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281 results for “Rapid evolution”

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zenodo48/100

Data from: Padfield et al. (2016) Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters.

<p>This repository provides the data from the TPC and logistic growth curves from the paper:</p> <p>Padfield, D., Yvon‐Durocher, G., Buckling, A., Jennings, S., &amp; Yvon‐Durocher, G. (2016). Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters, 19(2), 133-142.</p> <p>metadata.pdf gives a more detailed&nbsp;explanation of the data.</p>

opencc-by-4.0Jun 2018View details →
zenodo44/100

Data from: "Rapid molecular evolution of Spiroplasma symbionts of Drosophila"

<p>This repository contains data and information to reproduce the findings reported in the paper.</p> <p>File descriptions:</p> <ul> <li>OTU_sequences.fasta &ndash; all <em>Spiroplasma</em> sequences that contained an <a href="https://pfam.xfam.org/family/OTU">OTU domain</a> as predicted by <a href="https://www.ebi.ac.uk/Tools/pfa/pfamscan/">PfamScan</a></li> <li>OTU_alignments.fasta &ndash; alignment of OTU domains performed using <a href="https://mafft.cbrc.jp/alignment/software/">Mafft</a></li> <li>RIP_sequences.fasta &ndash; all <em>Spiroplasma</em> sequences that contained an <a href="https://pfam.xfam.org/family/RIP">RIP domain</a> as predicted by <a href="https://www.ebi.ac.uk/Tools/pfa/pfamscan/">PfamScan</a></li> <li>RIP_alignments.fasta &ndash; alignment of RIP domains performed using the <a href="http://hmmer.org/">HMMER package</a></li> <li>Spiroplasma_supermatrix.fasta &ndash; Fasta alignment of concatenated single copy <em>Spiroplasma</em> loci conserved across the investigated strains. Loci that showed signs of recombination were not included</li> <li>Spiroplasma_partitions.txt &ndash; Lists the loci that make up the <em>Spiroplasma</em> supermatrix</li> <li>Spiroplasma_partitioning.scheme.txt &ndash; Partitioning scheme employed in our Maximum Likelihood analysis of the supermatrix. This was the best fitting partitioning scheme as determined with <a href="http://www.iqtree.org/">IQ-TREE</a></li> <li>Protocol_1.pdf &ndash; Chloroform&ndash;Ethanol protocol used for extracting <em>Spiroplasma</em> DNA for&nbsp;<em>s</em>Hy-Tx</li> </ul>

opencc-by-4.0Jun 2020View details →
zenodo44/100

Range expansion is slower and more variable with rapid evolution across a spatial gradient in temperature

<p><span>Rapid evolution in colonizing populations can alter our ability to predict future range expansions. Recent theory suggests that the dynamics of replicate range expansions are less variable, and hence more predictable, with increased selection at the expanding range front. Here, we test whether selection from environmental gradients across space produces more consistent range expansion speeds, using the experimental evolution of replicate duckweed populations colonizing landscapes with and without a temperature gradient. We found that range expansion across a temperature gradient was slower on average, with range-front populations displaying higher population densities, and genetic signatures and trait changes consistent with directional selection. Despite this, we found that with a spatial gradient range expansion speed became more variable and less consistent among replicates over time. Our results therefore challenge current theory, highlighting that chance can still shape the genetic response to selection to influence our ability to predict range expansion speeds.</span></p>

opencc-by-4.0Jan 2024View details →
dryad40/100

Data from: Repetitive DNA profiles reveal evidence of rapid genome evolution and reflect species boundaries in ground beetles

Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the genome's component parts. Comparative study of entire genome architecture in model organisms is shedding light on mechanisms underlying genome regulation, evolution, and diversification; but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the <i>breve</i> species group of <i>Bembidion</i>, and vary across broader taxonomic sampling in <i>Bembidion</i> subgenus <i>Plataphus</i>. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the genome, revealing evidence of rapid genome evolution (including among sister pairs) not evident from analysis of traditional data sources such as multi-gene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the evolutionary history of <i>Plataphus</i>. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and genome evolution.

opencc-zeroApr 2020View details →
dryad40/100

Data from: Resurrected seeds from herbarium specimens reveal rapid evolution of drought resistance in a selfing annual

