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2,445 results for “Genetics: population”
Data for: Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow (Ammospiza caudacuta)
<p class="MsoNormal">Determining factors that shape a species' population genetic structure is beneficial for identifying effective conservation practices. We assessed population structure and genetic diversity for Saltmarsh Sparrow (<em>Ammospiza caudacuta</em>), an imperiled tidal marsh specialist, using 13 microsatellite markers and 964 individuals sampled from 24 marshes across the breeding range. We show that Saltmarsh Sparrow populations are structured regionally by isolation-by-distance, with gene flow occurring among marshes within ~110-135 km of one another. Isolation-by-resistance and isolation-by-environment also shape genetic variation; several habitat and landscape features are associated with genetic diversity and genetic divergence among populations. Human development in the surrounding landscape isolates breeding marshes, reducing genetic diversity and increasing population genetic divergence, while surrounding marshland and patch habitat quality (proportion high marsh and sea-level-rise trend) have the opposite effect. The distance of the breeding marsh to the Atlantic Ocean also influences genetic variation, with marshes farther inland being more divergent than coastal marshes. In northern marshes, hybridization with Nelson's Sparrow (<em>A. nelsoni</em>) strongly influences Saltmarsh Sparrow genetic variation, by increasing genetic diversity in the population; this has a concomitant effect of increasing genetic differentiation of marshes with high levels of introgression. From a conservation perspective, we found that the majority of population clusters have low effective population sizes, suggesting a lack of resiliency. To conserve the representative breadth of genetic and ecological diversity and to ensure redundancy of populations, it will be important to protect a diversity of marsh types across the latitudinal gradient of the species range, including multiple inland, coastal and urban populations, which we have shown to exhibit signals of genetic differentiation. It will also require maintaining connectivity at a regional level, by promoting high marsh habitat at the scale of gene flow (~130 km), while also ensuring "stepping stone" populations across the range. </p>
Low genetic diversity and shallow population structure in the broom hare, Lepus castroviejoi (Lagomorpha:Leporidae)
<p><span class="TextRun SCXW115721130 BCX4"><span class="NormalTextRun SCXW115721130 BCX4">Microsatellite dataset of 322 hare samples from five species: 76 samples from the broom hare (</span></span><em><span class="TextRun SCXW115721130 BCX4"><span class="NormalTextRun SCXW115721130 BCX4">Lepus </span><span class="NormalTextRun SCXW115721130 BCX4">castroviejoi</span></span></em><span class="TextRun SCXW115721130 BCX4"><span class="NormalTextRun SCXW115721130 BCX4">); 81 for the European hare (<em>L. europaeus</em>); 68 for the Iberian hare (<em>L. granatensis</em>); 77 for the mountain hare (<em>L. timidus</em>); and 20 for the Italian hare (<em>L. corsicanus</em>).</span></span></p>
Data from: Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales
<p>Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate population persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and thus has direct implications for the spatial scales of management plans. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach based on mitochondrial control region sequences and 4,339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units – the Atlantic, eastern Gulf, and western Gulf – that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighboring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.</p>
Dataset for: Utilizing high-resolution genetic markers to track population-level exposure of migratory birds to renewable energy development
<p class="MsoNormal"><span>With new motivation to increase the proportion of energy demands met by zero-carbon sources, there is a greater focus on efforts to assess and mitigate the impacts of renewable energy development on sensitive ecosystems and wildlife, of which birds are of particular interest. One challenge for researchers, due in part to a lack of appropriate tools, has been estimating the effects from such development on individual breeding populations of migratory birds. To help address this, we utilize a newly developed, high-resolution genetic tagging method to rapidly identify the breeding population of origin of carcasses recovered from renewable energy facilities and combine them with maps of genetic variation across geographic space (called 'genoscapes') for five species of migratory birds known to be exposed to energy development, to assess the extent of population-level effects on migratory birds. We demonstrate that most avian remains collected were from the largest populations of a given species. In contrast, those remains from smaller, declining populations made up a smaller percentage of the total number of birds assayed. Results suggest that application of this genetic tagging method can successfully define population-level exposure to renewable energy development and may be a powerful tool to inform future siting and mitigation activities associated with renewable energy programs.</span></p>
Data from: Past population control biases interpretations of contemporary genetic data: implications for future invasive Sitka black-tailed deer management in Haida Gwaii
