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562 results for “genetic divergence”
Data from: Genetic and morphometric divergence in threespine stickleback in the Chignik catchment, Alaska
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Data from: Genetic divergence between two phenotypically distinct bottlenose dolphin ecotypes suggests separate evolutionary trajectories
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Data from: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates
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Data from: Molecular population genetics of the melanic plumage polymorphism in arctic skuas (Stercorarius parasiticus): evidence for divergent selection on plumage colour
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Data from: Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding
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Data from: Genetic and epigenetic divergence between disturbed and undisturbed subpopulations of a Mediterranean shrub: a 20-year field experiment
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Data from: Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus
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Data from: Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator
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Data from: Genetic divergence predicts reproductive isolation in damselflies
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Data from: Genetics of adaptation: experimental test of a biotic mechanism driving divergence in traits and genes
The genes underlying adaptations are becoming known, yet the causes of selection on genes -- a key step in the study of the genetics of adaptation -- remains uncertain. We address this issue experimentally in a threespine stickleback species pair showing exaggerated divergence in bony defensive armor in association with competition-driven character displacement. We used semi-natural ponds to test the role of a native predator in causing divergent evolution of armor and two known underlying genes. Predator presence/absence altered selection on dorsal spines and allele frequencies at the Msx2a gene across a generation. Evolutionary trajectories of alleles at a second gene, Pitx1, and the pelvic spine trait it controls, were more variable. Our experiment demonstrates how manipulation of putative selective agents help to identify causes of evolutionary divergence at key genes, rule out phenotypic plasticity as a sole determinant of phenotypic differences, and eliminate reliance on fitness surrogates. Divergence of predation regimes in sympatric stickleback is associated with coevolution in response to resource competition, implying a cascade of biotic interactions driving species divergence. We suggest that as divergence proceeds, an increasing number of biotic interactions generate divergent selection, causing more evolution in turn. In this way, biotic adaptation perpetuates species divergence through time during adaptive radiation in an expanding number of traits and genes.
Data on assessing the effects of genetic divergence and morphology on Anolis lizard mating
<p>The brown anole (<i>Anolis sagrei</i>) is a widespread neotropical lizard found on many islands in the West Indies as well as the coast of Central America. Across their range, brown anole populations show extensive ecomorphological trait variation and substantial genetic divergence. It is unclear, however, whether this genetic and morphological divergence results in reproductive isolation between populations. We investigated variation in mating behavior across populations by analyzing four hours of video of each of 234 captive male-female <i>A. sagrei </i>pairs encompassing all 36 possible pairings from six sampled islands. For each pair of individuals, we tested for an association between the occurrence of mating, morphological traits, and genetic relatedness of their populations. We found no support for the hypotheses that ecological and/or non-ecological divergence is driving premating reproductive isolation in <i>A. sagrei</i>. We did find that males with relatively short heads tend to mate more quickly and hypothesize potential explanations that warrant future investigation.</p>
Genetic divergence across glacial refugia despite interglacial gene flow in a crested newt
<p>MtDNA-based phylogeography has illuminated the impact of the Pleistocene Ice Age on species distribution dynamics and the build-up of genetic divergence. The well-known shortcomings of mtDNA in biogeographical inference can be compensated by integrating multilocus data and species distribution modelling into phylogeography. We re-visit the phylogeography of the Italian crested newt (<i>Triturus carnifex</i>), a species distributed in two of Europe's main glacial refugia, the Balkan and Italian Peninsulas. While a new 51 nuclear DNA marker dataset supports the existence of three lineages previously suggested by mtDNA (Balkan, northern Italy and southern Italy), the nuclear DNA dataset also provides improved resolution where these lineages have obtained secondary contact. We observe geographically restricted admixture at the contact between the Balkan and northern Italy gene pools and identify a potential mtDNA ghost lineage here. At the contact between the northern and southern Italy gene pools we find admixture over a broader area, as well as asymmetric mtDNA introgression. Our species distribution model is in agreement with a distribution restricted to distinct refugia during Pleistocene glacial cycles and postglacial expansion with secondary contact. Our study supports: (1) the relevance of the north-western Balkan Peninsula as a discrete glacial refugium; (2) the importance of north-eastern Italy and the northern Apennine as suture zones; and (3) the applicability of a refugia-within-refugia scenario within the Italian Peninsula.</p>
The many population genetic and demographic routes to islands of genomic divergence
