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343 results for “genomic divergence”
Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee
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Data from: Genomic divergence in allopatric Northern Cardinals of the North American warm deserts is linked to behavioral differentiation
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Evolution of the correlated genomic variation landscape across a divergence continuum in the genus Castanopsis
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Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis
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High heterogeneity in genomic differentiation between phenotypically divergent songbirds: A test of mitonuclear co-introgression
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Data for: The 3-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence
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Assemblies and annotations from the paper "Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria"
<p>These files are the assemblies and annotations produced and analyzed in the revised version of the manuscript entitled "Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria".</p>
Data from: Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)
<p>As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 SNPs and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and processes shaping them. We found evidence of high (mean FST=0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans-Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1-3Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16, and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium despite no local reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near fixed and potentially adaptive trans-Atlantic differences concurrent with a background of high genome-wide differentiation supports subspecies designation in Atlantic salmon.</p>
Data from: Contrasting signatures of genomic divergence during sympatric speciation
<p>The transition from "well-marked varieties" into "well-defined species" has puzzled evolutionary biologists ever since Darwin — especially when extensive gene flow between incipient species is possible due to the lack of physical barriers (sympatric speciation). Gene flow counteracts the build-up of genome-wide differentiation, which is both a hallmark of speciation and forms the underlying basis of irreversible reproductive barriers (incompatibilities) that ultimately complete the speciation process. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs. However, empirical data to test this prediction remain rare and are often difficult to synthesize across animal taxa due to idiosyncrasies in their biology and evolutionary histories. Here, within a young species complex of Neotropical cichlid fish (<i>Amphilophus spp.</i>), we analyzed genomic divergence among populations and species, and the genetic architecture of traits that have been suggested to be important for this divergence, by generating a new genome assembly and re-sequencing 453 genomes. We found that species differing in mono/oligogenic traits affecting ecological performance and/or mate choice show remarkably localized genomic differentiation. In contrast, differentiation between species that diverged in polygenic traits is widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation-with-gene-flow as previously suggested, whereas, unexpectedly, polygenic architectures can promote rapid and stable speciation in sympatry.</p>
Data from: Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp
Population divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide datasets allows discrimination between alternative scenarios for these processes even in non-model taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum (bSFS), the second on the Pairwise Sequentially Markovian Coalescent (PSMC)) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia, and are separated into northern and southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of post divergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, non-model organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.
Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species
<p>The wild currant tomato <i>Solanum pimpinellifolium </i>inhabits a wide range of abiotic habitats across its native range of Ecuador and Peru. Although it has served as a key genetic resource for the improvement of domestic cultivars, little is known about the genetic basis of traits underlying local adaptation in this species, nor what abiotic variables are most important for driving differentiation. Here we use redundancy analysis (RDA) and other multivariate statistical methods (structural equation modeling (SEM) and generalized dissimilarity modeling (GDM)) to quantify the relationship of genomic variation (6,830 single nucleotide polymorphisms) with climate and geography, among 140 wild accessions. RDA, SEM, and GDM each identified environment as explaining more genomic variation than geography, suggesting that local adaptation to heterogeneous abiotic habitats may be an important source of genetic diversity in this species. Environmental factors describing temporal variation in precipitation and evaporative demand explained the most SNP variation among accessions, indicating that these forces may represent key selective agents. Lastly, by studying how SNP-environment associations vary throughout the genome (44,064 SNPs), we mapped the location and investigated the functions of loci putatively contributing to climatic adaptations. Together our findings indicate an important role for selection imposed by the abiotic environment in driving genomic differentiation between populations. </p>
Data from: Vocal divergence is concordant with genomic evidence for strong reproductive isolation in grasshopper mice (Onychomys)
Behavioral barriers to gene flow often evolve faster than intrinsic incompatibilities, and can eliminate the opportunity for hybridization between interfertile species. While acoustic signal divergence is a common driver of premating isolation in birds and insects, its contribution to speciation in mammals is less studied. Here we characterize the incidence of, and potential barriers to, hybridization among three closely related species of grasshopper mice (genus Onychomys). All three species use long-distance acoustic signals to attract and localize mates; O. arenicola and O. torridus are acoustically similar and morphologically cryptic whereas O. leucogaster is larger and acoustically distinct. We used genotyping-by-sequencing (GBS) to test for evidence of introgression in 227 mice from allopatric and sympatric localities in the western United States and northern Mexico. We conducted laboratory mating trials for all species pairs to assess reproductive compatibility, and recorded vocalizations from O. arenicola and O. torridus in sympatry and allopatry to test for evidence of acoustic character displacement. Hybridization was rare in nature and, contrary to prior evidence for O. torridus/O. arenicola hybrids, only involved O. leucogaster and O. arenicola. In contrast, lab crosses between O. torridus
Data from: The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback
<p>The repeated occurrence of similar phenotypes in independent lineages (i.e., parallel evolution) in response to similar ecological conditions can provide compelling insights into the process of adaptive evolution. An intriguing question is to what extent repeated phenotypic changes are underlain by repeated changes at the genomic level and whether patterns of genomic divergence differ with the geographic context in which populations evolve. Here, we combine genomic, morphological and ecological datasets to investigate the genomic signatures of divergence across populations of threespine stickleback (<i>Gasterosteus aculeatus</i>) that adapted to contrasting ecological niches (benthic or limnetic) in either sympatry or allopatry. We found that genome-wide differentiation (F<sub>ST</sub>) was an order of magnitude higher and substantially more repeatable for sympatric benthic and limnetic specialists compared to allopatric populations with similar levels of ecological divergence. We identified genomic regions consistently differentiated between sympatric ecotypes that were also differentiated between or associated with benthic vs. limnetic niche in allopatric populations. These candidate regions were enriched on three chromosomes known to be involved in the benthic-limnetic divergence of threespine stickleback. Some candidate regions overlapped with QTL for body shape and trophic traits such as gill raker number, traits that strongly differ between benthic and limnetic ecotypes. In sum, our study shows that magnitude and repeatability of genomic signatures of ecological divergence in threespine stickleback highly depend on the geographic context. The identified candidate regions provide starting points to identify functionally important genes for the adaptation to benthic and limnetic niches.</p>
