means that bird brains are significantly more likely to be relatively large, or relatively small, compared to body size.
What was going on here? Fristoe, born in Alaska, had a few ideas.
In fact, Fristoe suggests that the Alaska state bird, the ptarmigan, might be a good poster child for the small-brained species. Endearing though she is -- with her plushy bosom, feathered feet and unusual chuckling call -- she's not exactly known for her smarts. The ptarmigan can, however, chow down on twigs and willow leaves with the best of them.
"In our paper, we find that small-brained species in these environments employ strategies that are unachievable with a large brain," Fristoe said. "First, these species are able to persist by foraging on readily available but difficult to digest resources such as dormant plant buds, the needles of conifers, or even twigs.
"These foods can be found even during harsh winter conditions, but they are fibrous and require a large gut to digest," he said. "Gut tissue, like brain tissue, is energetically demanding, and limited budgets mean that it is challenging to maintain a lot of both.
"We also found that these species have high reproductive rates, producing many offspring every year," Fristoe said. "This would allow their populations to recover from high mortality during particularly challenging conditions. Because big-brained species tend to invest more time in raising fewer offspring, this is a strategy that is not available to them."
In other words, maybe big brains are not all that.
"Brains are not evolving in isolation -- they are part of a broader suite of adaptations that help organisms be successful in their lives," Botero said. "Because of trade-offs between different aspects of that total phenotype, we find that two different lineages may respond to selection from environmental oscillations in completely different ways.
"Given that our own species uses its brain to cope with these changes, it is not really surprising that biologists, ourselves included, have historically exhibited a bias toward thinking about environmental variability as a force that drives the expansion of brain size," Botero said. "But the interesting thing that we find here is that when we take a broader view, we realize that other strategies also work -- and remarkably, the alternative here involves making a brain actually smaller!"
abstract The ecological contexts that promote larger brains have received considerable attention, but those that result in smaller-than-expected brains have been largely overlooked. Here, we use a global sample of 2062 species to provide evidence that metabolic and life history tradeoffs govern the evolution of brain size in birds and play an important role in defining the ecological strategies capable of persisting in Earth’s most thermally variable and unpredictable habitats. While some birds cope with extreme winter conditions by investing in large brains (e.g., greater capacity for planning, innovation, and behavioral flexibility), others have small brains and invest instead in traits that allow them to withstand or recover from potentially deadly events. Specifically, these species are restricted to large body sizes, diets consisting of difficult-to-digest but readily available foods, and high reproductive output. Overall, our findings highlight the importance of considering strategic tradeoffs when investigating potential drivers of brain size evolution.
thermal niche evolution across replicated anolis lizard adaptive radiations
alex r. gunderson et al. 2018
doi.org/10.1098/rspb.2017.2241
genetic diversity
predicting population extinctions in darwin’s finches
heather l. farrington et al. 2019
doi.org/10.1007/s10592-019-01175-3
analysis of century-old museum specimens found that six of eight extinct populations had more genetic diversity than similar museum specimens from which descendants survive today. In most other species, low genetic diversity is a signal of a population in decline.
Researchers examined 212 tissue samples from museum specimens and living birds. Some of the museum specimens in the study were collected by Darwin himself in 1835. Only one of the extinct populations, a species called the vegetarian finch, had lower genetic diversity compared to modern survivors.
Lawson said the findings are explained by the fact that these birds can migrate in between populations.
Specifically, researchers believe a biological phenomenon called sink-source dynamics is at play in which larger populations of birds from other islands act as a "source" of immigrants to the island population that is naturally shrinking, the "sink." Without these immigrant individuals, the natural population on the island likely would continue to dwindle to local extinction. The immigrants have diverse genetics because they are coming from a variety of healthier islands, giving this struggling "sink" population inflated genetic diversity.
Petren said the findings serve as a warning that the genetics of individuals in fragmented populations might not tell the whole story about a species. And that is important for scientists who increasingly use genetics to account for the flow of genes between populations when determining a threatened species' likelihood of extinction.
"The promise of genetics is to sample a few individuals to understand the whole population. But it's a cautionary note that you might be sampling a fragment. You could be misled," he said.
abstract Genetic data are increasingly used for fast, efficient, and cost-effective monitoring of natural populations and assessment of extinction risk in species management. A single modern molecular snapshot is typically used to infer population size and vulnerability, yet for species with unknown and potentially complex genetic metapopulation structure, this technique may not effectively predict vulnerability. Darwin’s finches, which are well-represented in museum collections, offer a unique opportunity to test the effectiveness of predicting extinction vulnerability in species with complex structure, such as naturally fragmented populations. In this study, we compared ancient DNA from ~ 100 year old extinct and extant Darwin’s finch populations in the Galápagos Islands to determine whether single time point genetic assessments in the past accurately predicted extinction risk, or if other factors such as metapopulation dynamics could mask population declines. Of eight extinct populations, only one had significantly reduced genetic variation compared to an extant population of similar characteristics. Contrary to our prediction that populations would have decreased genetic diversity prior to extinction when compared to persisting populations, at least one measure of genetic diversity was significantly higher in six of the eight extinct populations when compared to extant populations. Simulations lend support to the hypothesis that unaccounted for metapopulation structure may explain the observed pattern in many species. Therefore, models of genetic diversity reflecting population extinction potential may be inadequate for highly-mobile species with metapopulation dynamics such as the Galápagos finches.
epidermal tissue adapts to restrain progenitors carrying clonal p53 mutations
kasumi murai et al. 2018
doi.org/10.1016/j.stem.2018.08.017
•p53 mutant progenitors outcompete wild-type cells to colonize normal epidermis
•The epidermis adapts to the mutant clones, slowly returning toward normal
•Low-dose UV light drives p53 mutant clone expansion in the short term
•Prolonged UV exposure generates mutant clones that may outcompete p53 mutant cells
Aging human tissues, such as sun-exposed epidermis, accumulate a high burden of progenitor cells that carry oncogenic mutations. However, most progenitors carrying such mutations colonize and persist in normal tissue without forming tumors. Here, we investigated tissue-level constraints on clonal progenitor behavior by inducing a single-allele p53 mutation (Trp53R245W; p53∗/wt), prevalent in normal human epidermis and squamous cell carcinoma, in transgenic mouse epidermis. p53∗/wt progenitors initially outcompeted wild-type cells due to enhanced proliferation, but subsequently reverted toward normal dynamics and homeostasis. Physiological doses of UV light accelerated short-term expansion of p53∗/wt clones, but their frequency decreased with protracted irradiation, possibly due to displacement by UV-induced mutant clones with higher competitive fitness. These results suggest multiple mechanisms restrain the proliferation of p53∗/wt progenitors, thereby maintaining epidermal integrity.
targeted sequencing reveals expanded genetic diversity of human transfer rnas
matthew d. berg et al. 2019
doi.org/10.1080/15476286.2019.1646079
A molecule called tRNA, or transfer ribonucleic acid, is an essential component of the human genome that acts as a translator. It reads the genetic code and translates it into proteins -- one of the key building blocks of the human body.
When researchers and clinicians investigate the genome's relation to disease, they have traditionally focused on mutations in the code for proteins. But now researchers at Western University have shown that the genes encoding tRNAs can also have mutations that cause the code to be misread, and in greater numbers than previously thought.
Think of it like a translator app on your phone -- if it has errors in its software, the output is going to be all wrong, even if the original text is correct.
