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173 results for “evolutionary dynamics”
Evolutionary dynamics of structural variation at a key locus for color pattern diversification in cichlid fishes
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Data from: Eco-evolutionary metapopulation dynamics of Batesian mimicry: Conditions for mimics without models
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Data from: Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents
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Eco-evolutionary dynamics modulate plant responses to global change depending on plant diversity and species identity
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Summary data for plots in: Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations
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Trophic cascades alter eco-evolutionary dynamics and body size evolution
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Data from: Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences
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Data for: Morphological covariance and onset of foot prehensility as indicators of integrated evolutionary dynamics in the herons (Ardeidae)
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Eco‐evolutionary dynamics driven by fishing: from single species models to dynamic evolution within complex food webs
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Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae) - test dataset
<p><strong>Objectives :</strong></p> <p>Examine salinity tolerance and adaptations to low salinities in a freshwater strain of Ectocarpuson physiological and molecular levels.</p> <p><strong>Cohort :</strong></p> <p>Two clonal strains of Ectocarpus sp. (Ectocarpales, Phaeophyceae), the genome-sequenced marine strain (MS) (accession CCAP 1310/4, origin San Juan de Marcona, Peru) and a freshwater strain (FWS, accession CCAP 1310/196, origin Hopkins River Falls, Victoria, Australia) were used.</p> <p><strong>Mass spectrometer :</strong></p> <p><br> Gas chromatography-mass spectrometry (GC-MS) as described by Ritteret al.(2008) : samples were analysed with a Hewlett-Packard 5873 Mass Selective Detector interfaced to a Hewlett-Packard 6890 Series+ gas chromatograph (Agilent, Les Ullis, France).</p>
Impact of Pleistocene eustatic fluctuations on evolutionary dynamics in Southeast Asian biodiversity hotspots
Pleistocene Climatic Fluctuations (PCF) are frequently highlighted as important evolutionary engines that triggered cycles of biome expansion and contraction. While there is ample evidence of the impact of PCF on biodiversity for continental biomes, the consequences in insular systems depend on the geology of the islands and the ecology of the taxa inhabiting them. The idiosyncratic aspects of insular systems are exemplified by the islands of the Sunda Shelf in Southeast Asia (Sundaland), where PCF-induced eustatic fluctuations had complex interactions with the geology of the region, resulting in high species diversity and endemism. Emergent land in Southeast Asia varied drastically with sea level fluctuations during the Pleistocene. Climate-induced fluctuations in sea level caused temporary connections between insular and continental biodiversity hotspots in Southeast Asia. These exposed lands likely had freshwater drainage systems that extended between modern islands: the Paleoriver Hypothesis. Built upon the assumption that aquatic organisms are among the most suitable models to trace ancient river boundaries and fluctuations of landmass coverage, the present study aims to examine the evolutionary consequences of PCF on the dispersal of freshwater biodiversity in Southeast Asia. Time-calibrated phylogenies of DNA-delimited species were inferred for six species-rich freshwater fish genera in Southeast Asia (Clarias, Channa, Glyptothorax, Hemirhamphodon, Dermogenys, Nomorhamphus). The results highlight rampant cryptic diversity and the temporal localization of most speciation events during the Pleistocene, with 88% of speciation events occurring during this period. Diversification analyses indicate that sea level-dependent diversification models poorly account for species proliferation patterns for all clades excepting Channa. Ancestral area estimations point to Borneo as the most likely origin for most lineages, with two waves of dispersal to Sumatra and Java during the last 5 Myrs. Speciation events are more frequently associated with boundaries of the paleoriver watersheds, with 60%, than islands boundaries, with 40%. In total, one-third of speciation events are inferred to have occured within paleorivers on a single island, suggesting that habitat heterogeneity and factors other than allopatry between islands substantially affected diversification of Sundaland fishes. Our results suggest that species proliferation in Sundaland is not wholly reliant on Pleistocene sea-level fluctuations isolating populations on different islands.