Population genomics reveals repeated signals of adaptive divergence in the Atlantic salmon of northeastern Europe
<p>Our ability to examine genetic variation across entire genomes have enabled many studies searching for the genetic basis of local adaptation. These studies have identified numerous loci as candidates for differential local selection, however relatively few have examined the overlap among candidate loci identified from independent studies of the same species in different geographic areas or evolutionary lineages. We used an allelotyping approach with a 220K SNP array to characterize the population genetic structure of Atlantic salmon in northeastern Europe and ask whether the same genomic segments emerged as outliers among populations in different geographic regions. Genome-wide data recapitulated the phylogeographic structure previously inferred from mtDNA and microsatellite markers. Independent analyses of three genetically and geographically distinct groups of populations repeatedly inferred the same 17 haploblocks to contain loci under differential local selection. The most strongly supported of these replicated haploblocks had known strong associations with life history variation or immune response in Atlantic salmon. Our results are consistent with these genomic segments harbouring large-effect loci which have a major role in Atlantic salmon diversification and are ideal targets for validation studies.</p>
Data from: Isolation by instability: historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna
Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene-flow in areas with high climatic instability promoting isolation of populations, defined here as "isolation by instability", highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.
Data from: Müllerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection
<p>Hybrid zones, where distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Studying clines in genetic loci and adaptive traits across hybrid zones is a powerful method for understanding how selection drives differentiation within a single species, but can also be used to compare parallel divergence in different species responding to a common selective pressure. Here, we study parallel divergence of wing colouration in the butterflies <i>Heliconius erato</i> and <i>H</i><i>. melpomene</i>, which are distantly related Müllerian mimics that show parallel geographic variation in both discrete variation in pigmentation, and quantitative variation in structural colour. Using geographic cline analysis, we show that clines in these traits are positioned in the roughly the same geographic region for both species, which is consistent with direct selection for mimicry. However, the width of the clines varies markedly between species. This difference is explained in part by variation in the strength of selection acting on colour traits within each species, but may also be influenced by differences in the dispersal rate and total strength of selection against hybrids between the species. Genotyping-by-sequencing also revealed weaker population structure in <i>H. melpomene</i>, suggesting the hybrid zones may have evolved differently in each species; which may also contribute to the patterns of phenotypic divergence in this system Overall, we conclude that multiple factors are needed to explain patterns of clinal variation within and between these species, although mimicry has probably played a central role.</p>
Data from: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta
Background: Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta,is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergence subspecies. Here we delineate the evolutionary processes driving genetic diversity and population differentiation in this species. Results: Using whole genome re-sequencing data from 517 Boechera stricta accessions, we identify four genetic groups that diverged around 30 - 180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY) and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome we also find regions with both high FST and DXY among groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms. Conclusions: Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.
Data from: Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genome-wide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z-chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate-mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate-mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.
Data from: Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens)
The little greenbul, a common rainforest passerine from sub-Saharan Africa, has been the subject of long-term evolutionary studies to understand the mechanisms leading to rainforest speciation. Previous research found morphological and behavioural divergence across rainforest–savannah transition zones (ecotones), and a pattern of divergence with gene flow suggesting divergent natural selection has contributed to adaptive divergence and ecotones could be important areas for rainforests speciation. Recent advances in genomics and environmental modelling make it possible to examine patterns of genetic divergence in a more comprehensive fashion. To assess the extent to which natural selection may drive patterns of differentiation, here we investigate patterns of genomic differentiation among populations across environmental gradients and regions. We find compelling evidence that individuals form discrete genetic clusters corresponding to distinctive environmental characteristics and habitat types. Pairwise FST between populations in different habitats is significantly higher than within habitats, and this differentiation is greater than what is expected from geographic distance alone. Moreover, we identified 140 SNPs that showed extreme differentiation among populations through a genomewide selection scan. These outliers were significantly enriched in exonic and coding regions, suggesting their functional importance. Environmental association analysis of SNP variation indicates that several environmental variables, including temperature and elevation, play important roles in driving the pattern of genomic diversification. Results lend important new genomic evidence for environmental gradients being important in population differentiation.
Data from: Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species
Quantifying introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what drives the longevity of putatively asexual groups. Here, we capitalize on three recent innovations—ultraconserved element (UCE) sequencing, bioinformatic techniques for identifying genome-specific variation in polyploids, and model-based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. Our analyses support a scenario in which the genomes sampled in unisexual salamanders last shared a common ancestor with genomes in their parental species ~3.4 million years ago, followed by a period of divergence between homologous genomes. Recently, secondary introgression has occurred at different times with each sexual species during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage is the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have undergone long periods of divergence without introgression. Unlike other sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could explain why these salamanders are among the oldest described unisexual animals.
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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.