Find research datasets worth reusing

Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds

Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site‐associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half‐century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well‐described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations.

Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities

Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15,000 genome-wide SNPs. Levels of genome-wide diversity were similar across cities, but varied across neighborhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (< 500 m) due to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.

Data from: Reticulate evolution within a spruce (Picea) species complex revealed by population genomic analysis

The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Here, we report a population genomics approach to test the role of hybridization and introgression in the evolution of the Picea likiangensis species complex. Based on 84,793 SNPs detected in transcriptomes of 82 trees collected from 35 localities, we identified 18 hybrids (including backcrosses) distributed within the range boundaries of the four taxa. Coalescent simulations, for each pair of taxa and for all taxa taken together, rejected several tree-like divergence models and supported instead a reticulate evolution model with secondary contacts occurring during Pleistocene glacial cycles after initial divergence in the late Pliocene. Significant gene flow occurred among some taxa after secondary contact according to an analysis based on modified ABBA-BABA statistics that accommodated a rapid diversification scenario. A novel finding was that introgression between certain taxa can contribute to increasing divergence (and possibly reproductive isolation) between those taxa and other taxa within a complex at some loci. These results illuminate the reticulate nature of evolution within the P. likiangensis complex and highlight the value of population genomic data in detecting the effects of introgression in the rapid diversification of related taxa.

Data from: Population genomics and morphometric assignment of western honey bees (Apis mellifera L.) in the Republic of South Africa

Backgrounds: Apis mellifera scutellata and A.m. capensis (the Cape honey bee) are western honey bee subspecies indigenous to the Republic of South Africa (RSA). Both bees are important for biological and economic reasons. First, A.m. scutellata is the invasive "African honey bee" of the Americas and exhibits a number of traits that beekeepers consider undesirable. They swarm excessively, are prone to absconding (vacating the nest entirely), usurp other honey bee colonies, and exhibit heightened defensiveness. Second, Cape honey bees are socially parasitic bees; the workers can reproduce thelytokously. Both bees are indistinguishable visually. Therefore, we employed Genotyping-by-Sequencing (GBS), wing geometry and standard morphometric approaches to assess the genetic diversity and population structure of these bees to search for diagnostic markers that can be employed to distinguish between the two subspecies. Results: Apis mellifera scutellata possessed the highest mean number of polymorphic SNPs (among 2,449 informative SNPs) with minor allele frequencies >0.05 (Np = 88%). The RSA honey bees generated a high level of expected heterozygosity (Hexp = 0.24). The mean genetic differentiation (FST; 6.5%) among the RSA honey bees revealed that approximately 93% of the genetic variation was accounted for within individuals of these subspecies. Two genetically distinct clusters (K = 2) corresponding to both subspecies were detected by Model-based Bayesian clustering and supported by Principal Coordinates Analysis (PCoA) inferences. Selected highly divergent loci (n = 83) further reinforced a distinctive clustering of two subspecies across geographical origins, accounting for approximately 83% of the total variation in the PCoA plot. The significant correlation of allele frequencies at divergent loci with environmental variables suggested that these populations are adapted to local conditions. Only 17 of 48 wing geometry and standard morphometric parameters were useful for clustering A.m. capensis, A.m. scutellata, and hybrid individuals. Conclusions: We produced a minimal set of 83 SNP loci and 17 wing geometry and standard morphometric parameters useful for identifying the two RSA honey bee subspecies by genotype and phenotype. We found that genes involved in neurology/behavior and development/growth are the most prominent heritable traits evolved in the functional evolution of honey bee populations in RSA.

opencc-zeroDec 2018View details →

Data from: Population genomics of rapid evolution in natural populations: polygenic selection in response to power station thermal effluents

Background: Examples of rapid evolution are common in nature but difficult to account for with the standard population genetic model of adaptation. Instead, selection from the standing genetic variation permits rapid adaptation via soft sweeps or polygenic adaptation. Empirical evidence of this process in nature is currently limited but accumulating. Results: We provide genome-wide analyses of rapid evolution in two Fundulus heteroclitus populations subjected to recently elevated temperatures due to coastal power station thermal effluents. Bayesian and multivariate analyses of population genomic structure reveal a substantial portion of genetic variation that is most parsimoniously explained by selection at the site of thermal effluents. An FST outlier approach in conjunction with additional conservative requirements identify significant allele frequency differentiation that exceeds neutral expectations among exposed and closely related reference populations. Genomic variation patterns near these candidate loci reveal that individuals living near thermal effluents have rapidly evolved from the standing genetic variation through small allele frequency changes at many loci in a pattern consistent with polygenic selection on the standing genetic variation. Conclusions: While the ultimate trajectory of selection in these populations is unknown, our findings suggest that polygenic models of adaptation may play important roles in large, natural populations experiencing recent selection due to environmental changes that cause broad physiological impacts.