Data from: A test for rate-coupling of trophic and cranial evolutionary dynamics in New World bats
<p>Data supporting article Shi et al. 2021, Evolution: <a href="https://doi.org/10.1111/evo.14188">https://doi.org/10.1111/evo.14188</a></p> <p>Morphological evolution is often assumed to be causally related to underlying patterns of ecological trait evolution. However, few studies have directly tested whether evolutionary dynamics of and major shifts in ecological resource use are coupled with morphological shifts that may facilitate trophic innovation. Using diet and multivariate cranial (microCT) data, we tested whether rates of trophic and cranial evolution are coupled in the radiation of New World bats. <span>We developed a generalizable information-theoretic method for describing evolutionary rate heterogeneity across large candidate sets of multi-rate models of evolution, without relying on a single best-fitting model</span>. We found considerable variation in trophic evolutionary dynamics, in sharp contrast to a largely homogeneous cranial evolutionary process. This dichotomy is surprising given documented functional associations between overall skull morphology and trophic ecology. We suggest that assigning discrete trophic states may underestimate trophic generalism, and that this radiation could be characterized by generally labile crania that result in a homogeneous dynamic of overall high morphological rates. Overall, we discuss how trophic classification could substantively impact our interpretation of how these dynamics covary in adaptive radiations.</p>
Data from: Evolutionary dynamics of a rapidly receding southern range boundary in the threatened California Red-Legged Frog (Rana draytonii)
Populations forming the edge of a species range are often imperiled by isolation and low genetic diversity, with proximity to human population centers being a major determinant of edge stability in modern landscapes. Since the 1960s, the California red-legged frog (Rana draytonii) has undergone extensive declines in heavily urbanized southern California, where the range edge has rapidly contracted northward while shifting its cardinal orientation to an east-west trending axis. We studied the genetic structure and diversity of these frontline populations, tested for signatures of contemporary disturbance, specifically fire, and attempted to disentangle these signals from demographic events extending deeper into the past. Consistent with the genetic expectations of the 'abundant-center' model, we found that diversity, admixture, and opportunity for random mating increases in populations sampled successively further away from the range boundary. Demographic simulations indicate that bottlenecks in peripheral isolates are associated with processes extending tens to a few hundred generations in the past, despite the demographic collapse of some due to recent fire-flood events. While the effects of recent disturbance have left little genetic imprint on these populations, they likely contribute to an extinction debt that will lead to continued range contraction unless management intervenes to stall or reverse the process.
Data from: Evolutionary dynamics of specialisation in herbivorous stick insects
Understanding the evolutionary dynamics underlying herbivorous insect mega-diversity requires investigating the ability of insects to shift and adapt to different host plants. Feeding experiments with nine related stick insect species revealed that insects retain the ability to use ancestral host plants after shifting to novel hosts, with host plant shifts generating fundamental feeding niche expansions. These expansions were however not accompanied by expansions of the realized feeding niches, as species on novel hosts are generally ecologically specialized. For shifts from angiosperm to chemically challenging conifer hosts, generalist fundamental feeding niches even evolved jointly with strong host plant specialization, indicating that host plant specialization is not driven by constraints imposed by plant chemistry. By coupling analyses of plant chemical compounds, fundamental and ecological feeding niches in multiple insect species, we provide novel insights into the evolutionary dynamics of host range expansion and contraction in herbivorous insects.
Data from: Evolutionary dynamics of quantitative variation in an adaptive trait at the regional scale: the case of zinc hyperaccumulation in Arabidopsis halleri
Metal hyperaccumulation in plants is an ecological trait whose biological significance remains debated, in particular because the selective pressures that govern its evolutionary dynamics are complex. One of the possible causes of quantitative variation in hyperaccumulation may be local adaptation to metalliferous soils. Here we explored the population genetic structure of Arabidopsis halleri at fourteen metalliferous and non-metalliferous sampling sites in Southern Poland. The results were integrated with a quantitative assessment of variation in zinc hyperaccumulation to trace local adaptation. We identified a clear hierarchical structure with two distinct genetic groups at the upper level of clustering. Interestingly, these groups corresponded to different geographic sub-regions, rather than to ecological types (i.e. metallicolous vs non-metallicolous). Also, approximate Bayesian computation analyses suggested that the current distribution of A. halleri in Southern Poland could be relictual as a result of habitat fragmentation caused by climatic shifts during the Holocene, rather than due to recent colonization of industrially polluted sites. In addition, we find evidence that some non-metallicolous lowland populations may have actually derived from metallicolous populations. Meanwhile, the distribution of quantitative variation in zinc hyperaccumulation did separate metallicolous and non-metallicolous accessions, indicating more recent adaptive evolution and diversifying selection between metalliferous and non-metalliferous habitats. This suggests that zinc hyperaccumulation evolves both ways – towards higher levels at non-metalliferous sites and lower levels at metalliferous sites. Our results open a new perspective on possible evolutionary relationships between A. halleri edaphic types that may inspire future genetic studies of quantitative variation in metal hyperaccumulation.
Data from: Sexual signal loss: the link between behavior and rapid evolutionary dynamics in a field cricket
1. Sexual signals may be acquired or lost over evolutionary time, and are tempered in their exaggeration by natural selection. 2. In the Pacific field cricket, Teleogryllus oceanicus, a mutation ("flatwing") causing loss of the sexual signal, the song, spread in < 20 generations in two of three Hawaiian islands where the crickets have been introduced. Flatwing (as well as some normal-wing) males behave as satellites, moving towards and settling near calling males to intercept phonotactic females. 3. From 2005-2012, we surveyed crickets and their responses to conspecific song, noting the morph and number of males and females before and after experimental playbacks. The three Hawaiian islands consistently contained different proportions of flatwing crickets, ranging from about 90% of males on Kauai to 50% on Oahu to rare on the Big Island of Hawaii. 4. Flatwing and normal-wing males do not appear to differ in responsiveness to playback, a behavior that should influence the likelihood of a male encountering a phonotactic female. Instead, male and female crickets from populations in which little to no calling song is perceptible during development tended to seek out callers more readily than crickets that developed in noisier environments. Such increased phonotaxis makes females more likely to find either the caller to which they are responding or to encounter a flatwing (or normal male satellite) that has also been attracted to the song. 5. Our evidence suggests that pre-existing behavioral plasticity (manifest as flexible responses to social – particularly acoustic – information in the environment) is associated with the rapid spread of the flatwing trait. Different social environments select for differential success of flatwing or normal-wing males, which in turn alters the social environment itself.