<p>Premise of study: Increased aridity and drought associated with climate change are exerting unprecedented selection pressures on plant populations. Whether populations can rapidly adapt, and which life history traits might confer increased fitness under drought, remain outstanding questions. </p> <p>Methods: We utilized a resurrection ecology approach, leveraging dormant seeds from herbarium collections to assess whether populations of <em>Plantago patagonica</em> from the semi-arid Colorado Plateau have rapidly evolved in response to approximately ten years of intense drought in the region. We quantified multiple traits associated with drought escape and drought resistance and assessed the survival of ancestors and descendants under simulated drought. </p> <p>Key Results: Descendant populations displayed a significant shift in resource allocation, in which they invested less in reproductive tissues and relatively more in both above- and below-ground vegetative tissues. Plants with greater leaf biomass survived longer under terminal drought; moreover, even after accounting for the effect of increased leaf biomass, descendant seedlings survived drought longer than their ancestors. </p> <p>Conclusions: Our results document rapid adaptive evolution in response to climate change in a selfing annual and suggest that shifts in tissue allocation strategies may underlie adaptive responses to drought in arid or semi-arid environments. This work also illustrates a novel approach, documenting that under specific circumstances, seeds from herbarium specimens may provide an untapped source of dormant propagules for future resurrection experiments.</p>

opencc-zeroOct 2023View details →
dryad40/100

Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales

<p>The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change.</p> <p>We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes.</p> <p>Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high <em>in</em> <em>situ</em> diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than other regions. The relatively common lineage dispersals out of temperate hotspots highlights strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae.</p> <p>The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid <em>in</em> <em>situ</em> diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high <em>in</em> <em>situ</em><strong> </strong>diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.</p>

opencc-zeroJan 2024View details →
dryad40/100

Data for: Microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance

<p>Plants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco-evolutionary processes on a shared host plant. We tested the role of a plant-beneficial soil bacterium (<em>Acidovorax radicis</em>) in altering eco-evolutionary interactions between different aphid genotypes (Sitobion avenae; genotypes Sickte and Fescue) feeding on barley (<em>Hordeum vulgare</em>). We measured fecundity, longevity and population growth of two aphid genotypes reared separately or together (population mixture) on three different barley varieties that were inoculated with or without <em>A. radicis</em>. Results showed that across all plant varieties <em>A. radicis</em> increased plant growth and suppressed aphid populations via reduced longevity and fecundity. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Using Lotka-Volterra modelling, we demonstrated that while <em>A. radicis</em> inoculation decreased growth rates for both aphid genotypes it increased the competitiveness of one genotype against the other. In general, in the presence of <em>A. radicis</em>, the Fescue aphid genotype became more inhibitory of Sickte aphids, while Sickte aphids facilitated the growth of Fescue aphids. Our work demonstrates that plant rhizosphere microbiomes exert community-level influences by mediating eco-evolutionary interactions between herbivores and host plants. By altering competitive interaction outcomes among aphids and thus impacting processes such as rapid evolution, soil microbes contribute to the short- and long-term structure and functioning of terrestrial habitats.</p>

opencc-zeroJan 2024View details →
dryad40/100

Data from: Rapid, parallel evolution of field mustard (Brassica rapa) under experimental drought

<p>Climate change is driving evolutionary and plastic responses in populations, but predicting these responses remains challenging. Studies that combine experimental evolution with ancestor-descendant comparisons allow assessment of the causes, parallelism, and adaptive nature of evolutionary responses, although such studies remain rare, particularly in a climate change context. Here, we created experimental populations of Brassica rapa derived from the same natural population and exposed these replicated populations to experimental drought or watered conditions for four generations. We then grew ancestors and descendants concurrently, following the resurrection approach. Experimental populations under drought showed rapid evolution of earlier flowering time and increased specific leaf area, consistent with a drought escape strategy and observations in natural populations. Evolutionary shifts followed the direction of selection and increased fitness under drought, indicative of adaptive evolution. Evolution to drought also occurred largely in parallel among replicate populations. Further, traits showed phenotypic plasticity to drought, but the direction and effect size of plasticity varied. Our results demonstrate parallel evolution to experimental drought, suggesting that evolution to strong, consistent selection may be predictable. Broadly, our study demonstrates the utility of combining experimental evolution with the resurrection approach to investigate responses to climate change.</p>

opencc-zeroNov 2021View details →
zenodo40/100

Data and custom codes from "Rapid evolution in salmon life-history induced by direct and indirect effects of fishing"