opengpl-2.0May 2015View details →

Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'

Authors Zhian N. Kamvar, Jonah C. Brooks, and Niklaus J. Grünwald

opencc-zeroOct 2023View details →

Of Mojave milkweed and mirrors: The population genomic structure of a species impacted by solar energy development

A rapid renewable energy transition has facilitated the development of large, ground‐mounted solar energy facilities worldwide. Deserts, and other sensitive aridland ecosystems, are the second most common land‐cover type for solar energy development globally. Thus, it is necessary to understand existing diversity within environmentally sensitive desert plant populations to understand spatiotemporal effects of solar energy siting and design. Overall, few population genomic studies of desert plants exist, and much of their biology is unknown. To help fill this knowledge gap, we sampled Mojave milkweed (Asclepias nyctaginifolia) in and around the Ivanpah Solar Electric Generating Station (ISEGS) in the Mojave Desert of California to understand the species' population structure, standing genetic variation, and how that intersects with solar development. We performed Restriction‐site Associated Sequencing (RADseq) and discovered 9942 single nucleotide polymorphisms (SNPs). Using these data, we found clear population structure over small spatial scales, suggesting each site sampled comprised a genetically distinct population of Mojave milkweed. While mowing, in lieu of blading, the vegetation across the solar energy facility's footprint prevented the immediate loss of the ISEGS Mojave milkweed population, we show that the effects of land‐cover change, especially those impacting desert washes, may impact long‐term genetic diversity and persistence. Potential implications of this include a risk of overall loss of genetic diversity, or even hastened extirpation. These findings highlight the need to consider the genetic diversity of impacted species when predicting the impact and necessary conservation measures of large‐scale land‐cover changes on species with small population sizes.

opencc-zeroOct 2023View details →

Applying genomic approaches to identify historic population declines in European forest bats

<ol> <li>Anthropogenically-driven environmental changes over the past two centuries have led to severe biodiversity loss, most prominently in the form of loss of populations and individuals. Better tools are needed to assess the magnitude of these wildlife population declines. Anecdotal evidence suggests European bat populations have suffered substantial declines in the past few centuries. However, there is little empirical evidence of these declines that can be used to put more recent population changes into historic context and set appropriate targets for species recovery. </li> <li>This study is a collaboration between academics and conservation practitioners to develop molecular approaches capable of providing quantitative evidence of historic population changes and their drivers that can inform the assessment of conservation status and conservation management. We generated a genomic dataset for the Western barbastelle, Barbastella barbastellus, a globally Near Threatened and regionally Vulnerable bat species, including colonies from across the species' British and Iberian ranges. We used a combination of landscape genetics and approximate Bayesian computation model-based inference of demographic history to identify both evidence of population size changes and possible drivers of these changes. </li> <li>We found that levels of genetic diversity and inbreeding were related to broadleaf woodland cover around the colony location. Genetic connectivity was impeded by artificial lights and facilitated by the combination of rivers and broadleaf woodland cover. </li> <li>The demographic history analysis showed that both the northern and southern British barbastelle populations have declined by 99% over the past 330–548 years. These declines may have been triggered by loss of large oak trees and native woodlands due to shipbuilding during the early colonial period.</li> <li> Synthesis and applications. Genomic approaches can be applied to provide a better understanding of the conservation status of threatened species, within historic and contemporary context, and inform their conservation management. This study shows how we can bridge the implementation gap and promote the application of genomics in conservation management through co-designing studies with conservation practitioners and co-developing applied management targets and recommendations.</li> </ol>

opencc-by-4.0Nov 2023View details →

Population Genomics Analysis of 30 Samples from Each of Multiple Populations Reveals Signatures of Selection from Breeding for Rapid Growth and Apical Dominance in Paulownia fortunei

Paulownia fortunei is an ecologically and economically valuable tree cultivated for its rapid growth and high-quality timber. To enhance Paulownia germplasm, we have developed the elite variety QingT with patented advantages in growth rate and apical dominance. To illuminate the genetic basis of QingT's superior traits, here we harness comparative population genomics to analyze genomic variation patterns between QingT and common Paulownia. We performed whole-genome re-sequencing of 30 QingT and 30 common samples, detecting 15.6 million SNPs and 2.6 million indels. Phylogeny and population structure analyses robustly partitioned common and QingT into distinct groups which indicate robust genome stabilization. QingT exhibited reduced heterozygosity and linkage disequilibrium decay compared to common Paulownia, reflecting high recombination, indicating hybridizing effects with common white-flowered string is the source of its patented advantages. Genome selection scans uncovered 25 regions of 169 genes with elevated nucleotide diversity, indicating selection sweeps among groups. Functional analysis of sweep genes revealed upregulation of ribosomal, biosynthesis and growth pathways in QingT, implicating enhanced protein production and developmental processes in its rapid growth phenotype. This study's insights comprehensively chart genomic variation during Paulownia breeding, localizing candidate loci governing agronomic traits, and underpinnings of future molecular breeding efforts to boost productivity.