<p>Invasive species management practices often include genetic analyses to better inform decision-making and resource allocation. Yet, past management actions may artificially bias recovered patterns of genetic variation; for example, a population bottleneck caused by contemporary culling may mirror some patterns associated with historical isolation. Here, we aimed to disentangle the impacts of past management activities from natural processes for Sitka black-tailed deer (<em>Odocoileus</em> <em>hemionus</em> <em>sitkensis</em>), an invasive species that has been repeatedly culled on two islands, SGang Gwaay and Reef, within the Haida Gwaii archipelago (Canada). We applied a recently developed Genotyping-in-Thousands by sequencing panel to contemporary (e.g., blood, serum, tissue, muscle, feces) and archived deer samples, the latter collected prior to management activity within the system (c. 1997–1998), which allowed us to contextualize conflicting patterns of isolation and connectivity previously observed on SGang Gwaay and Reef. Successful genotyping (92.6%) and population genetic analysis of 292 individuals at 236 SNPs revealed signals of historical isolation on SGang Gwaay and Reef, provided evidence of a founder effect during initial colonization, and indicated an absence of ongoing gene flow. Furthermore, our spatiotemporal analyses consistently supported a priori predictions associated with bottlenecks within post-cull populations, such as within-island loss of genetic variation, elevated within-island kinship, and increased levels of among-island genetic differentiation. These findings are promising for future management of deer on SGang Gwaay and Reef, suggesting that eradications on these islands may be durable. More broadly, our work highlights the importance of understanding management history before interpreting contemporary population genetic data.</p>
Preservation of genetic diversity in a highly fragmented population of the gray-sided vole Myodes rufocanus in an intensive farming region
<p class="MsoNormal"><span>Individual dispersal plays an important role in preserving genetic diversity in density-fluctuating populations of arvicoline rodents. When habitats are fragmented and dispersal between habitats is severely constrained, genetic diversity can be lost. Here, I investigated whether genetic diversity in the gray-sided vole <em>Myodes rufocanus </em>was preserved in an intensive farming region in Japan, where voles inhabited isolated windbreak forests along the borders of plowed lands. Genetic structure was examined in 673 vole samples (330 in spring and 343 in fall) collected at 34 windbreak forests located 0.35–20 km apart. A part of the control region (425 bp) of mitochondrial DNA (mtDNA) was sequenced in 673 voles, yielding 76 haplotypes. Genetic differentiation of maternally inherited mtDNA among trapping sites was markedly lower in males than in females in both seasons, indicating strong male-biased dispersal. Genotypes at six microsatellite DNA loci were determined in 494 voles (245 in spring and 249 in fall) from 18 trapping sites, and loci harbored 16–24 alleles. The mean number of alleles per locus (allelic diversity) at trapping sites was positively correlated with the number of examined individuals (density) in both seasons, and the relationship was very similar to that of a previous study performed in much less fragmented populations. Genetic differentiation of microsatellite DNA among trapping sites decreased considerably from spring to fall. In a STRUCTURE analysis with a most probable cluster number of two, closer trapping sites showed more similar mean values of cluster admixture proportions. The present findings indicate that gene flow among isolated windbreak forests, which occurred mainly by dispersal of males, was not restrained in this intensive farming region. Furthermore, the results suggest that genetic diversity in the study population was preserved as well as in less fragmented populations.</span></p>
Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids
<p>Introgression is a potential source of valuable genetic variation and interspecific introgression lines are important resources for plant breeders to access novel alleles. Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from natural interspecific hybridization and provide opportunities to study the nature and transmission pattern of donor chromatin in recipient genomes. Here, we analyze transmission of donor chromatin in reciprocal backcrosses between <em>G. hirsutum</em> and <em>G. barbadense</em>. Across the genome, recurrent backcrossing in both backgrounds yielded donor chromatin at slightly higher frequencies than the Mendelian expectation in BC<sub>5</sub>F<sub>1</sub> plants, while the average frequency of donor alleles in BC<sub>5</sub>F<sub>2</sub> segregating families was less than expected. In the two subgenomes of polyploid cotton, the rate of donor chromatin introgression was similar. Although donor chromatin was tolerated over much of the recipient genomes, 21 regions recalcitrant to donor alleles were identified. Only limited correspondence is observed between the recalcitrant regions in the two backgrounds, suggesting the effect of species background on introgression of donor segments. Genetic breakdown was progressive, with floral abscission and seed inviability ongoing during backcrossing cycles. Regions of either high or low introgression tended to be in terminal chromosomal regions that are generally rich in both genes and crossover events, with long stretches around the centromere having limited crossover activity resulting in relatively constant low introgression frequencies. Constraints on fixation and selection of donor alleles highlights the challenges of utilizing introgression breeding in crop improvement.</p>
