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537 results for “genome structure”
Data from: Genome-wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep (Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia)
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Data for: Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure
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Data from: High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery
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Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the Chocolate Tree
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A classification framework for Bacillus anthracis defined by global genomic structure
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Data from: Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci
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Genome-structural analyses support an allotetraploid origin of the walnut family from within Myricaceae and shared genome duplications reveal substitution rate variation
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Data from: Genome-wide insights into population structure and genetic history of Tunisian local cattle using the Illumina BovineSNP50 Beadchip
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Data from: On the roles of landscape heterogeneity and environmental variation in determining population genomic structure in a dendritic system
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Data from: Northern Bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy
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Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing
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Data from: Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland
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Data from: Genomics detects population structure within and between ocean basins in a circumpolar seabird: the white-chinned petrel
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Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution
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Genomic assessment of global population structure in a highly migratory and habitat versatile apex predator, the tiger shark (Galeocerdo cuvier)
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Genomic inbreeding and population structure of northern pike (Esox lucius) in Xinjiang, China
<p>Northern pike (Esox lucius) is originally only distributed in the Irtysh River, and now spread into many habitats in Xinjiang, China. A total of four populations were collected from north to south in Xinjiang, including Irtysh River (RIR), Ulungu Lake (LUL), a small lake nearby Ulungu River (LJD) and Bosten Lake (LBO). We estimated population genomic parameters, performed gene flow analysis, and estimated the effective population size of each population.</p>
Genome-wide SNPs detect no evidence of genetic population structure for reef manta rays (Mobula alfredi) in southern Mozambique
Little is known about the extent of genetic connectivity along continuous coastlines in manta rays or whether site visitation is influenced by relatedness. Such information is pertinent to defining population boundaries and understanding localised dispersal patterns and behaviour. Here, we use 3057 genome-wide single nucleotide polymorphisms (SNPs) to evaluate population genetic structure and assess levels of relatedness at aggregation sites of reef manta rays (Mobula alfredi) in southern Mozambique (n = 114). Contrary to indications of limited dispersal along the southern Mozambican coastline inferred from photo identification and telemetry studies, our results show no evidence of population structure (non-significant FST <0.001) for M. alfredi along this coast. We also found no evidence that individuals sampled at the same site were more related than expected by chance for males, females or across both sexes, suggesting kinship may not influence visitation pattern s at these sites. We estimated the effective population size (Ne) of this population to be 375 (95% CI = 369-380). Comparison to a distant eastern Indian Ocean site (Western Australia; n = 15) revealed strong genetic differentiation between Mozambique and Western Australia (FST = 0.377), identifying the Indian Ocean basin as a barrier to dispersal. Our findings show that genetic connectivity in M. alfredi extends for several hundred kilometres along continuous coastlines. We therefore recommend the population in Mozambique be considered a discrete management unit and future conservation plans should prioritize integrated strategies along the entire southern coastline.
Data from: Spatiotemporally explicit demographic modelling supports a joint effect of historical barriers to dispersal and contemporary landscape composition on structuring genomic variation in a red-listed grasshopper
Inferring the processes underlying spatial patterns of genomic variation is fundamental to understand how organisms interact with landscape heterogeneity and to identify the factors determining species distributional shifts. Here, we employ genomic data (ddRADSeq) to test biologically-informed models representing historical and contemporary demographic scenarios of population connectivity for the Iberian cross-backed grasshopper Dociostaurus hispanicus, a species with a narrow distribution that currently forms highly fragmented populations. All models incorporated biological aspects of the focal taxon that could hypothetically impact its geographical patterns of genomic variation, including (a) spatial configuration of impassable barriers to dispersal defined by topographic landscapes not occupied by the species, (b) distributional shifts resulted from the interaction between the species bioclimatic envelope and Pleistocene glacial cycles, and (c) contemporary distribution of suitable habitats after extensive land clearing for agriculture. Spatiotemporally-explicit simulations under different scenarios considering these aspects and statistical evaluation of competing models within an Approximate Bayesian Computation (ABC) framework supported spatial configuration of topographic barriers to dispersal and human-driven habitat fragmentation as the main factors explaining the geographical distribution of genomic variation in the species, with no apparent impact of hypothetical distributional shifts linked to Pleistocene climatic oscillations. Collectively, this study supports that both historical (i.e., topographic barriers) and contemporary (i.e., anthropogenic habitat fragmentation) aspects of landscape composition have shaped major axes of genomic variation in the studied species and emphasizes the potential of model-based approaches to gain insights into the temporal scale at which different processes impact the demography of natural populations.
Data from: Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus
The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America where the Viannia subgenus predominates, so far only L. (Viannia) braziliensis and L. (V.) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. (V.) naiffi and L. (V.) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads. The methods used were tested using short sequence reads for L. braziliensis M2904 against its published reference as a comparison. This assembly and annotation pipeline identified 70 additional genes not annotated on the original M2904 reference. Phylogenetic and evolutionary comparisons of L. guyanensis and L. naiffi with ten other Viannia genomes revealed four traits common to all Viannia: aneuploidy, 22 orthologous groups of genes absent in other Leishmania subgenera, elevated TATE transposon copies, and a high NADH-dependent fumarate reductase gene copy number. Within the Viannia, there were limited structural changes in genome architecture specific to individual species: a 45 Kb amplification on chromosome 34 was present in all bar L. lainsoni, L. naiffi had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had a possible minichromosome derived from the 3' end of chromosome 34. This combination of genome assembly, phylogenetics and comparative analysis across an extended panel of diverse Viannia has uncovered new insights into the origin and evolution of this subgenus and can help improve diagnostics for leishmaniasis surveillance.
Data from: Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms
Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority due to recent outbreaks of Avian Influenza. Ringing studies that trace large-scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism (SNP) markers in combination with population genetics and phylogeographic approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations world-wide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual-based structuring algorithms discern geographical structuring. Model-based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.
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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.