<p>Data and custom codes from Czorlich, Y., Aykanat, T., Erkinaro, J., Orell, P. &amp; Primmer, C.R. (2021)&nbsp;<em>Rapid evolution in salmon life-history induced by direct and indirect effects of fishing. </em>Science.</p> <p><strong>Codes:</strong></p> <p>The R file &quot;Fishing_effort_parallel.R&quot;&nbsp;was used to estimate fishing effort/intensity (beta in equation 8) given the length distribution, the gear-specific catchability&nbsp;and harvest rate</p> <p>&quot;Fishing_selection_estimate.R&quot; was&nbsp;used to estimate fishery-induced selection at <em>vgll3.</em></p> <p><strong>Datasets:</strong></p> <p>Genetic_phenotypic_data.xlsx: Genetic and phenotypic data about salmon from the Teno mainstem population</p> <p>sonar_data.xlsx: Number of salmon per length class&nbsp;entering the river in 2018 and 2019. The length classes of salmon caught in those years by one of the fishing methods are also included</p> <p>annual_catch_data.xlsx: Total mass (kg) of salmon caught by each fishing method between 1975 to 2014.</p> <p>Environmental_data.xlsx: Data about Barents Sea temperature, biomass of key species, fishing data</p> <p>individual_weight_salmon_catches.xlsx: Individual weight of salmon caught with different fishing gears in the last decades</p> <p><strong>Data sources:</strong></p> <p>- Genetic data (Tenojoki population, random sampling): From Czorlich et al. 2018,&nbsp;https://datadryad.org/stash/dataset/doi:10.5061/dryad.7hm4708</p> <p>-&nbsp;Data about krill biomass (1980 &ndash; 2013) were taken from (<em>1</em>, <em>2</em>).</p> <p>- Capelin biomass estimated from acoustic survey and the landed capelin catches were derived from (<em>3</em>) for 1973 &ndash; 2013.</p> <p>- Herring biomass data were retrieved from (<em>4</em>) for the 1973-1998 period. Herring biomass was calculated from the number of 1-2 year old herring and the mean weight per age as reported in (<em>3</em>) for 1988 &ndash; 2013.</p> <p>- The annual biomass of cod (a predator of forage fish) was derived from VPA analyses ((<em>5</em>), table 3.24). Landed cod biomass was also taken from (<em>5</em>).</p> <p>- An index for mesozooplankton (a forage fish food source) corresponding to the sum of <em>Calanus</em> biomass indices from different parts of the Barents Sea was used (<em>6</em>).</p> <p>- The annual sea temperature in the Kola section of the Barents Sea measured in the upper 200 meters was from <a href="http://www.pinro.vniro.ru/">pinro.vniro.ru</a></p> <p>- The total number of nets used to catch salmon in the Finnmark coastal region was calculated for each year using data from (7)</p> <p>-&nbsp;Other data&nbsp;were generated for this study, please check the Material and Methods.&nbsp;</p> <p><em>References:</em></p> <p>1. E. Eriksen, P. Dalpadado, Long-term changes in Krill biomass and distribution in the Barents Sea: Are the changes mainly related to capelin stock size and temperature conditions? <em>Polar Biology</em>. <strong>34</strong>, 1399&ndash;1409 (2011).</p> <p>2. &nbsp;&nbsp;&nbsp;&nbsp; ICES, &ldquo;Report of the Working Group on the Integrated Assessments of the Barents Sea. ICES CM 2017/SSGIEA:04. 186 pp.&rdquo; (2017).</p> <p>3. &nbsp;&nbsp;&nbsp;&nbsp; ICES, &ldquo;Report of the Arctic Fisheries Working Group (AFWG). ICES CM 2015/ACOM:05. 639 pp.&rdquo; (2015).</p> <p>4. &nbsp;&nbsp;&nbsp;&nbsp; R. Toresen, O. J. &Oslash;stvedt, Variation in abundance of Norwegian spring-spawning herring (Clupea harengus, Clupeidae) throughout the 20th century and the influence of climatic fluctuations. <em>Fish and Fisheries</em>. <strong>85</strong>, 385&ndash;391 (2000).</p> <p>5. &nbsp;&nbsp;&nbsp;&nbsp; ICES, &ldquo;Report of the Arctic Fisheries Working Group (AFWG). ICES CM 2016/ACOM:06. 621 pp.&rdquo; (2016).</p> <p>6. &nbsp;&nbsp;&nbsp;&nbsp; L. C. Stige et al., Spatiotemporal statistical analyses reveal predator-driven zooplankton fluctuations in the Barents Sea. <em>Progress in Oceanography</em>. <strong>120</strong>, 243&ndash;253 (2014).</p> <p>7.&nbsp; &nbsp; &nbsp; E. Niemel&auml;, T. Kalske, E. Hassinen, &ldquo;Numbers of fishing gears used in Kolarctic salmon project area, numbers of allowed sites for salmon fishing and numbers of salmon fishermen in Finnmark; development until the year 2013&rdquo; (2013).</p>

