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173 results for “evolutionary dynamics”
Code from: A theoretical framework for trait-based eco-evolutionary dynamics: population structure, intraspecific variation, and community assembly
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Data from: Keystone individuals alter ecological and evolutionary consumer-resource dynamics
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Data from: Landscape-scale eco-evolutionary dynamics: selection by seed predators and fire determine a major reproductive strategy
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Data from: The interaction between the Linnean and Darwinian shortfalls affects our understanding of the evolutionary dynamics driving diversity patterns of New World coralsnakes
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Data from: Estimating dispersal and evolutionary dynamics in diploporan blastozoans (Echinodermata) across the Great Ordovician Biodiversification Event
<p><b>Echinoderms make up a substantial component of Ordovician marine invertebrates, yet their speciation and dispersal history as inferred within a rigorous phylogenetic and statistical framework is lacking. We use Biogeographic Stochastic Mapping (BSM; implemented in the R package BioGeoBEARS) to infer ancestral area relationships and the number and type of dispersal events through the Ordovician for diploporan blastozoans and related species. The BSM analysis was divided into three time slices to analyze how dispersal paths changed before and during the Great Ordovician Biodiversification Event (GOBE) and within the Late Ordovician mass extinction intervals. The best-fit biogeographical model incorporated jump dispersal, indicating this was an important speciation strategy. Reconstructed areas within the phylogeny indicate the first diploporan blastozoans likely originated within Baltica or Gondwana. Dispersal, jump dispersal, and sympatry dominated the BSM inference through the Ordovician, while dispersal paths varied in time. Long-distance dispersal events in the Early Ordovician indicate distance was not a significant predictor of dispersal, whereas increased dispersal events between Baltica and Laurentia are apparent during the GOBE, indicating these areas were important to blastozoan speciation. During the Late Ordovician, there is an increase in dispersal events among all paleocontinents. The drivers of dispersal are attributed to oceanic and epicontinental currents. Speciation events plotted against geochemical data indicate that blastozoans may not have responded to climate cooling events and other geochemical perturbations, but additional data will continue to shed light into the drivers of early Paleozoic blastozoan speciation and dispersal patterns.</b></p>
Data from: Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga)
Low rates of sequence evolution associated with purifying selection can be interrupted by episodic changes in selective regimes. Visual pigments are a unique system in which we can investigate the functional consequences of genetic changes, therefore connecting genotype to phenotype in the context of natural and sexual selection pressures. We study the RH2 and RH1 visual pigments (opsins) across 22 bird species belonging to two ecologically convergent clades, the New World warblers (Parulidae) and Old World warblers (Phylloscopidae) and evaluate rates of evolution in these clades along with data from 21 additional species. We demonstrate generally slow evolution of these opsins: both Rh1 and Rh2 are highly conserved across Old World and New World warblers. However, Rh2 underwent a burst of evolution within the New World genus Setophaga, where it accumulated substitutions at 6 amino acid sites across the species we studied. Evolutionary analyses revealed a significant increase in dN/dS in Setophaga, implying relatively strong selective pressures to overcome long-standing purifying selection. We studied the effects of each substitution on spectral tuning and found they do not cause large spectral shifts. Thus, substitutions may reflect other aspects of opsin function, such as those affecting photosensitivity and/or dark–light adaptation. Although it is unclear what these alterations mean for colour perception, we suggest that rapid evolution is linked to sexual selection, given the exceptional plumage colour diversification in Setophaga.
Data from: The evolutionary dynamics of adaptive virginity, sex-allocation and altruistic helping in haplodiploid animals
In haplodiploids, females can produce sons from unfertilized eggs without mating. However, virgin reproduction is usually considered to be a result of a failure to mate, rather than an adaptation. Here we build an analytical model for evolution of virgin reproduction, sex-allocation, and altruistic female helping in haplodiploid taxa. We show that when mating is costly (e.g. when mating increases predation risk), virginity can evolve as an adaptive female reproductive strategy. Furthermore, adaptive virginity results in strongly divergent sex-ratios in mated and virgin queen nests ('split sex ratios'), which promotes the evolution of altruistic helping by daughters in mated queen nests. However, when helpers evolve to be efficient and increase nest production significantly, virgin reproduction is selected against. Our results suggest that adaptive virginity could have been an important stepping stone on the pathway to eusociality in haplodiploids. We further show that virginity can be an adaptive reproductive strategy also in primitively social haplodiploids if workers bias the sex ratio toward females. By remaining virgin, queens are free to produce sons, the more valuable sex in a female-biased population. Our work brings a new dimension to the studies linking reproductive strategies with social evolution.