"This actually changes the way we think about the genetic code," said lead author Mathew Berg, a PhD Candidate at Western's Schulich School of Medicine & Dentistry. "We have shown that variation in tRNA has the potential to lead to a protein being made improperly, which can lead to misfolding and malfunction of the protein."
The research team, led by Schulich Medicine & Dentistry Professors Christopher Brandl, Robert Hegele and Patrick O'Donoghue, say this is significant because many human diseases like Alzheimer's disease and diseases of the heart muscle are linked to misfolded proteins.
"Genetic variation is one of the major reasons why some people acquire a disease while others do not and we expect that an individual with 10 abnormal tRNAs might be more likely to acquire a disease than someone with one," said Brandl. "Another interesting aspect of what we saw is that the profile of tRNAs in even the limited group we looked at was very diverse. No two individuals were the same."
The researchers point out that all previous evidence suggested that there were minimal variations in the tRNA genes, likely attributed to the fact that it hadn't been looked at this closely before. Based on previous evidence, the team only expected to find one or two mutants in the tRNA.
The group, including PhD Candidate Dan Giguere, came up with a new way to sequence and read the tRNA to get a better picture of the variation that exists between individuals. This deep sequencing data gathered at Western showed that human tRNA variation was previously underestimated by more than 30-fold.
In a group of 84 people in London, Ontario they found that individuals contain on average 66 variants in their tRNA genes.
"Because tRNA variation has been hard to analyze, it has largely been overlooked in genetic association studies. Our work suggests that it is important to look at the tRNA genes and we also provide the tools to do so," said Brandl.
Next, the group wants to get a better understanding of exactly how these genes are contributing to disease and determine whether it can be reversed. They also expect that they'll find even greater variation by looking at more diverse populations from other areas around the world.
abstract Transfer RNAs are required to translate genetic information into proteins as well as regulate other cellular processes. Nucleotide changes in tRNAs can result in loss or gain of function that impact the composition and fidelity of the proteome. Despite links between tRNA variation and disease, the importance of cytoplasmic tRNA variation has been overlooked. Using a custom capture panel, we sequenced 605 human tRNA-encoding genes from 84 individuals. We developed a bioinformatic pipeline that allows more accurate tRNA read mapping and identifies multiple polymorphisms occurring within the same variant. Our analysis identified 522 unique tRNA-encoding sequences that differed from the reference genome from 84 individuals. Each individual had ~66 tRNA variants including nine variants found in less than 5% of our sample group. Variants were identified throughout the tRNA structure with 17% predicted to enhance function. Eighteen anticodon mutants were identified including potentially mistranslating tRNAs; e.g., a tRNASer that decodes Phe codons. Similar engineered tRNA variants were previously shown to inhibit cell growth, increase apoptosis and induce the unfolded protein response in mammalian cell cultures and chick embryos. Our analysis shows that human tRNA variation has been underestimated. We conclude that the large number of tRNA genes provides a buffer enabling the emergence of variants, some of which could contribute to disease.
the evolutionary signal in metagenome phyletic profiles predicts many gene functions
vedrana vidulin et al. 2018
doi.org/10.1186/s40168-018-0506-4
hidden genetic variation shapes the structure of functional elements in drosophila
mahul chakraborty et al. 2017
doi.org/10.1038/s41588-017-0010-y
whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate
luana s. f. lins et al. 2017
doi.org/10.1139/gen-2017-0188
a path to more enduring happiness: take a detour from specific emotional goals
maria a. rodas et al. 2018
doi.org/10.1002/jcpy.1042
the case for ecological neutral theory
james rosindell et al. 2012
doi.org/10.1016/j.tree.2012.01.004
density-dependent adult recruitment in a low-density tropical tree
james r. kellner, stephen p. hubbell 2018
doi.org/10.1073/pnas.1800353115
phenotypic diversity
low-fidelity assembly of influenza a virus promotes escape from host cells
michael d. vahey, daniel a. fletcher 2018
doi.org/10.1016/j.cell.2018.10.056
"If you have an environment that is changing rapidly over time, if you were reliant on genetic adaptations, you might be in some trouble, because it takes a certain amount of time for mutations to accumulate." But phenotypic diversity generates changes relatively quickly. Each time a virus replicates, the next generation displays a host of variation, some of which might be suited to the environment where it finds itself.
Scientists have known for decades that a flu virus in a human body can be a lot different than viruses grown in a lab. As opposed to the uniform, spherical, textbook-style viruses in a petri dish, in humans they vary in shape and composition -- particularly the abundance of certain proteins -- even if they are genetically very similar.
It has been difficult to study the exact number and location of these proteins on any individual virus, however. The go-to method in cell biology would involve attaching a fluorescent protein to the area of interest; the light makes the area easier to image and study.
But trying to attach fluorescent proteins to the molecules that make up a flu virus is like trying to get a third person on a tandem bike: There just isn't room. The fluorescent proteins are about the same size as the flu proteins; introducing such a relatively large element throws the virus out of whack.
A paper by Michael Vahey, assistant professor in the School of Engineering & Applied Science at Washington University in St. Louis and Daniel A. Fletcher, Purnendu Chatterjee Chair in Engineering Biological Systems and Chair of Bioengineering at the University of California, Berkeley, demonstrates that flu proteins can be tagged using a different method. The process has already yielded information that hints to one advantage at minimum for having so many flu phenotypes, that is, various shapes and configurations found in genetically identical flu particles.
The paper was published November 9 in the journal Cell.
"Under what circumstances is it adaptive, and how so?" Vahey asked. "This is a first step toward understanding that. But it's not a complete picture."
In order to move past the labeling difficulties, Vahey adapted a method that is typically used to label a specific area on a protein called, appropriately, "site-specific labeling." Instead of using a fluorescent protein, he inserted sequences five- to 10-amino-acids-long into the proteins that make up Influenza A virus. This is the most common flu virus, and also the most dangerous to humans.
After inserting these short sequences, he introduced enzymes and small amounts of fluorescent dyes. These enzymes take different dye molecules and connect them to the engineered viral proteins, giving researchers the ability to see individual proteins without disrupting how they -- or the virus they make up -- functions.
Of particular interest to researchers are the proteins hemagglutinin (HA) and neuraminidase (NA). HA is responsible for allowing a flu virus to attach to a cell and NA is responsible for decoupling the virus from the cell so that it can go on to infect others. (This is where designations such as H1N1 or H3N2 come from; the surface of the virus has different types of HA and NA that are referred to by specific numbers, or subtypes).
"Once we have the ability to label individual viruses, we can image them and quantify how much of each protein they have per particle, and what the size of that particle is," Vahey said.
Utilizing site-specific labeling overcomes a longstanding challenge in the study of flu viruses. Now that they could take a more detailed look, Vahey and Fletcher decided to do just that, setting up an experiment that might help them understand whether or not the variation seen in individual flu viruses might be adaptive, helping the virus to spread infection.
The researchers studied individual flu viruses released from cells, some of which were treated with a substance that blocks NA from doing its job, releasing the virus from a cell. (This is how the antiviral drug Tamiflu works. If the virus cannot release itself from the cell, it cannot spread and reproduce).
Then they compared the virus particles that were able to detach from the untreated cells to those that were able to detach from the cells treated with the NA inhibitor.
Hooking up: One way the flu may species-hop
You've heard of avian flu and swine flu. That's because Influenza is zoonotic, it can be transferred from one animal to another. The heterogeneous nature of the virus may help it do this.