opencc-by-4.0Jan 2022View details →
dryad40/100

Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability

<p>While selfing populations harbor little genetic variation limiting evolutionary potential, the causes are unclear. We experimentally evolved large, replicate populations of <em>Mimulus guttatus </em>for nine generations in greenhouses with or without pollinating bees and studied DNA polymorphism in descendants. Populations without bees adapted to produce more selfed seed yet exhibited striking reductions in DNA polymorphism despite large population sizes. Importantly, the genome-wide pattern of variation cannot be explained by a simple reduction in effective population size, but instead reflects the complicated interaction between selection, linkage, and inbreeding. Simulations demonstrate that the spread of favored alleles at few loci depresses neutral variation genome-wide in large populations containing fully selfing lineages. It also generates greater heterogeneity among chromosomes than expected with neutral evolution in small populations. Genome-wide deviations from neutrality were documented in populations with bees, suggesting widespread influences of background selection. After applying outlier tests to detect loci under selection, two genome regions were found in populations with bees, yet no adaptive loci were otherwise mapped. Large amounts of stochastic change in selfing populations compromise evolutionary potential and undermine outlier tests for selection. This occurs because genetic draft in highly selfing populations makes even the largest changes in allele frequency unremarkable.</p>

opencc-zeroMay 2022View details →
zenodo40/100

Borg tandem repeats undergo rapid evolution and are under strong selection to create new intrinsically disordered regions in proteins

<p>This repository contains files that accompany the Schoelmerich <em>et al.&nbsp;</em>(2022) bioRxiv preprint.</p> <p>These files include</p> <p>- all Borg proteins used for protein family clustering (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/all_Borg_proteins.fasta">all_Borg_proteins.fasta</a>)</p> <p>- 37 additional aaTR-proteins from manually curated Borg contigs (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/37_Borg_aaTR-proteins.fasta?versionId=bfdfe7b6-e3b5-48b8-b7e6-a20304097e7d">37_Borg_aaTR-proteins.fasta</a>)</p> <p>- IQ-TREE&nbsp;of Borg DNA polymerases and reference sequences from doi: 10.1093/nar/gkaa760 (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/DNAPolB_iqtree.treefile?versionId=c588a98c-822d-4a2f-a92d-7dcb3b1675f0">DNAPolB_iqtree.treefile</a>)</p> <p>- Borg Sm ribonucleoprotein sequences (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/21_Borg_Sm_ribonucleoproteins.fasta">21_Borg_Sm_ribonucleoproteins.fasta</a>)</p> <p>- Borg MHC sequences (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/14_Borg_MHC_proteins.fasta">14_Borg_MHC_proteins.fasta</a>)</p> <p>- AlphaFold2 predicted structural models&nbsp;of Borg Sm ribonucleoproteins and MHCs with aaTRs</p>

opencc-by-4.0May 2022View details →
dryad40/100

Data from: Weedy and seedy: The rapid evolution of life-history characteristics in an introduced daisy