Data from: Does past evolutionary history under different mating regimes influence the demographic dynamics of interspecific competition?
Interspecific interactions are contingent upon organism phenotypes, and thus phenotypic evolution can modify interspecific interactions and affect ecological dynamics. Recent studies have suggested that male-male competition within a species selects for capability to reproductively interfere with a closely related species. Here we examine the effect of past evolutionary history under different mating regimes on the demographic dynamics of interspecific competition in Callosobruchus seed beetles. We used previously established experimental evolution lines of C. chinensis that evolved under either forced lifelong monogamy or polygamy for 17 generations, and examined the demographic dynamics of competition between these C. chinensis lines and a congener, C. maculatus. Callosobruchus chinensis was competitively excluded by C. maculatus in all trials. Time series data analyses suggested that reproductive interference from C. chinensis was relatively more important in the trials involving polygamous C. chinensis than those involving monogamous C. chinensis, in accordance with the potentially higher reproductive interference capability of polygamous C. chinensis. However, the estimated signs and magnitudes of interspecific interactions were not fully consistent with this explanation, implying the evolution of not only reproductive interference but also other interaction mechanisms. Our study thus suggests multifaceted effects of sexually-selected traits on interspecific competitive dynamics.
Data from: Mechanical sensitivity reveals evolutionary dynamics of mechanical systems
A classic question in evolutionary biology is how form–function relationships promote or limit diversification. Mechanical metrics, such as kinematic transmission (KT) in linkage systems, are useful tools for examining the evolution of form and function in a comparative context. The convergence of disparate systems on equivalent metric values (mechanical equivalence) has been highlighted as a source of potential morphological diversity under the assumption that morphology can evolve with minimal impact on function. However, this assumption does not account for mechanical sensitivity—the sensitivity of the metric to morphological changes in individual components of a structure. We examined the diversification of a four-bar linkage system in mantis shrimp (Stomatopoda), and found evidence for both mechanical equivalence and differential mechanical sensitivity. KT exhibited variable correlations with individual linkage components, highlighting the components that influence KT evolution, and the components that are free to evolve independently from KT and thereby contribute to the observed pattern of mechanical equivalence. Determining the mechanical sensitivity in a system leads to a deeper understanding of both functional convergence and morphological diversification. This study illustrates the importance of multi-level analyses in delineating the factors that limit and promote diversification in form–function systems.
Data from: Eco-evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations
Although numerous hypotheses exist to explain the overwhelming presence of sexual reproduction across the tree of life, we still cannot explain its prevalence when considering all inherent costs involved. The Red Queen hypothesis states that sex is maintained because it can create novel genotypes with a selective advantage. This occurs when the interactions between species induce frequent environmental change. Here we investigate whether coevolution and eco-evolutionary feedback dynamics in a predator-prey system allows for indirect selection and maintenance of sexual reproduction in the predator. Combining models and chemostat experiments of a rotifer-algae system we show a continuous feedback between population and trait change along with recurrent shifts from selection by predation and competition for a limited resource. We found that a high propensity for sex was indirectly selected and was maintained in rotifer populations within environments containing these eco-evolutionary dynamics; whereas within environments under constant conditions, predators evolved rapidly to lower levels of sex. Thus, our results indicate that the influence of eco-evolutionary feedback dynamics on the overall evolutionary change has been underestimated.
Data from: Genome-wide evolutionary dynamics of influenza B viruses on a global scale
The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally.
Data from: Eco-evolutionary dynamics of sexual selection and sexual conflict
1.The research framework of eco‐evolutionary dynamics is increasing in popularity, as revealed by a steady stream of review articles and a recent and influential book, but primary empirical research is lagging behind. Moreover, the few empirical case studies demonstrating eco‐evolutionary dynamics might not be entirely representative. 2.Much current research on eco‐evolutionary dynamics is focused on how ecological interactions lead to natural selection on phenotypic traits ("eco‐evo"), and in turn how the evolutionary change in such traits feed back on ecological dynamics ("evo‐eco"). A key feature of eco‐evolutionary dynamics is thus a feedback loop between ecology (e. g. population dynamics) and evolution (i. e. genetic change). 3.In contrast to previous research on eco‐evolutionary dynamics driven by natural selection, the role of eco‐evolutionary feedbacks in sexual selection and sexual conflict are largely unknown. Here, I review theory and the limited empirical evidence in this area and identify some promising future lines of research. 4.I update a past review on contemporary evolution of secondary sexual traits in natural populations and formulate six explicit and rigorous criteria for contemporary evolution of secondary sexual traits by natural or sexual selection or sexual conflict. I then discuss the other key prediction of eco‐evolutionary dynamics (i. e. evolution by sexual selection or sexual conflict shapes ecological dynamics). My overview reveal that our current knowledge in this area is limited and mainly come from theoretical models and laboratory experiments. 5.A major challenge in eco‐evolutionary dynamics is therefore to link ecological and population dynamics with sexual selection and sexual conflict. This is not an easy task but might be possible with carefully chosen study systems and methods.
