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227 results for “demographic history”
Nationwide genomic biobank in Mexico unravels demographic history and complex trait architecture from 6,057 individuals: GWAS summary statistics
<p>Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories as well as complex trait architectures remain hidden due to the lack of Big Data. To fill this gap, the Mexican Biobank project genotyped 1.8 million markers in 6,057 individuals from 32 states and 898 sampling localities across Mexico with linked complex trait and disease information creating a valuable nationwide genotype-phenotype database. Through a suite of state-of-the-art methods for ancestry deconvolution and inference of identity-by-descent (IBD) segments, we inferred detailed ancestral histories for the last 200 generations in different Mesoamerican regions, unravelling native and colonial/post-colonial demographic dynamics. We observed large variations in runs of homozygosity (ROH) among genomic regions with different ancestral origins reflecting their demographic histories, which also affect the distribution of rare deleterious variants across Mexico. We analysed a range of biomedical complex traits and identified significant genetic and environmental factors explaining their variation, such as ROH found to be significant predictors for trait variation in BMI and triglycerides.<br> ======================================</p> <p>This dataset contains GWAS summary statistics for the Mexico Biobank Project. Summary statistics for 22 binary and quantitative traits are provided from the full cohort of 5721 individuals from across Mexico, and a subset of 1061 individuals inferred to have more than 90% Native American ancestry.</p>
Data from: Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)
<p>Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (<em>Plectropomus</em> <em>leopardus</em> [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that <em>P. leopardus</em> in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10–120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.</p>
Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago
<p><strong>Aim</strong>: The biodiversity of the Malay Archipelago is the product of the region's rich biogeographical history with periods of island connectivity and isolation during the Pleistocene glacial cycles. Here, the case of two endemic suid species, the Javan (<em>Sus verrucosus</em>) and Bawean (<em>S. blouchi</em>) warty pigs, was used to illustrate how biogeographic processes and recent anthropogenic pressures can shape demographic histories with significant implications for species conservation.</p> <p><strong>Location</strong>: Malay Archipelago, with focus on Bawean and Java.</p> <p><strong>Methods</strong>: We employed genome-wide single nucleotide polymorphisms from the Porcine SNP60 v2 BeadChip to assess interspecific genetic differentiation, to estimate divergence times, and to perform demographic model selection.</p> <p><strong>Results</strong>: In contrast to the hypothesis of recent divergence during the last glacial maximum, <em>S. blouchi</em> was found to have diverged from <em>S. verrucosus</em> at least 166k years ago following a founder event. The contemporary <em>S. blouchi</em> population was characterised by a recent bottleneck that reduced the effective population size to less than 20. The genomic assessment supports the single species status of <em>S. blouchi</em>, as was previously proposed based on morphometrics. The demographic history of <em>S. verrucosus</em> showed evidence of secondary contact with the sympatric banded pig (<em>S. scrofa vittatus</em>) that colonised Java 70k years ago.</p> <p><strong>Main</strong> <strong>conclusions</strong>: While the Javan and Bawean warty pigs have persisted throughout the Pleistocene climatic oscillations, contemporary pressures from human activities threaten their survival and immediate action should be taken to grant legal protection to both <em>S. verrucosus</em> and <em>S. blouchi</em>. This study highlighted the use of demographic history modelling using genomic data to identify evolutionary significant units and inform conservation.</p>
Biogeographic barriers and historical climate affect phylogeographic structure and demographic history of the common gartersnake
<p><strong>Aim</strong>: Current distributions of widespread North American (NA) species have been shaped by Pleistocene glacial cycles, latitudinal temperature gradients, sharp longitudinal habitat transitions, and the vicariant effects of major mountain and river systems that subdivide the continent. Within these transcontinental species, genetic diversity patterns might not conform to established biogeographic breaks compared to more spatially restricted taxa due to intrinsic differences (e.g., greater dispersal ability in generalist species) or spatiotemporal differences (e.g., wide-ranging species predate younger barriers). In this study, we highlight the effects of these extrinsic variables on genetic structuring by investigating the phylogeographic history of a widespread generalist squamate found throughout NA. </p> <p><strong>Location</strong>: North America</p> <p><strong>Taxon</strong>: Common gartersnake, <em>Thamnophis sirtalis</em></p> <p><strong>Methods</strong>: We evaluate the effects of major river basins and the forest-grassland transition into the Interior Plains on genetic structure patterns using phylogenetic, spatially informed population structure, and demographic analyses of SNP data, and address range expansion history with ecological niche modeling using locality and historic climate data.