opencc-zeroDec 2023View details →

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

<div> Coffea arabica, an allotetraploid hybrid of C. eugenioides and C. canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ∼30.5 kya, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica. </div>

opencc-zeroJan 2024View details →

Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations

Genetic diversity is fundamental to the adaptive potential and survival of species. Although its importance has long been recognized in science, it has a history of neglect within policy – until now. The new Global Biodiversity Framework recently adopted by the Convention on Biological Diversity, states that genetic diversity must be maintained at levels assuring adaptive potential of populations, and includes metrics for systematic monitoring of genetic diversity in so called indicators. Similarly, indicators for genetic diversity are being developed at national levels. Here, we apply new indicators for Swedish national use to one of the northernmost salmonid fishes, the Arctic charr (Salvelinus alpinus). We sequence whole genomes to monitor genetic diversity over four decades in three landlocked populations inhabiting protected alpine lakes in central Sweden. We find levels of genetic diversity, inbreeding and load to differ among lakes but remain stable over time. Effective population sizes are generally small (<500), suggesting a limited ability to maintain adaptive variability if genetic exchange with nearby populations became eliminated. We identify genomic regions potentially shaped by selection; SNPs exhibiting population divergence exceeding expectations under drift and a putative selective sweep acting within one lake to which the competitive brown trout was introduced during the sampling period. Identified genes appear involved in immunity and salinity tolerance. Present results suggest that genetically vulnerable populations of Arctic charr have maintained neutral and putatively adaptive genetic diversity despite small effective sizes, attesting the importance of continued protection and assurance of gene flow among populations.

opencc-zeroJan 2024View details →

Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics

Background Hydrangea petiolaris Siebold & Zucc., also known as climbing hydrangea, is a vine native to the woodlands of Korea, Japan, and Sakhalin Island. It is an economically important ornamental plant with fertile and sterile flowers. Despite the recent increase in Hydrangea breeding and interest in germplasm conservation, relatively little is known about the relationships between Hydrangea species. Results We employed Illumina NovaSeq 6000 sequencing technology to generate a total of 39,945,480 reads, which were assembled into 137,715 contigs. A total of 109,092 filtered transcripts were used to identify microsatellites, and 54,587 microsatellite repeat motifs were revealed within 33,556 contigs. Among these, 4,510 transcripts harboring microsatellites had Gene Ontology annotations, and numerous microsatellite-containing transcripts exhibited associations with genes, including those encoding PPR proteins, aldehyde dehydrogenases, and bHLH transcription factors, related to the restorer of fertility (Rf) genes, which play a critical role in restoring fertility in plants with cytoplasmic male sterility. Validation of transcriptomic SSR markers demonstrated high levels of polymorphism, revealing significant genetic diversity within populations. However, null alleles and deviations from Hardy‒Weinberg equilibrium at specific loci suggested caution in genotyping accuracy. Population-level analysis disclosed high genetic differentiation and distinct clustering of populations. Conclusions The H. petiolaris transcriptomic SSR markers offer valuable insight for gaining insights into the population genetics, evolutionary background, and practical strategies for conserving this species. Moreover, the microsatellite loci we have identified and their associations with annotated genes hold promise for creating functional markers specifically tailored for H. petiolaris. These markers include valuable resources of transcriptomic SSR markers suitable for population genetic investigations and have a reasonable degree of applicability across different taxa.

opencc-zeroMar 2024View details →

Genomic analysis of population history for Hawaiian monk seals

The Hawaiian monk seal, one of the world's most endangered pinnipeds, has faced decades of declines and been the focus of intensive conservation efforts. A myriad of conservation threats has led to range-wide population declines, but population trends among islands can vary widely in response to heterogeneous threats. Populations in the Northwestern Hawaiian Islands have been declining whereas Main Hawaiian Islands numbers are expanding. Molecular data can provide information to disentangle population structure and dynamics; however, previous studies have yielded insufficient resolution in such a genetically depauperate species. Advances in genomic technology and affordability offer a novel opportunity to revisit questions about Hawaiian monk seal trends with high resolution markers that provide better discrimination ability in low diversity species. Here, we investigated region- and island-level population structuring and connectivity. We used BestRAD sequencing on 169 seals from 14 islands that span the archipelago to estimate genetic diversity, genetic differentiation, population structure, and migration rates. We did not find robust evidence for island-level population structure. For the first time, our dataset provided resolution to differentiate regional populations with low but significant genetic differentiation. Further, DAPC analyses illustrated population structure with evidence for connectivity, which mirrored our migration rate estimates. Future conservation decisions will need to consider the balance of maintaining connectivity between regions while not homogenizing and losing valuable yet rare, regional unique variation.