<ol> <li>The way that organisms diverge into reproductively isolated species is a major question in biology. The recent accumulation of genomic data provides promising opportunities to understand the genomic landscape of divergence, which describes the distribution of differences across genomes. Genomic areas of unusually high differentiation have been called genomic islands of divergence. Their formation has been attributed to a variety of mechanisms, but a prominent hypothesis is that they result from divergent selection over a small portion of the genome, with surrounding areas homogenised by gene flow. Such islands have often been interpreted as being associated with divergence with gene flow. However other mechanisms related to genomic structure and population history can also contribute to the formation of genomic islands of divergence.</li> <li>We currently lack a quantitative framework to examine the dynamics of genomic landscapes under the complex and nuanced conditions that are found in natural systems. Here, we develop an individual-based simulation to explore the dynamics of diverging genomes under various scenarios of gene flow, selection and genotype-phenotype maps.</li> <li>Our modelling results are consistent with empirical observations demonstrating the formation of genomic islands under genetic isolation. Importantly, we have quantified the range of conditions that produce genomic islands. We demonstrate that the initial level of genetic diversity, drift, time since divergence, linkage disequilibrium, strength of selection and gene flow are all important factors that can influence the formation of genomic islands. Because the accumulation of genomic differentiation over time tends to erode the signal of genomic islands, genomic islands are more likely to be observed in recently divergent taxa, although not all recently diverged taxa will necessarily exhibit islands of genomic divergence. Gene flow primarily slows the swamping of islands of divergence with time.</li> <li>By using this framework, further studies may explore the relative influence of particular suites of events that contribute to the emergence of genomic islands under sympatric, parapatric and allopatric conditions. This approach represents a novel tool to explore quantitative expectations of the speciation process, and should prove useful in elucidating past and projecting future genomic evolution of any taxa.</li> </ol>
Datasets for: Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations
<p><b>Background</b>: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (<i>Ctenolabrus rupestris</i>) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies.</p> <p><b>Results:</b> After construction of a <i>de novo </i>assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33 235 genome wide SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global <i>F<sub>ST</sub></i> among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~1% within Scandinavia. SNPs showing large divergence (<i>F<sub>ST</sub></i>>0.15) were picked as candidate diagnostic markers for population assignment. 173 of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species' Scandinavian distribution range. 69 of these SNPs were significantly (<i>p</i><0.05) differentiated (mean <i>F<sub>ST_173_loci</sub></i><i>=</i>0.065<i>, F<sub>ST_69_</sub></i><i><sub>loci</sub></i><i>=</i>0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin.</p> <p><b>Conclusions:</b> Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.</p>
Patterns of genetic divergence and demographic history shed light on island-mainland population dynamics and melanic plumage evolution in the white-winged fairywren
<p>The existence of distinct traits in island versus mainland populations offers opportunities to gain insights into how eco-evolutionary processes operate under natural conditions. We used two island colonization events in the white-winged fairywren (<i>Malurus </i><i>leucopterus</i>) to investigate the genomic and demographic origin of melanic plumage. This avian species is distributed across most of Australia, and males of the mainland subspecies (<i>M. l. leuconotus</i>) exhibit a blue nuptial plumage in contrast to males of two island subspecies – <i>M. l. leucopterus </i>on Dirk Hartog Island<i> </i>and <i>M. l. edouardi</i>on Barrow Island – that exhibit a black nuptial plumage. We used reduced-representation sequencing to explore differentiation and demographic history in this species and found clear patterns of divergence between mainland and island populations, with additional substructuring on the mainland. Divergence between the mainland and Dirk Hartog was approximately 10 times more recent than the split between the mainland and Barrow Island, supporting two independent colonizations. In both cases, estimated gene flow between the mainland and the islands was low, contributing to signals of divergence among subspecies. Our results present demographic reconstructions of mainland-island dynamics and associated plumage variation in white-winged fairywrens, with broader implications regarding our understanding of convergent evolution in insular populations.</p>
Data from: The influence of life-history strategy on genetic differentiation and lineage divergence in darters (Percidae: Etheostomatinae)
Recent studies determined that darters with specialized breeding strategies can exhibit deep lineage divergence over fine geographic scales without apparent physical barriers to gene flow. However, the extent to which intrinsic characteristics interact with extrinsic factors to influence population divergence and lineage diversification in darters is not well understood. This study employed comparative phylogeographic and population genetic methods to investigate the influence of life-history on gene flow, dispersal ability, and lineage divergence in two sympatric sister darters with differing breeding strategies. Our results revealed highly disparate phylogeographic histories, patterns of genetic structure, and dispersal abilities between the two species suggesting that life-history may contribute to lineage diversification in darters, especially by limiting dispersal among large river courses. Both species also showed striking differences in demographic history, indicating that extrinsic factors differentially affected each species during the Pleistocene. Collectively, our results indicate that intrinsic and extrinsic factors have influenced levels of gene flow among populations within both species examined. However, we suggest that life-history strategy may play a more important role in lineage diversification in darters than previously appreciated, a finding that has potentially important implications for understanding diversification of the rich North American freshwater fish fauna.