Microsatellite genotypes of Japanese abies species: Insights from population genetics and SDM
<p><span>Range shifts during the Pleistocene shaped the unique phylogeographical structures of many species. Pleistocene range shifts gave currently allopatric species opportunities to occur in sympatry, likely resulting in ancient introgressions between related taxa. In our study, we investigate the range shifts and introgression patterns of three Japanese <em>Abies </em>species (<em>A. firma, A. homolepis, and A. veitchii</em>) by employing an extensive survey of 43 populations. This survey includes comprehensive analysis of both mitochondrial (mtDNA) and nuclear (18 microsatellites) genomes, in combination with species distribution modeling (SDM). It is important to note that these two types of markers provide distinct and complementary information, as they have different modes of inheritance and mutation rates. Bayesian clustering analysis indicates that the three species were clearly separated, with the exception of the <em>A. homolepis </em>var. <em>umbellata</em> population, which is considered a natural hybrid between <em>A. homolepis</em> and <em>A. firma</em>. However, mtDNA haplotypes of the four northern populations of <em>A. firma</em> were entirely replaced by two major haplotypes of <em>A. homolepis </em>and <em>A. veitchii.</em> The results of Neighbor-net, NewHybrids, STRUCTURE analyses, and SDM suggest that historical introgression between species occurred in each geographic region, with mtDNA capture being the likely mechanism. However, contrary to these findings, the ABC coalescent analysis did not support an ancient introgression. Therefore, further validation with genome-wide level data is needed to clarify this issue. Our conclusion is that climate-induced range shifts during the Pleistocene/Holocene likely played a crucial role in the observed patterns of introgression in these species.</span></p>
Phenotypic and genetic diversity data recorded in island and mainland populations worldwide
<p><span>We used this dataset to assess the strength of isolation due to geographic and macroclimatic distance across island and mainland systems, comparing published measurements of phenotypic traits and neutral genetic diversity for populations of plants and animals worldwide. </span>The dataset includes 112 studies of 108 species (72 animals and 36 plants) in 868 island populations and 760 mainland populations, with population-level taxonomic and biogeographic information, totalling 7438 records.</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>
Soil composition, phenotypic and genetic data to: Adaptive differentiation on serpentine soil in diploid versus autotetraploid populations of Biscutella laevigata (Brassicaceae)
<p><span>Serpentine soils exhibit extreme properties (e.g. high magnesium content) influencing plant growth and survival and have been repeatedly documented to promote adaptive edaphic differentiation in plants. Individuals from four pairs of nearby diploid and autotetraploid populations of <em>Biscutella laevigata</em> sampled on serpentine vs non-serpentine soils in a factorial design are used to assess the genetic and phenotypic changes associated with edaphic origin and ploidy level. Individual samples from natural populations were subjected to soil elemental analysis and genotyping using restriction site-associated DNA sequences (RAD-seq) to link genetic variation with contrasting soils and ploidy levels. In diploids, genetic variation was consistent with demographic contraction and a pattern of isolation by environment with respect to the ratio of calcium / magnesium concentrations, whereas tetraploids presented evidence of expansion with limited edaphic differentiation. The genetic basis of tolerance and adaptation to serpentine was further assessed experimentally on seed-grown individuals from all populations subjected to high (serpentine-like) vs low (control) concentrations of magnesium in hydropony. Fitness-related phenotypic traits under experimental cultivation were consistent with adaptive differentiation among diploid ecotypes but not among the tetraploids that similarly grow in both habitats and consistently present higher investment in roots. Further work comparing experimentally resynthesized polyploids to natural diploids and polyploids has to tease the role of whole genome duplication apart from the impact of post-polyploidy evolution.</span></p>
Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake
<p class="MsoNormal">Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation reflecting long-term impacts of genetic drift, yet this widely used approach has been questioned in the genomics era. Here we leverage a chromosome-level assembly and whole genome resequencing data (N=110 individuals) from an endangered rattlesnake (<em>Sistrurus catenatus</em>) to evaluate the relationship between genome-wide neutral and functional diversity over long- and short-term timescales. As predicted for populations at long-term equilibrium, we found a positive correlation between population-level estimates of neutral genetic diversity (π) and the mean number of highly detrimental loss-of-function mutations, and a negative relationship between neutral genetic diversity and an estimate of genetic load. In contrast, we found only a weak, non-significant positive correlation between levels of neutral and adaptive variation. Additional analyses using estimates of drift at more recent time scales (> 100 generations) show expected correlations between both measures of genetic load, but a lack of a significant correlation with levels of adaptive variation. Individual-based demographic metrics that capture drift impacts over recent time scales confirm these results. Broadly, our results confirm that estimates of diversity and demography based on neutral genetic variation provide an accurate measure of a key component of genetic erosion – genetic load – in populations of a threatened vertebrate. Our findings also provide nuance to the neutral-functional diversity controversy by demonstrating that neutral genetic diversity is useful in predicting some, but not all, components of functional genetic diversity.</p>