"Typically the receptor that the virus binds to in not identical in, say a bird and a human," said Michael Vahey, assistant professor in the School of Engineering & Applied Science but flu virus binds to receptors almost like Velcro. "There are many different hooks, the more you have, the harder it is to peel it off." In the case of Influenza, the "hooks" are hemagglutinin, (HA).
It's possible that a variant animal flu virus with a high number of HA can successfully attach to a human cell, creating new ways to make humans miserable with the flu.
"What we found is that viruses that are smaller, or have more NA, are more resistant to the NA inhibitor," Vahey said. "They were more likely to be able to detach from a cell that has been challenged with Tamiflu." They could then go on to infect more cells.
The results suggest that these two variations -- being smaller than average, or having more NA -- could be beneficial for a virus that found itself in a person who had been treated with Tamiflu. It's one example of how having lots of diversity among individual viruses might be advantageous.
On the other hand, viruses with more HA, or that are larger, can bind more strongly to cells. "Under any particular circumstance, it might be beneficial to be anywhere within that range," Vahey said. "In the case of Tamiflu treatment, you're inhibiting NA such that the viruses that happen to have more NA and also happen to be smaller now have a little bit of a leg up."
More broadly, Vahey said, "If you have an environment that is changing rapidly over time, if you were reliant on genetic adaptations, you might be in some trouble, because it takes a certain amount of time for mutations to accumulate." But phenotypic diversity generates changes relatively quickly. Each time a virus replicates, the next generation displays a host of variation, some of which might be suited to the environment where it finds itself.
Down the line, the importance of phenotype may have implications for the development of new flu vaccines. "Typically in the development of a flu vaccine, you're concerned about how genetic changes in the virus may reduce the effectiveness of the vaccine," Vahey said. "This could be an additional consideration, how variation in viral phenotype may contribute."
abstract
•Influenza A virus forms morphologically and compositionally heterogeneous progeny
•Heterogeneity is encoded in assembly and can depend on the growth environment
•Progeny of individual virions are as variable as the progeny of large populations
•Phenotypic variability helps subsets of the population to escape NA inhibitors
Influenza viruses inhabit a wide range of host environments using a limited repertoire of protein components. Unlike viruses with stereotyped shapes, influenza produces virions with significant morphological variability even within clonal populations. Whether this tendency to form pleiomorphic virions is coupled to compositional heterogeneity and whether it affects replicative fitness remains unclear. Here, we address these questions by developing a strain of influenza A virus amenable to rapid compositional characterization through quantitative, site-specific labeling of viral proteins. Using this strain, we find that influenza A produces virions with broad variations in size and composition from even single infected cells. This phenotypic variability contributes to virus survival during environmental challenges, including exposure to antivirals. Complementing genetic adaptations that act over larger populations and longer times, this “low-fidelity” assembly of influenza A virus allows small populations to survive environments that fluctuate over individual replication cycles.
large teams develop science and technology; small teams disrupt it
lingfei wu et al. 2019
doi.org/10.1038/s41586-019-0941-9
researchers examined 60 years of publications and found that smaller teams were far more likely to introduce new ideas to science and technology, while larger teams more often developed and consolidated existing knowledge.
While both large and small teams are essential for scientific progress, the findings suggest that recent trends in research policy and funding toward big teams should be reassessed.
"Big teams are almost always more conservative. The work they produce is like blockbuster sequels; very reactive and low-risk." said study co-author James Evans, professor of sociology, director of the Knowledge Lab at UChicago and a leading scholar in the quantitative study of how ideas and technologies emerge. "Bigger teams are always searching the immediate past, always building on yesterday's hits. Whereas the small teams, they do weird stuff -- they're reaching further into the past, and it takes longer for others to understand and appreciate the potential of what they are doing."
Knowledge Lab is a unique research center that combines "science of science" approaches from sociology with the explosion of digital information now available on the history of research and discovery. By using advanced computational techniques and developing new tools, Knowledge Lab researchers reconstruct and examine how knowledge over time grows and influences our world, generating insights that can fuel future innovation.
The Nature study collected 44 million articles and more than 600 million citations from the Web of Science database, 5 million patents from the U.S. Patent and Trademark Office, and 16 million software projects from the Github platform. Each individual work in this massive dataset was then computationally assessed for how much it disrupted versus developed its field of science or technology.
"Intuitively, a disruptive paper is like the moon during the lunar eclipse; it overshadows the sun -- the idea it builds upon -- and redirects all future attention to itself," said study co-author Lingfei Wu, a postdoctoral researcher with the University of Chicago and Knowledge Lab. "The fact that most of the future works only cite the focal paper and not its references is evidence for the 'novelty' of the focal paper. Therefore, we can use this measure, originally proposed by Funk and Owen-Smith, as a proxy for the creation of new directions in the history of science and technology."
Across papers, patents and software products, disruption dramatically declined with the addition of each additional team member. The same relationship appeared when the authors controlled for publication year, topic or author, or tested subsets of data, such as Nobel Prize-winning articles. Even review articles, which simply aggregate the findings of previous publications, are more disruptive when authored by fewer individuals, the study found.
The main driver of the difference in disruption between large and small teams appeared to be how each treat the history of their field. Larger teams were more likely to cite more recent, highly cited research in their work, building upon past successes and acknowledging problems already in their field's zeitgeist. By contrast, smaller teams more often cited older, less popular ideas, a deeper and wider information search that creates new directions in science and technology.
"Small teams and large teams are different in nature," Wu said. "Small teams remember forgotten ideas, ask questions and create new directions, whereas large teams chase hotspots and forget less popular ideas, answer questions and stabilize established paradigms."
The analysis shows that both small and large teams play important roles in the research ecosystem, with the former generating new, promising insights that are rapidly developed and refined by larger teams. Some experiments are so expensive, like the Large Hadron Collider or the search for dark energy, that they can only be answered by a single, massive collaboration. But other complex scientific questions may be more effectively pursued by an ensemble of independent, risk-taking small teams rather than a large consortium, the authors argue.
"In the context of science, funders around the world are funding bigger and bigger teams," Evans said. "What our research proposes is that you really want to fund a greater diversity of approaches. It suggests that if you really want to build science and technology, you need to act like a venture capitalist rather than a big bank -- you want to fund a bunch of smaller and largely disconnected efforts to improve the likelihood of major, pathbreaking success."
"Most things are going to fail, or are not going to push the needle within a field. As a result it's really about optimizing failure," Evans added. "If you want to do discovery, you have to gamble."
abstract One of the most universal trends in science and technology today is the growth of large teams in all areas, as solitary researchers and small teams diminish in prevalence1,2,58. Increases in team size have been attributed to the specialization of scientific activities58, improvements in communication technology59,60, or the complexity of modern problems that require interdisciplinary solutions6,7,8. This shift in team size raises the question of whether and how the character of the science and technology produced by large teams differs from that of small teams. Here we analyse more than 65 million papers, patents and software products that span the period 1954–2014, and demonstrate that across this period smaller teams have tended to disrupt science and technology with new ideas and opportunities, whereas larger teams have tended to develop existing ones. Work from larger teams builds on more-recent and popular developments, and attention to their work comes immediately. By contrast, contributions by smaller teams search more deeply into the past, are viewed as disruptive to science and technology and succeed further into the future—if at all. Observed differences between small and large teams are magnified for higher-impact work, with small teams known for disruptive work and large teams for developing work. Differences in topic and research design account for a small part of the relationship between team size and disruption; most of the effect occurs at the level of the individual, as people move between smaller and larger teams. These results demonstrate that both small and large teams are essential to a flourishing ecology of science and technology, and suggest that, to achieve this, science policies should aim to support a diversity of team sizes.
the importance of cognitive diversity for sustaining the commons
jacopo a. baggio et al. 2019
doi.org/10.1038/s41467-019-08549-8
"Individuals often have different cognitive abilities," Baggio says. "For example, individuals with high general intelligence will be more able to discern patterns and dynamics of resources, and individuals with high social intelligence communicate more effectively and understand the mental state of others."
