Recherche

Dryad Translation missing: fr.blacklight.search.logo
Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing
Malenfant, René M.; Coltman, David W.; Davis, Corey S. — 2014-09-04 Single-nucleotide polymorphisms (SNPs) offer numerous advantages over anonymous markers such as microsatellites, including improved estimation of population parameters, finer-scale resolution of population structure and more precise genomic dissection of quantitative traits. However, many SNPs are needed to equal the resolution of a single microsatellite, and reliable large-scale genotyping of SNPs remains a challenge in nonmodel species. Here, we document the creation of a 9K Illumina Infinium BeadChip for polar bears (Ursus maritimus), which will be used to investigate: (i) the fine-scale population structure among Canadian polar bears and (ii) the genomic architecture of phenotypic traits in the Western Hudson Bay subpopulation. To this end, we used restriction-site associated DNA (RAD) sequencing from 38 bears across their circumpolar range, as well as blood/fat transcriptome sequencing of 10 individuals from Western Hudson Bay. Six-thousand RAD SNPs and 3000 transcriptomic SNPs were selected for the chip, based primarily on genomic spacing and gene function respectively. Of the 9000 SNPs ordered from Illumina, 8042 were successfully printed, and – after genotyping 1450 polar bears – 5441 of these SNPs were found to be well clustered and polymorphic. Using this array, we show rapid linkage disequilibrium decay among polar bears, we demonstrate that in a subsample of 78 individuals, our SNPs detect known genetic structure more clearly than 24 microsatellites genotyped for the same individuals and that these results are not driven by the SNP ascertainment scheme. Here, we present one of the first large-scale genotyping resources designed for a threatened species.
Dryad Translation missing: fr.blacklight.search.logo
Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013
Malenfant, René M.; Coltman, David L.; Richardson, Evan S.; Lunn, Nicholas J.; Davis, Corey S.; Coltman, David W.; Lunn, Nick J. — 2013-11-12 Polar bears (Ursus maritimus) in the Western Hudson Bay subpopulation have been declining in size and body condition for decades, as climate change causes earlier sea ice breakup, reduced hunting time on the ice, and an increasingly long fasting season. As Western Hudson Bay females have decreased in size, rates of litter production and average litter size have also decreased, while cub mortality and average time to independence have increased. Although these changes have potential evolutionary consequences, little is yet known about the adaptive genetic variation in body size or fat accumulation that would have to underlie any such change. In this study, we used high-throughput Illumina sequencing to develop SNPs from pooled blood and fat transcriptomes, using samples from five adult female polar bears and five (unrelated) dependent cubs. In total, we generated 371,258 transcripts of which 36,755 were deemed to be “full length” (i.e., covered more than 90% of their best BLAST hit), and we identified 63,020 SNPs. Since this study was conducted, we have used a subset of these SNPs to develop an Illumina BeadArray for quantitative genetics research in Western Hudson Bay.
Dryad Translation missing: fr.blacklight.search.logo
Data from: Spatial genetic structure of the mountain pine beetle (Dendroctonus ponderosae) outbreak in western Canada: historical patterns and contemporary dispersal
Samarasekera, G. D. N. Gayathri; Bartell, Nicholas V.; Lindgren, B. Staffan; Cooke, Janice E. K.; Davis, Corey S.; James, Patrick M. A.; Coltman, David W.; Mock, Karen E.; Murray, Brent W. — 2011-10-17 Environmental change has a wide range of ecological consequences, including species extinction and range expansion. Many studies have shown that insect species respond rapidly to climatic change. A mountain pine beetle epidemic of record size in North America has led to unprecedented mortality of lodgepole pine, and a significant range expansion to the northeast of its historic range. Our goal was to determine the spatial genetic variation found among outbreak population from which genetic structure, and dispersal patterns may be inferred. Beetles from 49 sampling locations throughout the outbreak area in western Canada were analysed at 13 microsatellite loci. We found significant north-south population structure as evidenced by: (i) Bayesian-based analyses, (ii) north-south genetic relationships and diversity gradients; and (iii) a lack of isolation-by-distance in the northernmost cluster. The north-south structure is proposed to have arisen from the processes of postglacial colonization as well as recent climate-driven changes in population dynamics. Our data support the hypothesis of multiple sources of origin for the outbreak and point to the need for population specific information to improve our understanding and management of outbreaks. The recent range expansion across the Rocky Mountains into the jack/lodgepole hybrid and pure jack pine zones of northern Alberta is consistent with a northern British Columbia origin. We detected no loss of genetic variability in these populations, indicating that the evolutionary potential of mountain pine beetle to adapt has not been reduced by founder events. This study illustrates a rapid range-wide response to the removal of climatic constraints, and the potential for range expansion of a regional population.