<p>Despite the importance of life-history characteristics in determining a species' success, we still lack basic information about some fundamental life-history elements found across the life cycle of introduced plants. Our study assesses rapid evolutionary divergence in life-history characteristics of the beach daisy, <em>Arctotheca populifolia,</em> by comparing introduced Australian and source South African plants and measuring eight key variables including seed mass, germination, reproductive output and survival. This is the first study that compares the life history of an introduced plant species with its single original source population, providing a precise and powerful method for detecting evolutionary divergence. We found that introduced <em>A. populifolia</em> has evolved a suite of weedy life-history characteristics in less than 90 years: the introduced plants use a live-fast die-young strategy of germination and survival and produce significantly more inflorescences and more seeds that germinate faster. This knowledge adds to the remarkable data that we already have on the rapid evolutionary divergence occurring in the morphology, physiology and defence of this introduced plant and highlights the speed and scope of evolutionary divergence possible in plants. To fully understand and manage the future of our plant species, we must consider their potential for ongoing change in key aspects of life history.</p>

opencc-zeroSep 2022View details →
dryad40/100

Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly

<p><span>Both local adaptation and adaptive phenotypic plasticity can influence the match between phenotypic traits and local environmental conditions. Theory predicts that environments stable for multiple generations promote local adaptation, while highly heterogeneous environments favor adaptive phenotypic plasticity. However, when environments have periods of stability mixed with heterogeneity, the relative importance of local adaptation and adaptive phenotypic plasticity is unclear. Here, we used <em>Drosophila suzukii</em> as a model system to evaluate the relative influence of genetic and plastic effects on the match of populations to environments with periods of stability from three to four generations. This invasive pest insect can develop within different fruits, and persists throughout the year in a given location on a succession of distinct host fruits, each one being available for only a few generations. Using reciprocal common environment experiments of natural <em>D. suzukii</em> populations collected from cherry, strawberry and blackberry, we found that both oviposition preference and offspring performance were higher on medium made with the fruit from which the population originated, than on media made with alternative fruits. This pattern, which remained after two generations in the laboratory, was analyzed using a statistical method we developed to quantify the contributions of local adaptation and adaptive plasticity in determining fitness. Altogether, we found that genetic effects (local adaptation) dominate over plastic effects (adaptive phenotypic plasticity). Our study demonstrates that spatially and temporally variable selection does not prevent the rapid evolution of local adaptation in natural populations. The speed and strength of adaptation may be facilitated by several mechanisms including a large effective population size and strong selective pressures imposed by host plants.</span></p>

opencc-zeroNov 2022View details →
dryad40/100

Rapid evolution of a brood parasite's egg pattern does not lead to large increases in mimetic fidelity

<p>In coevolutionary mimicry systems, mimics evolve to resemble models. When model fitness is reduced by close mimicry (such as when models are hosts and mimics are brood parasites), selection should drive mimics to evolve greater similarity to models over time, and models to evolve away from mimics ('chase-away evolution'), potentially resulting in mimetic fidelity remaining constant over time. Evidence for reciprocal evolution of models and mimics and its effect on mimetic fidelity is limited, however, likely because long-term data are required to observe such trends. Here, we test for these dynamics in an avian brood parasite system. The brood-parasitic cuckoo finch (Anomalospiza imberbis) lays eggs which mimic those of its host, the tawny-flanked prinia (Prinia subflava). In defence, prinias have evolved complex egg patterns which facilitate recognition of parasitic eggs. Prinia egg patterns are more complex than cuckoo finch egg patterns, and so selection should favour elevated complexity in parasite eggs (i.e. mimics evolving towards models) and even greater complexity in host eggs (i.e. models evolving away from mimics). Using a dataset spanning 50 years, we show that egg pattern complexity has indeed increased in both species over this time period, reflecting rapid adaptive evolution of both models and mimics. Both species have evolved at similar rates. Accordingly, we find no detectible increase in mimetic fidelity over time. Thus, host evolution can counteract even rapid parasite evolution, and result in the persistence of imperfect mimicry.</p>