opencc-zeroMar 2024View details →

Genetic insight into a polygenic trait using a novel Genome Wide Association approach in a wild amphibian population

Body size variation is central in the evolution of life history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (Lissotriton graecus). By combining a Genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis. The putatively associated variants explained 12.8% to 44.5% of the total phenotypic variation in body size and were mapped to genes with functional roles in the regulation of gene expression and cell cycle processes. Our study is the first to provide insights into the genetic basis of complex traits in newts and provides a useful tool to identify loci potentially involved in fitness related traits in small data sets from natural populations in non-model species.

opencc-zeroApr 2024View details →

Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape

Phrynosoma mcallii (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analyzed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and Salton Sea. We recommend additional lands in the U.S. and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy (RMS). We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change and other long-term impacts.

opencc-zeroApr 2024View details →

Data from: Major group-B enterovirus populations deleted in the noncoding 5' region of genomic RNA modulate activation of the type I interferon pathway in cardiomyocytes and induce myocarditis

Major 5'-terminally deleted (5'TD) RNA forms of group-B coxsackievirus (CVB-5'TD) has been associated with myocarditis in both mice and humans. Although it is known that interferon-β (IFN-β) signaling is critical for an efficient innate immune response against CVB-induced myocarditis, the link between CVB-5'TD RNA forms and type I IFN signaling in cardiomyocytes remains to be explored. In a mouse model of CVB3/28-induced myocarditis, major early-emerging forms of CVB-5'TD RNA have been characterized as replicative viral populations that impair IFN-β production in the heart. Synthetic CVB3/28 RNA forms mimicking each of these major 5'TD virus populations were transfected in mice and have been shown to modulate innate immune responses in the heart and to induce myocarditis in mice. Remarkably, transfection of synthetic viral RNA with deletions in the secondary structures of the 5'-terminal CVB3 RNA domain I, modifying stem-loops "b", "c" or "d", were found to impair IFN-β production in human cardiomyocytes. In addition, the activation of innate immune response by Poly(I:C), was found to restore IFN-β production and to reduce the burden of CVB-5'TD RNA-forms in cardiac tissues, thereby reducing the mortality rate of infected mice. Overall, our results indicate that major early-emerging CVB3 populations deleted in the domain I of genomic RNA, in the 5' noncoding region, modulate the activation of the type I IFN pathway in cardiomyocytes and induce myocarditis in mice. These findings shed new light on the role of replicative CVB-5'TD RNA forms as key pathophysiological factors in CVB-induced human myocarditis.