Data from: Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with E. coli
Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.
Data from: Environmental fluctuations restrict eco-evolutionary dynamics in predator-prey system
Environmental fluctuations, species interactions and rapid evolution are all predicted to affect community structure and their temporal dynamics. Although the effects of the abiotic environment and prey evolution on ecological community dynamics have been studied separately, these factors can also have interactive effects. Here we used bacteria–ciliate microcosm experiments to test for eco-evolutionary dynamics in fluctuating environments. Specifically, we followed population dynamics and a prey defence trait over time when populations were exposed to regular changes of bottom-up or top-down stressors, or combinations of these. We found that the rate of evolution of a defence trait was significantly lower in fluctuating compared with stable environments, and that the defence trait evolved to lower levels when two environmental stressors changed recurrently. The latter suggests that top-down and bottom-up changes can have additive effects constraining evolutionary response within populations. The differences in evolutionary trajectories are explained by fluctuations in population sizes of the prey and the predator, which continuously alter the supply of mutations in the prey and strength of selection through predation. Thus, it may be necessary to adopt an eco-evolutionary perspective on studies concerning the evolution of traits mediating species interactions.
Data from: The architecture of river networks can drive the evolutionary dynamics of aquatic populations
It is widely recognized that physical landscapes can shape genetic variation within and between populations. However, it is not well understood how riverscapes, with their complex architectures, affect patterns of neutral genetic diversity. Using a spatially explicit agent-based modeling (ABM) approach, we evaluate the genetic consequences of dendritic river shapes on local population structure. We disentangle the relative contribution of specific river properties to observed patterns of genetic variation by evaluating how different branching architectures and downstream flow regimes affect the genetic structure of populations situated within river networks. Irrespective of the river length, our results illustrate that the extent of river branching, confluence position, and levels of asymmetric downstream migration dictate patterns of genetic variation in riverine populations. Indeed, comparisons between simple and highly branched rivers show a 20-fold increase in the overall genetic diversity and a 7-fold increase in the genetic differentiation between local populations. Given that most rivers have complex architectures, these results highlight the importance of incorporating riverscape information into evolutionary models of aquatic species and could help explain why riverine fishes represent a disproportionately large amount of global vertebrate diversity per unit of habitable area.
Data from: Evolutionary dynamics of interlinked public goods traits: an experimental study of siderophore production in Pseudomonas aeruginosa
Public goods cooperation is common in microbes, and there is much interest in understanding how such traits evolve. Research in recent years has identified several important factors that shape the evolutionary dynamics of such systems, yet few studies have investigated scenarios involving interactions between multiple public goods. Here we offer general predictions about the evolutionary trajectories of two public goods traits having positive, negative or neutral regulatory influence on one another's expression, and we report on a test of some of our predictions in the context of Pseudomonas aeruginosa's production of two interlinked iron-scavenging siderophores. First, we confirmed that both pyoverdine and pyochelin siderophores do operate as public goods under appropriate environmental conditions. We then tracked their production in lines experimentally evolved under different iron-limitation regimes known to favour different siderophore expression profiles. Under strong iron limitation, where pyoverdine represses pyochelin, we saw a decline in pyoverdine and a concomitant increase in pyochelin – consistent with expansion of pyoverdine-defective cheats derepressed for pyochelin. Under moderate iron limitation, pyochelin declined – again consistent with an expected cheat invasion scenario – but there was no concomitant shift in pyoverdine because cross-suppression between the traits is unidirectional only. Alternating exposure to strong and moderate iron-limitation caused qualitatively similar though lesser shifts compared to the constant-environment regimes. Our results confirm that the regulatory inter-connections between public goods traits can significantly modulate the course of evolution, yet also suggest how we can start to predict the impacts such complexities will have on phenotypic divergence and community stability.