Using a digital game to simulate a virtual ecosystem, the researchers found that when teams of people with high general intelligence, but low social intelligence faced a situation where resources became scarce, those teams depleted resources faster, harvested less potential resources and pushed the ecosystem to its limits.
But when both general and social intelligence were high, teams harvested a greater percentage of potential resources and kept the ecosystem from collapsing.
"It's a way to really start to understand how individuals and groups interact and what type of individuals are more prone or less prone to favor group benefits over individual costs," Baggio says.
General intelligence helped people figure out the rules of the game and how the resources, in this case digital tokens, regenerated, while social intelligence helped people cooperate to optimize performance, says Thomas Coyle, co-author of the study and professor of psychology at the University of Texas at San Antonio.
"In theory, people with higher levels of social intelligence are more effective in reducing conflict among group members and in getting people to work toward common goals," Coyle says. "Such 'people' skills are important for managing shared resources."
The work points to a need for education in diverse types of intelligence, says Jacob Freeman, an assistant professor of anthropology at Utah State University and study co-author.
"It suggests that our education systems should focus on cultivating both general and social intelligence to better equip groups to deal with complex, social-ecological challenges," Freeman says.
Coyle says researchers are still exploring ways to improve social intelligence.
For the study, the researchers used a digital game where people collected virtual tokens in exchange for actual money. Participants were 216 undergraduates from two large universities in the Western United States. They were randomly placed into one of two experimental conditions: either a game where the conditions began improving and tokens continued to be replenished, or one where conditions began deteriorating and tokens did not regenerate fast enough.
General intelligence was represented by ACT and SAT scores provided by the universities. Social intelligence was measured using a short story test that estimated the ability of individuals to infer others' intentions and feelings. The test is often used to predict social communication disorders, communication errors and the ability to infer the mental states of others
abstract Cognitive abilities underpin the capacity of individuals to build models of their environment and make decisions about how to govern resources. Here, we test the functional intelligences proposition that functionally diverse cognitive abilities within a group are critical to govern common pool resources. We assess the effect of two cognitive abilities, social and general intelligence, on group performance on a resource harvesting and management game involving either a negative or a positive disturbance to the resource base. Our results indicate that under improving conditions (positive disturbance) groups with higher general intelligence perform better. However, when conditions deteriorate (negative disturbance) groups with high competency in both general and social intelligence are less likely to deplete resources and harvest more. Thus, we propose that a functional diversity of cognitive abilities improves how effectively social groups govern common pool resources, especially when conditions deteriorate and groups need to re-evaluate and change their behaviors.
physiological evolution during adaptive radiation: a test of the island effect in anolis lizards
jhan c. salazar et al. 2019
doi.org/10.1111/evo.13741
The idea that evolution can be slow on islands is actually somewhat strange. Ever since Darwin's journey to the Galapagos, islands have been recognized as hotspots of rapid evolution, resulting in many ecologically diverse species. The reason why evolution often goes into overdrive on islands has to do with the ecological opportunity presented by simplified environments. When organisms wash up on remote islands, they find themselves freed of their usual competitors and predators, which frees them to rapidly diversify to fill new niches. This phenomenon of faster evolution is often referred to as the "island effect."
Yet, the researchers discovered that physiological evolution in Anolis lizards is actually much slower on islands than on the mainland. What is causing evolution to stall?
The same ecological opportunity that frees island organisms from predators also facilitates behavioral thermoregulation. "Whereas mainland lizards spend most of their time hiding from predators, island lizards move around more, and are able to spend much of their day precisely shuttling between sun and shade," said Muñoz, assistant professor in the Department of Biological Sciences in the College of Science.
If it gets too hot, island lizards simply go find a shady spot. If it gets too cold, they can dash onto a sunny perch. By thermoregulating, island lizards are not just buffering themselves from thermal variation. They are effectively shielding themselves from natural selection. If lizards aren't exposed to extreme temperatures, then selection on physiology is weakened. The result? Slower rates of physiological evolution. Effectively, island lizards use behavioral thermoregulation like SPF against natural selection!
Jhan Salazar said, "Our results show that faster evolution on islands is not a general rule." This slower physiological evolution on islands stands in stark contrast to morphology, which has been shown to evolve faster in island anoles. When it comes to morphology and physiology on islands, it seems we are looking at different sides of the same coin. The same ecological release from predators and competition that allowed for the truly impressive amount of morphological diversification that has appeared quickly among island anoles, seems to additionally allow for more behavioral thermoregulation which slows physiological evolution.
"We are discovering that organisms are the architects of their own selective environments meaning that behavior and evolution are locked together in a delicate dance. This pas de deux tells us something important about how diversity arises in nature," said Muñoz
abstract Phenotypic evolution is often exceptionally rapid on islands, resulting in numerous, ecologically diverse species. Although adaptive radiation proceeds along various phenotypic axes, the island effect of faster evolution has been mostly tested with regard to morphology. Here, we leveraged the physiological diversity and species richness of Anolis lizards to examine the evolutionary dynamics of three key traits: heat tolerance, body temperature, and cold tolerance. Contrary to expectation, we discovered slower heat tolerance evolution on islands. Additionally, island species evolve toward higher optimal body temperatures than mainland species. Higher optima and slower evolution in upper physiological limits are consistent with the Bogert effect, or evolutionary inertia due to thermoregulation. Correspondingly, body temperature is higher and more stable on islands than on the American mainland, despite similarity in thermal environments. Greater thermoregulation on islands may occur due to ecological release from competitors and predators compared to mainland environments. By reducing the costs of thermoregulation, ecological opportunity on islands may actually stymie, rather than hasten, physiological evolution. Our results emphasize that physiological diversity is an important axis of ecological differentiation in the adaptive radiation of anoles, and that behavior can impart distinct macroevolutionary footprints on physiological diversity on islands and continents.
alternative responses to rare selection events are differentially vulnerable to changes in the frequency, scope, and intensity of environmental extremes
thomas r. haaland, carlos a. botero 2019
doi.org/10.1002/ece3.5675
challenges the idea that species previously exposed to more variable conditions are more likely to survive extreme events.
"It is difficult to predict how organisms will respond to changes in extreme events because these events tend to be, by definition, quite rare," Botero said. "But we can have a pretty good idea of how any given species may respond to current changes in this aspect of climate -- if we pay attention to its natural history, and have some idea of the climatic regime it has experienced in the past."
Unexpected vulnerabilities
Researchers in the Botero laboratory use a variety of tools from ecology and evolutionary biology to explore how life -- from bacteria to humans -- copes with and adapts to repeated environmental change.