Population genetics of Daphnimorpha species
<p>A climate relict is of particular importance in evolutionary biology because of its long-term survival in the face of climatic oscillations. However, because their current distributions are usually restricted and fragmented, many climatic relicts have extinction risks. Daphnimorpha (Thymelaeaceae) is a Japanese endemic genus that comprises two species (<em>D</em>. <em>capitellata</em> and <em>D. kudoi</em>) showing a disjunct distribution in the southern part of Japan. These two species are endemic to a single mountain range. In this study, we conducted population genetic analyses using genome-wide single nucleotide polymorphism obtained from multiplexed inter-simple sequence repeat genotyping by sequencing to reveal the phylogeographic history and obtain conservation implications for the two species. The results showed these two species may have been isolated since the Tertiary period, indicating that they are climate relicts. In addition, <em>D. kudoi</em> showed clear genetic differentiation between two mountains (Mt. Nagata and Mt. Kuromi), with a decline in effective population sizes during the last glacial period. In contrast, <em>D. capitellata </em>showed no clear intraspecific genetic structure and its effective population size was relatively stable. These differences could be a result of differences in habitat preferences between the species. For conservation, we should manage the two species based on the three evolutionary significant units (ETUs; <em>D. capitellata, D. kudoi</em> population on Mt. Nagata, and <em>D. kudoi</em> population on Mt. Kuromi). Considering the limited gene flows among subpopulations and their small population sizes, all ETUs require conservative attention to maintain or increase their effective population sizes.</p>
Population genetics and comparative morphology of two serpentine Phlox species
<p>Hybridization between rare and widespread species can result in loss of genetic integrity for the rarer species, which can have management and conservation implications. One rare species, <em>Phlox hirsuta</em>, is a serpentine endemic in northern California, and it frequently co-occurs with a widespread congener, <em>P. speciosa</em>. Putative hybrids were recognized based on intermediate morphology, so the possibility of hybridization was explored using floral morphological and molecular data. Ninety-eight individuals of <em>P. hirsuta</em> and <em>P. speciosa</em> were collected from each of three populations, and floral features were measured and compared. Eleven microsatellite loci were amplified for species and putative hybrids, and inter- and intraspecific genetic diversity and relationships were investigated with multiple methods. Variation in morphological and molecular data was recognized. Floral variation was greater for <em>P. hirsuta</em> than <em>P. speciosa</em>. Putative hybrids were genetically allied with <em>P. speciosa</em>, but two individuals of <em>P. hirsuta</em> were resolved to have genetic similarity with <em>P. speciosa</em>. While hybridization is possible between the species, it is uncommon and appears to be primarily unidirectional, with <em>P. speciosa</em> as the hypothesized male parent and <em>P. hirsuta</em> as the hypothesized female parent. The small number of recognized hybrids may be due to ineffective interspecific pollination, early acting inbreeding depression, hybrids being less fit than parents, and/or small sample sizes. Reinforcement does not appear to play a role in secondary contact between species. Both microsatellite loci and floral morphology varied across the small geographic range of <em>P. hirsuta</em>, suggesting local differentiation and adaptation are possible over short distances.</p>
Genetic Screening for Filaggrin Mutation in Atopic Dermatitis and Ichthyosis Vulgaris in the African American Population
ClinicalTrials.gov study NCT01016106. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Effect of Dalcetrapib vs Placebo on CV Risk in a Genetically Defined Population With a Recent ACS
ClinicalTrials.gov study NCT02525939. IPD Sharing: NO. Countries: 32. Publications: 3.
Landscape genetics of an endangered salt marsh endemic: identifying population continuity and barriers to dispersal
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Data from: An established plant invader may still benefit from increasing genetic diversity – Insights from artificial populations in a common garden experiment
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Data from: Sustained positive consequences of genetic rescue of fitness and behavioural traits in inbred populations of Drosophila melanogaster
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Data from: Interacting effects of genetic variation for seed dormancy and flowering time on phenology, life history, and fitness of experimental Arabidopsis thaliana populations over multiple generations in the field
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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.