opencc-zeroNov 2022View details →
dryad40/100

Data from: Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought

<p>While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree of genetic parallelism of rapid evolutionary responses to climate change is limited. In this study, we combined the resurrection approach with an evolve and resequence design to examine genome-wide evolutionary changes following drought. We exposed genetically similar replicate populations of the annual plant <em>Brassica</em> <em>rapa</em> derived from a field population in southern California to four generations of experimental drought or watered conditions in a greenhouse. Genome-wide sequencing of ancestral and descendant population pools identified hundreds of SNPs that showed evidence of rapidly evolving in response to drought. Several of these were in stress response genes, and two were identified in a prior study of drought response in this species. However, almost all genetic changes were unique among experimental populations, indicating that the evolutionary changes were largely non-parallel, despite the fact that genetically similar replicates of the same founder population had experienced controlled and consistent selection regimes. This non-parallelism of evolution at the genetic level is potentially because of polygenetic adaptation allowing for multiple different genetic routes to similar phenotypic outcomes. Our findings help to elucidate the relationship between rapid phenotypic and genomic evolution and shed light on the degree of parallelism and predictability of genomic evolution to environmental change.</p>

opencc-zeroFeb 2023View details →
zenodo40/100

Reference data from the Pathomove simulation, for the manuscript "Novel pathogen introduction triggers rapid evolution in animal social movement strategies"

<p>This is a reference dataset of multiple runs of the &#39;Pathomove&#39; simulation, to accompany the manuscript &quot;Novel pathogen introduction rapidly alters the evolution of movement, restructuring animal societies&quot;. The datasets are in the form of R data objects saved as Rds files.</p> <p>This version of the data is intended to accompany a resubmission to <em>eLife</em>.</p>

openmit-licenseMar 2022View details →
dryad40/100

Data from: Reverse plasticity underlies rapid evolution by clonal selection within populations of fibroblasts propagated on a novel soft substrate

<p>Mechanical properties such as substrate stiffness are a ubiquitous feature of a cell's environment. Many types of animal cells exhibit canonical phenotypic plasticity when grown on substrates of differing stiffness, in vitro and in vivo. Whether such plasticity is a multivariate optimum due to hundreds of millions of years of animal evolution, or instead is a compromise between conflicting selective demands, is unknown. We addressed these questions by means of experimental evolution of populations of mouse fibroblasts propagated for approximately 90 cell generations on soft or stiff substrates. The ancestral cells grow twice as fast on stiff substrate as on soft substrate and exhibit the canonical phenotypic plasticity. Soft-selected lines derived from a genetically diverse ancestral population increased growth rate on soft substrate to the ancestral level on stiff substrate and evolved the same multivariate phenotype. The pattern of plasticity in the soft-selected lines was opposite of the ancestral pattern, suggesting that reverse plasticity underlies the observed rapid evolution. Conversely, growth rate and phenotypes did not change in selected lines derived from clonal cells. Overall, our results suggest that the changes were the result of genetic evolution and not phenotypic plasticity per se. Whole-transcriptome analysis revealed consistent differentiation between ancestral and soft-selected populations, and that both emergent phenotypes and gene expression tended to revert in the soft-selected lines. However, the selected populations appear to have achieved the same phenotypic outcome by means of at least two distinct transcriptional architectures related to mechanotransduction and proliferation.</p>

opencc-zeroOct 2023View details →
dryad40/100

Data from: Rapid, parallel evolution of field mustard (Brassica rapa) under experimental drought

Open the record for dataset details and reuse information.

publicNov 2021View details →
dryad40/100

Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly

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publicNov 2022View details →
dryad40/100

Data from: Rapid evolution of a native species following invasion by a congener

Open the record for dataset details and reuse information.

publicSep 2015View details →

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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.

allen-brain-atlas
neuroscienceopenDocumentation, web resources, and API references are available online.
Last verified 2026-04-30Open record

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.

abode-home-cage
behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.
Last verified 2026-04-30Open record

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.

dandi-nwb
electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.
Last verified 2026-04-30Open record

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.

ibl
behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.
Last verified 2026-04-29Open record

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.

openneuro
neuroscienceopenPublished datasets are available on demand over the internet.
Last verified 2026-04-29Open record