For the new study, Botero worked with his former student Haaland, now a postdoctoral fellow at the University of Zurich in Switzerland, to develop an evolutionary model of how populations respond to rare environmental extremes. (Think: 500-year floods.) These rare events can be tricky for evolution because it is difficult to adapt to hazards that are almost never encountered.
Through computer simulations, Haaland and Botero found that certain traits and experiences emerged as key indicators of vulnerability.
Specifically, they found:
Species that breed a single time in their lifetime tend to evolve conservative behaviors or morphologies, as if they were expecting to experience an environmental extreme every time.
In contrast, species in which a single individual can reproduce multiple times and in different contexts (say, a bird that nests several times in a season and in different trees), evolution favors behaving as if environmental extremes simply never happen.
The key insight of this new model is that species belonging to the former, "conservative" category can easily adapt to more frequent or widespread extremes but have trouble adjusting when those extremes become more intense. The opposite is true of species in the latter, "care-free" category.
Haaland and Botero also found that factors speeding up trait evolution are generally likely to hinder -- rather than favor -- adaptation to rare selection events. Part of the reason: High mutation rates tend to facilitate the process of adaptation to normal conditions during the long intervals in between environmental extremes.
"Our results challenge the idea that species that have been historically exposed to more variable environments are better suited to cope with climate change," Botero said.
"We see that simple changes in the pattern and intensity of environmental extremes could be lethal even for populations that have experienced similar events in the past. This model simply helps us better understand when and where we may have a problem."
Applicable to many environmental extremes
The simple framework that Haaland and Botero describe can be applied to any kind of environmental extreme including flooding, wildfires, heatwaves, droughts, cold spells, tornadoes and hurricanes -- any and all of which might be considered part of the "new normal" under climate change.
Take extreme heat as an example. The model can be used to predict what will happen to animal or plant species when there are more heat waves, when heatwaves last longer, or when typical heat waves affect larger areas.
"Regions in which heat waves used to be rare and patchy are likely to host primarily species that do not exhibit conspicuous adaptations to extreme heat," Botero said. "Our model indicates that the biggest threats of extinction in these particular locations will therefore be more frequent or widespread heat waves, and that the species of highest concern in these places will be endemics and species with small geographic distribution.
"Conversely, areas in which heat waves were historically common and widespread can be expected to host species that already exhibit adaptations for extreme heat," Botero added. "In this case, our model suggests that the typical inhabitants of these places are likely to be more vulnerable to hotter temperatures than to longer or more widespread heat waves."
Informing conservation actions
The new model gives wildlife managers and conservation organizations insight into the potential vulnerabilities of different species based on relatively simple assessments of their natural histories and historical environments.
For example, a 2018 study by Colin Donihue, visiting postdoctoral fellow at Washington University, found that Anolis lizards in the Caribbean tend to evolve larger toepads and shorter limb lengths in response to hurricanes because these traits help them cling better to branches during strong winds. The new model suggests that while these lizards are unlikely to be affected by more frequent hurricanes, their populations may nevertheless face a significant threat of extinction if future hurricanes become more intense. A possible solution to this problem might be to provide wind refuges across the island to allow parts of the population escape winds of very high intensity, Botero suggested.
"While this simple conservation action is unlikely to completely shift the balance from a 'conservative' to a 'care-free' evolutionary response to extreme events, it may nevertheless reduce the strongest vulnerability of these 'conservative' lizard populations," Botero said. "It might just buy them enough time to accumulate sufficient evolutionary changes in their toes and limbs to meet the new demands of their altered habitat."
abstract Extreme weather events are becoming more frequent, severe, and/or widespread as a consequence of anthropogenic climate change. While the economic and ecological implications of these changes have received considerable attention, the role of evolutionary processes in determining organismal responses to these critical challenges is currently unknown. Here we develop a novel theoretical framework that explores how alternative pathways for adaptation to rare selection events can influence population‐level vulnerabilities to future changes in the frequency, scope, and intensity of environmental extremes. We begin by showing that different life histories and trait expression profiles can shift the balance between additive and multiplicative properties of fitness accumulation, favoring different evolutionary responses to identical environmental phenomena. We then demonstrate that these different adaptive outcomes lead to predictable differences in population‐level vulnerabilities to rapid increases in the frequency, intensity, or scope of extreme weather events. Specifically, we show that when the primary mode of fitness accumulation is additive, evolution favors ignoring environmental extremes and lineages become highly vulnerable to extinction if the frequency or scope of extreme weather events suddenly increases. Conversely, when fitness accumulates primarily multiplicatively, evolution favors bet‐hedging phenotypes that cope well with historical extremes and are instead vulnerable to sudden increases in extreme event intensity. Our findings address a critical gap in our understanding of the potential consequences of rare selection events and provide a relatively simple rubric for assessing the vulnerabilities of any population of interest to changes in a wide variety of extreme environmental phenomena.
behavioural plasticity is associated with reduced extinction risk in birds
simon ducatez et al. 2020
doi.org/10.1038/s41559-020-1168-8
birds that were able to incorporate new foods into their diet or develop new techniques to obtain food were better able to withstand the environmental changes affecting their habitat, which represent their main threat of extinction.
Throughout the years, scientists have noticed numerous examples of these behaviours. Green herons have been repeatedly observed using bread or insects as bait to catch fish. Opportunistic carrion crows have been seen using cars as nut- or seashell-crackers. Great cormorants in New Zealand have been observed coordinating their fishing periods with the movements of commercial ferries in order to take advantage of the strong currents generated by the propellers to catch confused fish.
Proving a long-held theory about species vulnerability
The ability to innovate, a measure of 'behavioural plasticity', has long been thought to render species less vulnerable to the risk of extinction, but it has been difficult to test this thoroughly on a global level.
Louis Lefebvre, the senior author of the new study, who teaches in McGill's Biology Department, he has spent the last 20 years combing through the literature, searching for evidence of foraging innovations in the wild. Thanks to the tireless dedication of bird watchers from around the world who have reported these novel behaviours, he has been able to compile a database of over 3,800 bird foraging innovations.
"The large database we now have has allowed us to test, on almost all bird species of the world, the idea that the more you can change your feeding behaviour, the better you might be able to cope with destruction of your normal habitat," said Lefebvre. "We feel our results are solid, as we have taken into account as many co-variables and possible biases that we could think of."
More innovations mean a greater probability of population stability or increase
The researchers gathered information about the feeding innovations described in articles published in 204 ornithological journals between 1960 and 2018.They then compared the number of observed innovations of each species with the level of their risk of extinction according to the Red List of the International Union for Conservation of Nature (IUCN). Their modelling showed that extinction risk was reduced in species that displayed innovative behaviours, and as the number of these behaviours increased, extinction risk was reduced further.
"We long suspected that this relationship between innovation and survival must exist, but now we have been able to verify it quantitatively," says the study's first author, Simon Ducatez, a post-doctoral researcher at McGill University and at CREAF in Barcelona. "We have also been able to verify that the greater the number of innovations described for a species, the greater the probability that its populations are stable or increasing. The result is clear: the greater the innovative capacity, the lower the risk of extinction of the species."
Ability to find new food sources no guarantee of survival
The authors caution that behavioural plasticity only reduces birds' risk of extinction from habitat alteration, and that it does not affect sensitivity to invasive species or overexploitation. The study reveals that the ability to invent new behaviours represents a clear evolutionary advantage for birds coping with the destruction of their habitats, although it is not always a guarantee of survival.