</p> <p><strong>Results</strong>: We identify four phylogeographic lineages with varying degrees of connectivity between them. We find discordant population structure patterns between sex-linked and autosomal loci with respect to the relationship between the central NA lineage relative to coastal lineages. We find support for southeast Pleistocene refugia where recent secondary contact occurred during the Last Glacial Maximum and evidence for both northern and southern refugia in western NA.</p> <p><strong>Main Conclusion</strong>: Our results provide strong evidence for a Middle Pliocene origin for <em>Thamnophis</em> <em>sirtalis</em> in central-southeastern NA preceding its rapid expansion across the continent prior to middle Pleistocene climate-mediated lineage formation. We implicate major riverine networks within the Mississippi watershed in likely repeated westward expansion events across the Interior Plains. Finally, we corroborate prior conclusions that phenotypic differences between subspecies do not reflect shared evolutionary history and note that the degree of separation between inferred lineages warrants further investigation before any taxonomic revisions are proposed.</p>
Supplementary data for: "The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches"
<p>Supplementary data to https://doi.org/10.1101/2023.06.01.543285</p>
Population genomic analyses reveal hybridization and marked differences in genetic structure and demographic history of Scurria limpet sister species with parapatric distributions across the southeastern pacific
<p>The study of sister species that occur in parapatry around biogeographic transition zones can help understand the evolutionary processes that underlie the changes in species composition across biogeographic transition zones. The South Eastern Pacific (SEP) coast is a highly productive coastal system that exhibits a broad biogeographic transition zone around 30–35ºS. Here, we present a comparative genome-wide analysis of the sister species <em>Scurria viridula</em> and <em>Scurria zebrina</em>, that occur in parapatry and whose poleward and equatorward range edges intersect in the 30–35ºS SEP biogeographic transition zone. We sampled 118 specimens sourced from nine sites from Tocopilla (22ºS) to Chiloé (41ºS) including one site where both species overlap and analyzed over 8,000 biallelic single nucleotide polymorphisms. We found evidence of hybridization between these species in the contact zone and found significant but contrasting population structures for both species. Our results indicate that the genetic structure in <em>S. viridula</em>, which is currently expanding its range poleward, follows a simple isolation-by-distance model with no traces of natural selection (no evidence of outlier loci). In contrast, <em>S. zebrina</em>, which finds its equatorward range edge at the transition zone, displayed a pronounced genetic break approximately at 32-34ºS, along a region of marked environmental heterogeneity in association with a semi-permanent coastal upwelling regime. For <em>S. zebrina</em>, we also found 43 outlier loci associated with this genetic break, with a significant proportion of them clustering in a single linkage group. This marked difference in the presence of outlier loci between species suggests that they could be responding differently to local environmental challenges found at their overlapping geographic range edges, thus providing important new insights about genomic changes around biogeographic transition zones in sister species and the forces that shape genetic diversity in intertidal marine species. </p>
Multilocus evidence provides insight into the demographic history and asymmetrical gene flow between Ostrinia furnacalis and Ostrinia nubilalis (Lepidoptera: Crambidae) in the Yili area, Xinjiang, China
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Biogeographic barriers and historical climate affect phylogeographic structure and demographic history of the common gartersnake
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Demographic history shapes genomic ancestry in hybrid zones
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Data from: Phylogeographic and demographic patterns reveal congruent histories in seven Amazonian white-sand ecosystems birds
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The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests
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Data from: Patterns of genotype variation and demographic history in Lindera glauca (Lauraceae), an apomict-containing dioecious forest tree
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The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)
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High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species
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Data from: Genetic Diversity and Demographic History of an Upper Hill Dipterocarp (Shorea platyclados): Implications for Conservation
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Demographic history and adaptive evolution of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Western Australia
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The expression of demographic costs of reproduction varies among coexisting plants with different life history traits
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Population structure, patterns of natal dispersal, and demographic history in a declining aerial insectivore, the purple martin Progne subis
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Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses
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Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago
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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)
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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.