Dryad Translation missing: fr.blacklight.search.logo
Data from: Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs
Viengkone, Michelle; Derocher, Andrew Edward; Richardson, Evan Shaun; Malenfant, René Michael; Miller, Joshua Moses; Obbard, Martyn E.; Dyck, Markus G.; Lunn, Nick J.; Sahanatien, Vicki; Davis, Corey S. — 2017-10-03 Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single-nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine-scale structure. In Hudson Bay, Canada, three polar bear (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark–recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine-scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western—including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern—individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH (Akimiski Island in James Bay); and (iv) Northeast—individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine-scale population delineation in polar bears. https://creativecommons.org/publicdomain/zero/1.0/
Dryad Translation missing: fr.blacklight.search.logo
Data from: Clones or clans: the genetic structure of a deep-sea sponge, Aphrocallistes vastus, in unique sponge reefs of British Columbia, Canada
Brown, Rachel R.; Davis, Corey S.; Leys, Sally P. — 2017-03-13 Understanding patterns of reproduction, dispersal and recruitment in deep-sea communities is increasingly important with the need to manage resource extraction and conserve species diversity. Glass sponges are usually found in deep water (>1000 m) worldwide but form kilometre-long reefs on the continental shelf of British Columbia and Alaska that are under threat from trawling and resource exploration. Due to their deep-water habitat, larvae have not yet been found and the level of genetic connectivity between reefs and nonreef communities is unknown. The genetic structure of Aphrocallistes vastus, the primary reef-building species in the Strait of Georgia (SoG) British Columbia, was studied using single nucleotide polymorphisms (SNPs). Pairwise comparisons of multilocus genotypes were used to assess whether sexual reproduction is common. Structure was examined 1) between individuals in reefs, 2) between reefs and 3) between sites in and outside the SoG. Sixty-seven SNPs were genotyped in 91 samples from areas in and around the SoG, including four sponge reefs and nearby nonreef sites. The results show that sponge reefs are formed through sexual reproduction. Within a reef and across the SoG basin, the genetic distance between individuals does not vary with geographic distance (r = −0.005 to 0.014), but populations within the SoG basin are genetically distinct from populations in Barkley Sound, on the west coast of Vancouver Island. Population structure was seen across all sample sites (global FST = 0.248), especially between SoG and non-SoG locations (average pairwise FST = 0.251). Our results suggest that genetic mixing occurs across sponge reefs via larvae that disperse widely.
Dryad Translation missing: fr.blacklight.search.logo
Data from: Cross-platform compatibility of de novo-aligned SNPs in a non-model butterfly genus
Dryad
Campbell, Erin O.; Davis, Corey S.; Dupuis, Julian R.; Muirhead, Kevin; Sperling, Felix A.H.; Sperling, Felix A. H. — 2017-06-20 High-throughput sequencing methods for genotyping genome-wide markers are being rapidly adopted for phylogenetics of non-model organisms in conservation and biodiversity studies. However, the reproducibility of SNP genotyping and degree of marker overlap or compatibility between datasets from different methodologies have not been tested in non-model systems. Using double-digest restriction site associated DNA sequencing, we sequenced a common set of 22 specimens from the butterfly genus Speyeria on two different Illumina platforms, using two variations of library preparation. We then used a de novo approach to bioinformatic locus assembly and SNP discovery for subsequent phylogenetic analyses. We found a high rate of locus recovery despite differences in library preparation and sequencing platforms, as well as overall high levels of data compatibility after data processing and filtering. These results provide the first application of NGS methods for phylogenetic reconstruction in Speyeria, and support the use and long-term viability of SNP genotyping applications in non-model systems.