Indeed, the type of problem-solving skills that allow birds to face drastic changes in habitat does not seem to work against other types of threats such as over hunting. "It must be taken into account that the species with the greatest capacity for innovation have longer generation times, which makes them more vulnerable to hunting," explains Daniel Sol, researcher at CREAF and the CSIC in Barcelona. "This implies that, unlike what is usually assumed, the ability to innovate protects animals from some but not all of the rapid changes in the environment."
abstract Behavioural plasticity is believed to reduce species vulnerability to extinction, yet global evidence supporting this hypothesis is lacking. We address this gap by quantifying the extent to which birds are observed behaving in novel ways to obtain food in the wild; based on a unique dataset of >3,800 novel behaviours, we show that species with a higher propensity to innovate are at a lower risk of global extinction and are more likely to have increasing or stable populations than less innovative birds. These results mainly reflect a higher tolerance of innovative species to habitat destruction, the main threat for birds.
ecologically diverse clades dominate the oceans via extinction resistance
matthew l. knope et al. 2020
doi.org/10.1126/science.aax6398
examined approximately 20,000 genera (groups of related species) of fossil marine animals across the past 500 million years, and approximately 30,000 genera of living marine animals.
The findings clearly show that the species in the most diverse animal groups also tend to be more mobile and more varied in how they feed and live, notes lead study author Matthew Knope, assistant professor of biology at the University of Hawai`i at Hilo.
“Being a member of an ecologically flexible group makes you resistant to extinction, particularly during mass extinctions,” he says. “The oceans we see today are filled with a dizzying array of species in groups like fishes, arthropods, and mollusks, not because they had higher origination rates than groups that are less common, but because they had lower extinction rates over very long intervals of time.”
The “slow and steady” development of lineages through time has been a key factor in dictating which lineages have achieved the highest diversity.
Michal Kowalewski, professor of invertebrate paleontology at the University of Florida, who was not involved with the study, said the study highlights “the value of paleontological data for assessing core questions of biology.”
“Perhaps the fable of the tortoise and the hare is apt in explaining marine animal diversification: some groups jumped out to an early diversity lead only to be surpassed by other groups that were more ecologically diverse and less evolutionarily volatile, with steady diversification rates and strong resistance to mass extinctions,” adds Knope.
abstract Ecological differentiation is correlated with taxonomic diversity in many clades, and ecological divergence is often assumed to be a cause and/or consequence of high speciation rate. However, an analysis of 30,074 genera of living marine animals and 19,992 genera of fossil marine animals indicates that greater ecological differentiation in the modern oceans is actually associated with lower rates of origination over evolutionary time. Ecologically differentiated clades became taxonomically diverse over time because they were better buffered against extinction, particularly during mass extinctions, which primarily affected genus-rich, ecologically homogeneous clades. The relationship between ecological differentiation and taxonomic richness was weak early in the evolution of animals but has strengthened over geological time as successive extinction events reshaped the marine fauna.
evenness effects mask richness effects on ecosystem functioning at macro‐scales in lakes
christopher t. filstrup et al. 2019
doi.org/10.1111/ele.13407
suggests that species richness -- the number of different species in a given ecological community -- is not the only, nor necessarily the best, way to measure biodiversity impacts on ecosystems. A stronger measure to predict how well the ecosystem is functioning is how evenly the species are distributed.
For example, in Filstrup's research on algae in lakes, he looked at whether or not multiple species have about the same number of individuals in a community, no matter the number of different species. It's easy to understand that having similar numbers of species across a community is a good thing. What's unexpected is that "even" communities don't always lead to high-functioning or highly productive ecosystems, as scientists thought.
"Evenness of species tends to be overlooked, but we found it can be more important than richness when predicting how well ecosystems function," said Filstrup. "As scientists, we need to determine how ecosystems will respond to environmental change, including biodiversity loss, especially when it impacts things we care about, like water quality and aquatic food webs."
Consider the harm caused by overabundant and toxic algae in lakes. This is an example of a highly "uneven" ecological community where one species takes over. While some algal blooms are benign and promote a healthy food web, toxic algal blooms can lead to health problems and water quality issues. An example on the land are prairies that have more evenly distributed plant species that leads to higher productivity.
Ecosystems with reduced biodiversity may not be as resilient to new or changing stressors. In those situations, climate change and land use in watersheds are more impactful compared to ecosystems with more diverse communities. A species that dominates under one set of conditions may perform poorly under another set of conditions.
Filstrup leads the water quality program at NRRI and is focused on understanding changes to Minnesota lakes. For this study, however, he pulled in U.S. Environmental Protection Agency data from 1,130 lakes across the U.S. with researchers Katelyn King and Ian McCullough from Michigan State University.
"We thought we'd find these responses only in intense agricultural regions," said Filstrup. "But we found these strong but opposite responses to 'evenness' throughout very different regions of the country, suggesting this may be the rule rather than the exception."
abstract Biodiversity–ecosystem functioning (BEF) theory has largely focused on species richness, although studies have demonstrated that evenness may have stronger effects. While theory and numerous small‐scale studies support positive BEF relationships, regional studies have documented negative effects of evenness on ecosystem functioning. We analysed a lake dataset spanning the continental US to evaluate whether strong evenness effects are common at broad spatial scales and if BEF relationships are similar across diverse regions and trophic levels. At the continental scale, phytoplankton evenness explained more variance in phytoplankton and zooplankton resource use efficiency (RUE; ratio of biomass to resources) than richness. For individual regions, slopes of phytoplankton evenness–RUE relationships were consistently negative and positive for phytoplankton and zooplankton RUE, respectively, and most slopes did not significantly differ among regions. Findings suggest that negative evenness effects may be more common than previously documented and are not exceptions restricted to highly disturbed systems.
is local biodiversity declining or not? a summary of the debate over analysis of species richness time trends
bradley j. cardinale et al. 2018
doi.org/10.1016/j.biocon.2017.12.021
•Recent analyses of time-series data suggest biodiversity is not declining at local scales as often claimed.
•We argue existing time-series are inappropriate for testing hypotheses about biodiversity change.
•Datasets are low quality, lack spatial representation, and fail to account for key drivers of change.
•Failure to consider these problems has led to misinterpretations and unwarranted extrapolations.
•New analyses must use higher-quality datasets to test improved hypotheses about diversity change.
Recently, a debate has developed over how biodiversity is changing across the planet. While most researchers agree species extinctions are increasing globally due to human activity, some now argue that species richness at local scales is not declining as many biologists have claimed. This argument stems from recent syntheses of time-series data that suggest species richness is decreasing in some locations, increasing in others, but not changing on average. Critics of these syntheses (like us) have argued there are serious limitations of existing time-series datasets and their analyses that preclude meaningful conclusions about local biodiversity change. Specifically, authors of these syntheses have failed to account for several primary drivers of biodiversity change, have relied on data poor time-series that lack baselines needed to detect change, and have unreasonably extrapolated conclusions. Here we summarize the history of this debate, as well as key papers and exchanges that have helped clarify new issues and ideas. To resolve the debate, we suggest future researchers be more clear about the hypotheses of biodiversity change being tested, focus less on amassing large datasets, and more on amassing high-quality datasets that provide unambiguous tests of the hypotheses. Researchers should also keep track of the contributions that native versus non-native species make to biodiversity time trends, as these have different implications for conservation. Lastly, we suggest researchers be aware of pros and cons of using different types of data (e.g., time-series, spatial comparisons), taking care to resolve divergent results among sources to allow broader conclusions about biodiversity change.