Data from: High-dimensional variance partitioning reveals the modular genetic basis of adaptive divergence in gene expression during reproductive character displacement
Although adaptive change is usually associated with complex changes in phenotype, few genetic investigations have been conducted of adaptations that involve sets of high dimensional traits. Microarrays have supplied high-dimensional descriptions of gene expression, and phenotypic change resulting from adaptation often results in large-scale changes in gene expression. We demonstrate how genetic analysis of large-scale changes in gene expression generated during adaptation can be accomplished by determining by high-dimensional variance partitioning within classical genetic experimental designs. A microarray experiment conducted on a panel of recombinant inbred lines (RILs) generated from two populations of Drosophila serrata that have diverged in response to natural selection, revealed genetic divergence in 10.6% of 3762 gene products examined. Over 97% of the genetic divergence in transcript abundance was explained by only 12 genetic modules. The two most important modules, explaining 50% of the genetic variance in transcript abundance, were genetically correlated with the morphological traits that are known to be under selection. The expression of three candidate genes from these two important genetic modules was assessed in an independent experiment using qRT-PCR on 430 individuals from the panel of RILs, and confirmed the genetic association between transcript abundance and morphological traits under selection.
Data from: The extent and genetic basis of phenotypic divergence in life history traits in Mimulus guttatus
Differential natural selection acting on populations in contrasting environments often results in adaptive divergence in multivariate phenotypes. Multivariate trait divergence across populations could be caused by selection on pleiotropic alleles or through many independent loci with trait-specific effects. Here, we assess patterns of association between a suite of traits contributing to life history divergence in the common monkeyflower, Mimulus guttatus, and examine the genetic architecture underlying these correlations. A common garden survey of 74 populations representing annual and perennial strategies from across the native range revealed strong correlations between vegetative and reproductive traits. To determine whether these multitrait patterns arise from pleiotropic or independent loci, we mapped QTLs using an approach combining high-throughput sequencing with bulk segregant analysis on a cross between populations with divergent life histories. We find extensive pleiotropy for QTLs related to flowering time and stolon production, a key feature of the perennial strategy. Candidate genes related to axillary meristem development co-localize with the QTLs in a manner consistent with either pleiotropic or independent QTL effects. Further, these results are analogous to previous work showing pleiotropy-mediated genetic correlations within a single population of M. guttatus experiencing heterogeneous selection. Our findings of strong multivariate trait associations and pleiotropic QTLs suggest that patterns of genetic variation may determine the trajectory of adaptive divergence.
Data from: Morphological differentiation correlates with ecological but not genetic divergence in a Gehyra gecko.
Body size affects life history, the ecological niche of an organism and its interactions with other organisms. Resultantly, marked differences in body size between related organisms are often an indication of a species boundary. This is particularly evident in the Gehyra variegata species complex of geckos, which displays differential body sizes between genetically divergent species, but high levels of intra-specific morphological conservatism. We report on a Gehyra population that displays extraordinary body size differentiation in comparison with other G. variegata species. We used morphological and environmental data to show this population is phenotypically and ecologically distinct from its parapatric congener G. lazelli and that morphology and ecology are significantly correlated. Contrastingly, mtDNA analysis indicates paraphyly between the two groups and allele frequencies at six microsatellite loci show no population structure concordant with morpho/eco-type. These results suggest either ecological speciation or environmentally induced phenotypic polymorphism, in an otherwise morphologically conservative group.
Data from: Evidence of neutral and adaptive genetic divergence between European trout populations sampled along altitudinal gradients
Species with a wide geographical distribution are often composed of distinct subgroups which may be adapted to their local environment. European trout (Salmo trutta species complex) provide an example of such a complex consisting of several genetically and ecologically distinct forms. However, trout populations are strongly influenced by human activities, and it is unclear to what extent neutral and adaptive genetic differences have persisted. We sampled 30 Swiss trout populations from heterogeneous environments along replicated altitudinal gradients in three major European drainages. More than 850 individuals were genotyped at 18 microsatellite loci which included loci diagnostic for evolutionary lineages and candidate markers associated with temperature tolerance, reproductive timing and immune defence. We find that the phylogeographic structure of Swiss trout populations has not been completely erased by stocking. Distinct genetic clusters corresponding to the different drainages could be identified, although nonindigenous alleles were clearly present, especially in the two Mediterranean drainages. We also still detected neutral genetic differentiation within rivers which was often associated with the geographical distance between populations. Five loci showed evidence of divergent selection between populations with several drainage-specific patterns. Lineage-diagnostic markers, a marker linked to a quantitative trait locus for upper temperature tolerance in other salmonids and a marker linked to the major histocompatibility class I gene were implicated in local adaptation and some patterns were associated with altitude. In contrast, tentative evidence suggests a signal of balancing selection at a second immune relevant gene (TAP2). Our results confirm the persistence of both neutral and potentially adaptive genetic differences between trout populations in the face of massive human-mediated dispersal.
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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.