Dryad Translation missing: fr.blacklight.search.logo
Data from: Estimating genome-wide heterozygosity: effects of demographic history and marker type
Miller, Joshua M.; Malenfant, René M.; David, Patrice; Davis, Corey S.; Poissant, Jocelyn; Hogg, John T.; Festa-Bianchet, Marco; Coltman, David W. — 2013-09-17 Heterozygosity–fitness correlations (HFCs) are often used to link individual genetic variation to differences in fitness. However, most studies examining HFCs find weak or no correlations. Here, we derive broad theoretical predictions about how many loci are needed to adequately measure genomic heterozygosity assuming different levels of identity disequilibrium (ID), a proxy for inbreeding. We then evaluate the expected ability to detect HFCs using an empirical data set of 200 microsatellites and 412 single nucleotide polymorphisms (SNPs) genotyped in two populations of bighorn sheep (Ovis canadensis), with different demographic histories. In both populations, heterozygosity was significantly correlated across marker types, although the strength of the correlation was weaker in a native population compared with one founded via translocation and later supplemented with additional individuals. Despite being bi-allelic, SNPs had similar correlations to genome-wide heterozygosity as microsatellites in both populations. For both marker types, this association became stronger and less variable as more markers were considered. Both populations had significant levels of ID; however, estimates were an order of magnitude lower in the native population. As with heterozygosity, SNPs performed similarly to microsatellites, and precision and accuracy of the estimates of ID increased as more loci were considered. Although dependent on the demographic history of the population considered, these results illustrate that genome-wide heterozygosity, and therefore HFCs, are best measured by a large number of markers, a feat now more realistically accomplished with SNPs than microsatellites.
Dryad Translation missing: fr.blacklight.search.logo
Data from: Heritability of body size in the polar bears of Western Hudson Bay
Dryad
Malenfant, René M.; Davis, Corey S.; Richardson, Evan S.; Lunn, Nicholas J.; Coltman, David W. — 2022-04-26 Among polar bears (Ursus maritimus), fitness is dependent on body size through males' abilities to win mates, females' abilities to provide for their young, and all bears' abilities to survive increasingly longer fasting periods caused by climate change. In the Western Hudson Bay subpopulation (near Churchill, Manitoba, Canada), polar bears have declined in body size and condition, but nothing is known about the genetic underpinnings of body size variation, which may be subject to natural selection. Here, we combine a 4449-individual pedigree and an array of 5433 single-nucleotide polymorphisms (SNPs) to provide the first quantitative genetics study of polar bears. We used animal models to estimate heritability (h2) among polar bears handled between 1966 and 2011, obtaining h2 estimates of 0.34-0.48 for strictly skeletal traits and 0.18 for axillary girth (which is also dependent on fatness). We genotyped 859 individuals with the SNP array to test for marker-trait association and combined p-values over genetic pathways using gene-set analysis. Variation in all traits appeared to be polygenic, but we detected one region of moderately large effect size in body length near a putative noncoding RNA in an unannotated region of the genome. Gene-set analysis suggested that variation in body length was associated with genes in the regulatory cascade of cyclin expression, which has previously been associated with body size in mice. A greater understanding of the genetic architecture of body size variation will be valuable in understanding the potential for adaptation in polar bear populations challenged by climate change.

Instructions pour la recherche cartographique

1.Activez le filtre cartographique en cliquant sur le bouton « Limiter à la zone sur la carte ».
2.Déplacez la carte pour afficher la zone qui vous intéresse. Maintenez la touche Maj enfoncée et cliquez pour encadrer une zone spécifique à agrandir sur la carte. Les résultats de la recherche changeront à mesure que vous déplacerez la carte.
3.Pour voir les détails d’un emplacement, vous pouvez cliquer soit sur un élément dans les résultats de recherche, soit sur l’épingle d’un emplacement sur la carte et sur le lien associé au titre.
Remarque : Les groupes servent à donner un aperçu visuel de l’emplacement des données. Puisqu’un maximum de 50 emplacements peut s’afficher sur la carte, il est possible que vous n’obteniez pas un portrait exact du nombre total de résultats de recherche.

(auteur : Davis, Corey S.)

Limiter par :

Effacer tout

au