biodiversity gains? the debate on changes in local- vs global-scale species richness
richard b. primack et al. 2018
doi.org/10.1016/j.biocon.2017.12.023
inheritors of the earth: how nature is thriving in an age of extinction
chris thomas 2017
not recommended
endorsed by matt ridley, explains a lot
aggregated knowledge from a small number of debates outperforms the wisdom of large crowds
joaquin navajas et al. 2018
doi.org/10.1038/s41562-017-0273-4
measuring the crowd within: probabilistic representations within individuals
edward vul, harold pashler 2008
doi.org/10.1111/j.1467-9280.2008.02136.x
’it’s not a tumor’: a framework for capitalizing on individual diversity to boost target detection
jennifer e. corbett, jaap munneke 2018
doi.org/10.1177/0956797618784887
one and done? optimal decisions from very few samples
the “fundamental attribution error” is rational in an uncertain world
drew walker, kevin smith, edward vul
how diversity makes us smarter: being around people who are different from us makes us more creative, more diligent and harder-working
katherine w. phillips 2014
www.scientificamerican.com/article/how-diversity-makes-us-smarter/
why diversity programs fail
frank dobbin, alexandra kalev 2016
hbr.org/2016/07/why-diversity-programs-fail
successfully communicating a cocreated innovation
helen si wang et al. 2019
doi.org/10.1177/0022242919841039
Is the cocreation model a legitimate strategy to drive innovation and adoption of resulting products -- or is it flawed by design? Marketing communications is often regarded as one of the major influences on innovation adoption and creators typically take two approaches to marketing new products. They either share a consumer creation or genesis story (also called user-generated content or UGC) or use more traditional, firm-generated content (FGC) that often stresses a feature's products and benefits. This research shows that it is wise to combine these strategies but with an interesting twist on conventional advertising wisdom.
When sharing a genesis story, creators tend to take one of two tacks: 1) an approach-oriented message about how they achieved new or desired outcomes; or 2) an avoidance-oriented message that promises to help users avoid unpleasant or undesirable outcomes they themselves experienced. Advertising best practice stresses that a firm should use consistent messaging to communicate with customers.
This practice does not hold up to scrutiny in the area of co-created products, however. Instead, the researchers found that a mixed or "mismatch" communication strategy works best to speed individual and mass consumer adoption. A mismatch communication strategy means that if the product creator's claim is approach-oriented, the firm should use an avoidance-oriented and vice versa.
As an example, for the cocreated Starbucks® Doubleshot Energy Mexican Mocha Coffee Drink, the creators' authentic message was approach-oriented and focused on "Embracing winter... fueling me with all of the winter warmth and energy I want." When the researchers combined this with an avoidance firm message, "What the world can't miss this winter... say bye-bye to the winter chill and blues" to make a mismatch strategy, adoption levels increased compared to when the approach firm message was used -- "What the world desires this winter... makes you embrace all the winter warmth and joy."
Key findings from five studies include:
Products using a mismatch strategy were adopted 56.1% of the time compared to 26.3% of those using matching communication strategies.
This approach works best with low-expertise consumers who reference their own life stories when buying and using goods. High-expertise consumers are less motivated by this approach.
Firms using a mismatch communication strategy are 10% more likely to experience early takeoff, which is critical to the mass adoption of the innovation.
"This research offers important implications for managers and companies seeking to leverage the creative power of the crowd in developing innovations," says Wang. Noble adds, "Our findings challenge the conventional wisdom in many marketing campaigns. If you want takeoff, mismatch your message with the innovator creator's message."
abstract Despite the growing popularity of cocreation approaches to innovation, the bottom-line results of these efforts continue to frustrate many firms. Marketing communications are one important tool in stimulating consumer adoption, yet marketers to date have not taken advantage of a unique phenomenon associated with many cocreated innovations: the presence of a genesis story in the words of the creator, which can be combined in different ways with traditional marketing messaging. Using mixed methods, the authors demonstrate a crossover effect in which a “mismatch” of the fundamental motivations behind authentic creation narratives and traditional persuasive messages enhances adoption of the cocreated innovation. This effect is mediated by potential adopters’ self-referencing of their own stories about similar experiences or consumption episodes. Furthermore, the effect of a motivation mismatch strategy is attenuated for expert consumers. Finally, this motivation mismatch strategy triggers “takeoff” of cocreated innovations. This research offers substantial implications for research on cocreated innovation, narrative persuasion, and firm-generated and user-generated communication. It provides managers specific guidance on enhancing the success of cocreation programs through an integrated communications strategy.
nest carbon dioxide masks gaba-dependent seizure susceptibility in the naked mole-rat
michael zions et al. 2020
doi.org/10.1016/j.cub.2020.03.071
some people with seizures have something similar — are they evolved for a particular niche too?
African naked mole-rats are sometimes referred to as animal superheroes. They resist cancer, tolerate pain, and live a remarkably long time. They're also known for their ability to handle high levels of carbon dioxide and can go for several minutes without oxygen. But researchers reporting in Current Biology on April 30 say they may have found the mole-rats' kryptonite: they need high levels of carbon dioxide to function.
"While they thrive in their cramped nest quarters, the air composition just above the surface of their burrows in East Africa makes them vulnerable to seizures," said Dan McCloskey of The City University of New York. "Because that's what happens when naked mole-rats lose carbon dioxide."
In other words, the mole-rats don't just tolerate high levels of carbon dioxide in their crowded nests; it appears that they actually require it. When they reach the hot surface and start heat-induced hyperventilation in the fresh air, it sends them into seizures. In the study now reported, the researchers found that this curious need for carbon dioxide is explained by the presence of a missense mutation in a gene that encodes the major neuronal chloride transporter known as KCC2.
The researchers came to this discovery in an unexpected way. Naked mole-rats have little control over their body temperature and also are prone to seizing in response to heat, they knew. McCloskey and first author of the new study Michael Zions had been exploring this susceptibility to fever-like conditions as a model for fever-induced (febrile) seizures in human children.
The team joined forces with Kai Kaila and Martin Puskarjov, University of Helsinki, Finland. Kaila, an expert in febrile seizures, and Puskarjov had earlier found a mutation affecting KCC2 in families of people prone to them. What they now know is that mole-rats and those families with a genetic predisposition for febrile seizures carry the very same genetic change.
"We knew there was some value in the line of inquiry, but we had no idea that the similarities would go all the way down to the genetic level," Kaila said.
"The identification of the genetic polymorphism in the naked mole-rat KCC2 was a surprise," Puskarjov added. "Aside from a small subset of humans, naked mole-rats are now the only other mammals known to harbor this variant."
Further study yielded more surprises. When the researchers gave a naked mole-rat the anti-seizure drug diazepam, the drug triggered a seizure rather than preventing one. While the result was unexpected, it helped them make sense of years of unusual behavioral and electrophysiological data: the naked mole-rats were relying on carbon dioxide to help them compensate for deficiencies in their brain's inhibitory GABAergic system.
KCC2 is a chloride transporter: its normal job is to control the amount of chloride inside of neurons. In a typical adult mammal, chloride levels in central neurons are kept low. When the neurotransmitter GABA binds to a neuron, chloride enters and blocks the activity of the neuron. This ability to reduce neural activity is essential for many thousands of neurons to work together in coordinated fashion and avoid becoming overexcited. In the naked mole-rat and people with the mutation, KCC2 doesn't clear chloride from neurons as effectively. As a result, this inhibitory cascade doesn't work as well.