opencc-by-4.0Nov 2024View details →

Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti

*  These authors contributed equally: Alejandro N. Lozada-Chávez, Irma Lozada-Chávez. <h3> </h3> <h1>Supplementary Dataset</h1>   This repository contains the  Supplementary Data (from 1 to 12) cited in our paper "Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti" in Nature Ecology and Evolution: <a title="Aedes aegypti domestication." href="https://doi.org/10.1038/s41559-025-02643-5">https://doi.org/10.1038/s41559-025-02643-5</a> These datasets are available in the section "Supplementary Information" of our paper, but with the absence of the SD-9 due its large big size (~3Gb after decompressed). Here you can find the complete set of datasets in a single ZIP file: 41559_2025_2643_MOESM5_ESM_Supplementary_Data.zip   LIST OF DATASETS: 1) Supplementary Data 1. SNP statistics for populations through genomic regions (TXT).  2) Supplementary Data 2. Sequences of new detected nrEVEs (FASTA).  3) Supplementary Data 3. Phylogenetic trees for populations and individuals (NEWICK).  4) Supplementary Data 4. Information for 8,120 hard selective sweeps detected with RAiSD in out-of-Africa populations (TXT).  5) Supplementary Data 5. Information for 1,030 SNP outliers detected with PCAdapt within 2,266 genes (VCF format).  6) Supplementary Data 6. Matrix with DoS scores for 11,651 orthologous protein-coding genes in AaegL5 and each Ae. aegypti population (TXT).  7) Supplementary Data 7. Matrix with MKT scores for 11,651 orthologous protein-coding genes in AaegL5 and each Ae. aegypti population (TXT).  8) Supplementary Data 8. Matrix with DoS scores used to estimate relaxed selection (TXT).  9) Supplementary Data 9. Matrix with SNPs and genomic coordinates within adaptive protein-coding genes and ncRNAs that are shared or private for out-of-Africa populations against African populations (TXT).  10) Supplementary Data 10. Matrix with 483 nonsynonymous SNPs and their allele frequencies for our 40 populations Florida and Colombia (TXT). 11) Supplementary Data 11. Genomic coordinates of SNPs in AaegL5 obtained from the literature and VectorBase (TXT).  12) Supplementary Data 12. Source data of metrics used to plot Figure 4b (TXT).   UPDATES NOTE: <ul> <li>Repository version 3. Final version of datasets for the accepted manuscript.</li> <li>Repository version 2. Incomplete datasets: Files as prelimary versions and their content may vary. The SD-10 is not present (matrix with 483 SNPs) was added. The SD-7 is a broken file (cannot be opened).</li> <li>Repository version 1.  Incomplete datasets: Files as prelimary versions and their content may vary. Two final SD files are not present.</li> </ul>   CITATION OF THIS REPOSITORY: Lozada-Chávez, A. N., Lozada-Chávez, I., Alfano, N., Palatini, U., Sogliani, D., Elfekih, S., Degefa, T., Sharakhova, M. V., Badolo, A., Patchara, S., Casas-Martinez, M., Carlos, B. C., Carballar-Lejarazú, R., Lambrechts, L., Souza-Neto, J. A., & Bonizzoni, M. (2024). Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti [Data set]. Zenodo. https://doi.org/10.5281/zenodo.14948092

opencc-by-4.0Mar 2024View details →

SINGER-inferred targets for exceptional population differentiation in coalescence times in African populations in 1000 Genomes Project

This repo saves the gene targets which shows the signal of population differentiation in coalescence times in African populations in 1000 Genomes Project.  Here are the detailed explanations for the header of the files: chrom               The chromosome where the genomic window is located (e.g., chr1, chrX). window_start        The 0-based start position of the genomic window being analyzed. window_end          The 1-based end position of the genomic window (exclusive). score               Ratio between the overall diversity and the population specific diversity, in the genomic window. transcript_chrom    The chromosome where the transcript is located. transcript_start    The 0-based start position of the transcript. transcript_end      The 1-based end position of the transcript (exclusive). transcript_id       The unique identifier for the transcript (e.g., Ensembl or RefSeq ID). strand              The strand of the transcript: "+" for forward, "-" for reverse. coding_start        The start position of the coding region of the transcript (if applicable). coding_end          The end position of the coding region of the transcript (if applicable). RGB                 The RGB color used for visualization in genome browsers (format: R,G,B). block_count         The number of exons in the transcript. block_sizes         Comma-separated list of exon lengths (in base pairs). block_starts        Comma-separated list of exon start positions relative to transcript_start.

opencc-zeroDec 2021View details →

Population and seascape genomics of a critically endangered benthic elasmobranch, the blue skate Dipturus batis

The blue skate (Dipturus batis) has a patchy distribution across the North-East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries-induced population declines and extirpations. The viability of remnant populations remains uncertain, and could be impacted by continued fishing and bycatch pressure and the projected impacts of climate change. We genotyped 503 samples of D. batis, obtained opportunistically from the widest available geographic range, across 6,350 single nucleotide polymorphisms (SNPs) using a reduced-representation sequencing approach. Genotypes were used to assess the species' contemporary population structure, estimate effective population sizes, and identify putative signals of selection in relation to environmental variables using a seascape genomics approach. We identified genetic discontinuities between inshore (British Isles) and offshore (Rockall and Faroe Island) populations, with differentiation most pronounced across the deep waters of the Rockall Trough. Effective population sizes were largest in the Celtic Sea and Rockall, but low enough to be of potential conservation concern among Scottish and Faroese sites. Among the 21 candidate SNPs under positive selection was one significantly correlated with environmental variables predicted to be affected by climate change, including bottom temperature, salinity, and pH. The paucity of well annotated elasmobranch genomes precluded us from identifying a putative function for this SNP. Nevertheless, our findings suggest that climate change could inflict a strong selective force upon remnant populations of D. batis, further constraining its already restricted habitat. Furthermore, the results provide fundamental insights on the distribution, behaviour, and evolutionary biology of D. batis in the North-East Atlantic that will be useful for the establishment of conservation actions for this and other critically endangered elasmobranchs.