Data from: Evolving from static to dynamic signals: evolutionary compensation between two communicative signals
Signals that convey related information may impose selection on each other, creating evolutionary links between different components of the communicative repertoire. Here, we ask about the consequences of the evolutionary loss of one signal (a colour patch) on another (a motion display) in Sceloporus lizards. We present data on male lizards of four species: two pairs of sister taxa representing two independent evolutionary losses of the static colour patch (S. cozumelae and S. parvus; S. siniferus and S. merriami). Males of the two species that have undergone an evolutionary loss of blue-belly patches (S. cozumelae, S. siniferus) were less active than their blue-bellied sister taxa (S. parvus, S. merriami), consistent with the suggestion that the belly patches were lost to reduce conspicuousness of species with high predation pressure. In contrast, the headbob display appears to have become more, rather than less, conspicuous over evolutionary time. The colour patch is exhibited primarily during aggressive encounters, whereas headbob displays are multifunction signals used in several different contexts, including aggressive encounters. Males of species that have lost the colour patch produced more motion displays, and the structure of those motion displays were more similar to those produced during combat. In both evolutionary episodes, a static colour signal appears to have been replaced by dynamic motion displays that can be turned off in the presence of predators and other unwanted receivers. The predominant pattern is one of evolutionary compensation and interactions between multiple signals that convey related information.
Data from: Demography-dispersal trait correlations modify the eco-evolutionary dynamics of range expansion
Spreading populations are subject to evolutionary processes acting on dispersal and reproduction that can increase invasion speed and variability. It is typically assumed that dispersal and demography traits evolve independently, but abundant evidence points to correlations between them that may be positive or negative, genetic or environmental. We sought to understand how demography-dispersal correlations modify the eco-evolutionary dynamics of range expansion. We first explored this question with the beetle Callosobruchus maculatus, a laboratory model in which evolutionary acceleration of invasion has been demonstrated. We then built a simulation model to explore the role of trait correlations in this system and more generally. We found that positive correlations amplify the positive influence of evolution on speed and variability, while negative correlations (such as we found empirically) constrain that influence. Strong negative genetic correlations can even cause evolution to decelerate invasion. Heritable and environmental correlations had similar effects on some measures of invasion but different effects on others. Model results enabled us to retrospectively explain invasion dynamics and trait evolution in C. maculatus, and may similarly aid the interpretation of other field and laboratory studies. Non-independence of demography and dispersal is an important consideration for understanding and predicting outcomes of range expansion.
The dataset of the role of dormant propagule banks in shaping eco-evolutionary dynamics of community assembly
<p>Here is the dataset of the simulation data of the role of dormant propagule banks in shaping eco-evolutionary dynamics of community assembly. </p>
Molecular dynamics simulations for "Evolutionary Dynamics of RuBisCO: Emergence of the Small Subunit and its Impact Through Time"
<p>This repository contains the molecular dynamics simulation files for the extant and ancestral RuBisCOs, presented in Amritkar2024 et. al.</p> <p>There are two separate folders, one for the regular MD simulations and the other for MD simulations with gas trajectories.</p> <p>Both folders have the simulation trajectory `.dcd` files and the `.pdb` for their corresponding protein structures.</p> <p>The trajectory files are dried, i.e. water molecules have been removed from them.</p> <p>The data encompasses over 7 extant (pdb ids: 1BWV, 3ZXW, 6FTL, 6URA, 7SNV, 8RUC, 9RUB) and 8 ancestral (Anc-I/I', Anc-I', Anc-I, Anc-IAB, Anc-ICD, Anc-IA, Anc-IB, Anc-I-without-RbcS) RuBisCO complexes.</p> <p>This study performed three types of simulations: with water molecules (labeled as exp01), with water + CO2 molecules (labeled as exp02), and with water + O2 molecules (labeled as exp04).</p> <p>There are two replicates for the exp01 simulations and the simulation length for each is 250 ns.</p> <p>The <em>exp02</em> and <em>exp04</em> files are not present for the RbcS-less (Anc-I/I', Anc-I', Anc-I-without_RbcS, 6URA, and 9RUB) RuBisCOs. The simulation length for the gas simulations is 75 ns and one replicate.</p> <p>Each file is named "<em>RuBisCO-system"</em>."<em>simulation-type</em>".md"replicate-number".dry."<em>pdb or dcd</em>".</p> <p>The files are named with respect to each RuBisCO-id in small (No caps). Anc-I/I' is represented as "anciip" and Anc-I' is represented as "ancip".</p>
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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.