"Naked mole-rat brains lack some of the inhibition that a mammal needs. Instead, they're using the carbon dioxide to get back to where they have to be," Zions said. "They prefer CO2 levels that would panic a person, but are troubled by fresh air. They've leveraged a liability to literally dig themselves a niche."
As the researchers explain, an inhibition-impaired brain would normally be a handicap as it is in people prone to febrile seizures. It works for naked mole-rats because they rely on their carbon dioxide-rich environments to help keep their brain within normal parameters. "We believe they are utilizing nest carbon dioxide to offset their impoverished GABA system," Kaila said.
The researchers think the findings may provide an essential clue as to why the naked mole-rats are one of only two mammalian species to evolve eusociality, living together in highly cooperative colonies.
"Low carbon dioxide areas may cause hyperexcitability and overstimulation or anxiety. Their brain physiology urges them to go back to the nest rather than set out on their own," McCloskey said. Support for this idea comes from the researchers' discovery that the only other eusocial mammal, the Damaraland mole-rat, has a slightly different mutation in the exact same location on the KCC2 gene as the naked mole-rat.
In addition to the insights into mole-rat evolution, the findings may also have implications for people who carry the KCC2 variant, including those prone to febrile seizures and people with idiopathic generalized epilepsy, schizophrenia, or autism who in some cases also have the variant, according to the researchers. "The breathing patterns and carbon dioxide needs of these individuals is something to consider," Kaila said.
abstract African naked mole-rats were likely the first mammals to evolve eusociality, and thus required adaptations to conserve energy and tolerate the low oxygen (O2) and high carbon dioxide (CO2) of a densely populated fossorial nest. As hypercapnia is known to suppress neuronal activity, we studied whether naked mole-rats might demonstrate energy savings in GABAergic inhibition. Using whole-colony behavioral monitoring of captive naked mole-rats, we found a durable nest, characterized by high CO2 levels, where all colony members spent the majority of their time. Analysis of the naked mole-rat genome revealed, uniquely among mammals, a histidine point variation in the neuronal potassium-chloride cotransporter 2 (KCC2). A histidine missense substitution mutation at this locus in the human ortholog of KCC2, found previously in patients with febrile seizures and epilepsy, has been demonstrated to diminish neuronal Cl extrusion capacity, and thus impairs GABAergic inhibition. Seizures were observed, without pharmacological intervention, in adult naked mole-rats exposed to a simulated hyper- thermic surface environment, causing systemic hypocapnic alkalosis. Consistent with the diminished function of KCC2, adult naked mole-rats demonstrate a reduced efficacy of inhibition that manifests as triggering of seizures at room temperature by the GABAA receptor (GABAAR) positive allosteric modulator diazepam. These seizures are blocked in the presence of nest-like levels of CO2 and likely to be mediated through GABAAR activity, based on in vitro recordings. Thus, altered GABAergic inhibition adds to a growing list of adaptations in the naked mole-rat and provides a plausible proximate mechanism for nesting behavior, where a return to the colony nest restores GABA-mediated inhibition.
food availability drives plastic self-repair response in a basal metazoan- case study on the ctenophore mnemiopsis leidyi a. agassiz 1865
katharina tissy bading et al. 2017
doi.org/10.1038/s41598-017-16346-w
the effect of nanosecond pulsed high frequency discharges on the temperature evolution of ignition kernels
jonathan m. bonebrake et al. 2018
doi.org/10.1016/j.proci.2018.06.027
teeming: how superorganisms work together to build infinite wealth on a finite planet
tamsin woolley-barker 2018
the secret life of your microbiome: why nature and biodiversity are essential to health and happiness
susan prescott 2017
cool: how the brain’s hidden quest for cool drives our economy and shapes our world
steven quartz & anette asp 2015
the end of average: how we succeed in a world that values sameness
todd rose 2016
complexity: the evolution of earth’s biodiversity and the future of humanity
william c. burger 2016
range: why generalists triumph in a specialized world
david epstein 2019
sorry i’m late, i didn’t want to come: an introvert’s year of living dangerously
jessica pan 2019
gödel, escher, bach: an eternal golden braid
douglas hofstadter 1979
inclusify: the power of uniqueness and belonging to build innovative teams
stefanie johnson 2020
I said that setting goals is good, and one woman in the back of the room raised her hand and asked, “If you set targets, won’t people think they were just hired because of their race? I wouldn’t want to get a job because of my gender.”
I heard a great response to this from my friend Tara Dunn, the president of HighMark Law. She said, “Okay, if thirty percent of the time you don’t get the job because you’re a woman and thirty percent of the time you think you’re only getting the job because you’re a woman, and thirty percent of the time you really are not qualified, then you only have access to a tenth of the jobs out there. Just take the job.
Napoleon Bonaparte: “The people to fear are not those who disagree with you, but those who disagree with you and are too cowardly to let you know.”
great adaptations: star-nosed moles, electric eels, and other tales of evolution’s mysteries solved
kenneth catania 2020
why hiring the ‘best’ people produces the least creative results
scott page 2018
https://aeon.co/ideas/why-hiring-the-best-people-produces-the-least-creative-results
groups of diverse problem solvers can outperform groups of high-ability problem solvers
lu hong and scott page 2004
https://doi.org/10.1073/pnas.0403723101
the diversity bonus: how great teams pay off in the knowledge economy
scott e page 2017 9780691176888
not yet read
the difference: how the power of diversity creates better groups, firms, schools, and societies
to read next
diversity and complexity
to read next
why some people are impossibly talented
david robson 2019
bbc.com/worklife/article/20191118-what-shapes-a-polymath---and-do-we-need-them-more-than-ever
the polymath: unlocking the power of human versatility
waqas ahmed 2019
what if driving force of evolution is not niche variability but need for diversity? eventually suitable diverse form arrives in niche and happens to be more suited than general or previous form, so comes by chance to be more in that niche. the different species we see in different niches arise not because of the niches themselves but because the species arise or arrive suited to the niche? really need to read darwin’s words closely on this, as the general perception is that a niche causes speciation.
species diversity can drive speciation
researchgate.net/publication/7891932_Species_diversity_can_drive_speciation
“diversity begets diversity' hypothesis (Hypothesis 2; Van Valen, 1973; Rohde, 1992; Gillooly et al., 2004; Emerson & Kolm, 2005 )”
“One recurring theme is how diversity drives further diversity: do species create opportunities for speciation (MacArthur 1972; Strong et al. 1984; Farrell et al. 1992; Emerson & Kolm 2005; Janz et al. 2006)?”
but this disputes it
researchgate.net/publication/6016891_Species_diversity_can_drive_speciation_Comment
They argued that this positive relationship indicates speciation drives species richness. However, this speciation-driven hypothesis has been challenged by several other studies (Cadena et al. 2005, Kiflawi et al. 2007, Pereira et al. 2007, Whittaker et al. 2007, Witt and Maliakal-Witt 2007, Birand and Howard 2008, Gruner et al. 2008). The point of debate is not so much about how speciation could promote species diversity (this is rather obvious) but about whether the endemics–diversity relationship is a reliable testimony of this speciation-driven hypothesis.
Link: 01093-ff9f956a44c231f6f87c02669fbb7732.html