Data from: Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana
Anticipating the effect of climate change on plants requires understanding its evolutionary consequence on traits and genes in complex realistic environments. How seasonal variation has an impact on the dynamics of adaptation in natural populations remains unclear. We simulated adaptation to different climate change scenarios, grounding our analysis in experimental data and explicitly exploring seasonal variation. Seasonal variation dramatically affected the dynamics of adaptation: Marked seasonality led to genetic differentiation within the population to different seasonal periods, whereas low seasonality led to a single population with fast-evolving fitness. Our results suggest the prevalence of phenotypic plasticity across environmental conditions in determining how climate change will shift selection on traits and loci. In this unpredictable context, maintaining broad genomic diversity is critical.
Data from: Evolutionary history of Daphnia drives divergence in grazing selectivity and alters temporal community dynamics of producers
Consumers with different seasonal life histories encounter different communities of producers during specific seasonal phases. If consumers evolve to prefer the producers that they encounter, then consumers may reciprocally influence the temporal composition of producer communities. Here we study the keystone consumer Daphnia ambigua, whose seasonal life history has diverged due to intraspecific predator divergence across lakes of New England. We ask whether grazing preferences of Daphnia have diverged also, and test whether any grazing differences influence temporal composition patterns of producers. We reared clonal populations of Daphnia from natural populations representing the two diverged life history types for multiple generations. We conducted short-term (24 hours) and long-term (27 days) grazing experiments in equal polycultures consisting of 3 diatom and 2 green algae species, treated with no consumer, Daphnia from lakes with anadromous alewife, or from lakes with landlocked alewife. After 24 hours, life history and grazing preference divergence in Daphnia ambigua drove significant differences in producer composition. However, those differences disappeared at the end of the 27-day experiment. Our results illustrate that, despite potentially more complex long-term dynamics, a multitrophic cascade of evolutionary divergence from a predator can influence temporal community dynamics at the producer level.
Data from: Inference of Japanese encephalitis virus ecological and evolutionary dynamics from passive and active virus surveillance
A comprehensive monitoring strategy is vital for tracking the spread of mosquito-borne Japanese encephalitis virus (JEV), the leading cause of viral encephalitis in Asia. Virus detection consists of passive surveillance of primarily humans and swine, and/or active surveillance in mosquitoes, which may be a valuable proxy in providing insights into ecological processes underlying the spread and persistence of JEV. However, it has not been well characterized whether passive surveillance alone can capture the circulating genetic diversity to make reasonable inferences. Here, we develop phylogenetic models to infer JEV host changes, spatial diffusion patterns, and evolutionary dynamics from data collected through active and passive surveillance. We evaluate the feasibility of using JEV sequence data collected from mosquitoes to estimate the migration histories of genotypes GI and GIII. We show that divergence times estimated from this dataset were comparable to estimates from all available data. Increasing the amount of data collected from active surveillance improved time of most recent common ancestor estimates and reduced uncertainty. Phylogenetic estimates using all available data and only mosquito data from active surveillance produced similar results, showing that GI epidemics were widespread and diffused significantly faster between regions than GIII. In contrast, GIII outbreaks were highly structured and unlinked suggesting localized, unsampled infectious sources. Our results show that active surveillance of mosquitoes can sufficiently capture circulating genetic diversity of JEV to confidently estimate spatial and evolutionary patterns. While surveillance of other hosts could contribute to more detailed disease tracking and evaluation, comprehensive JEV surveillance programs should include systematic surveillance in mosquitoes to infer the most complete patterns for epidemiology, and risk assessment.
Data from: Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa
The production of beneficial public goods is common in the microbial world, and so is cheating – the exploitation of public goods by non-producing mutants. Here, we examine co-evolutionary dynamics between cooperators and cheats and ask whether cooperators can evolve strategies to reduce the burden of exploitation, and whether cheats in turn can improve their exploitation abilities. We evolved cooperators of the bacterium Pseudomonas aeruginosa, producing the shareable iron-scavenging siderophore pyoverdine, together with cheats, defective in pyoverdine production but proficient in uptake. We found that cooperators managed to co-exist with cheats in 56% of all replicates over approximately 150 generations of experimental evolution. Growth and competition assays revealed that co-existence was fostered by a combination of general adaptions to the media and specific adaptions to the co-evolving opponent. Phenotypic screening and whole-genome re-sequencing of evolved clones confirmed this pattern, and suggest that cooperators became less exploitable by cheats because they significantly reduced their pyoverdine investment. Cheats, meanwhile, improved exploitation efficiency through mutations blocking the costly pyoverdine-signalling pathway. Moreover, cooperators and cheats evolved reduced motility, a pattern that likely represents adaptation to laboratory conditions, but at the same time also affects social interactions by reducing strain mixing and pyoverdine sharing. Overall, we observed parallel evolution, where co-existence of cooperators and cheats was enabled by a combination of adaptations to the abiotic and social environment and their interactions.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.