Genome variability in European and American bison detected using the BovineSNP50 BeadChip

Pertoldi, Cino; Wójcik, Jan M.; Tokarska, Małgorzata; Kawałko, Agata; Kristensen, Torsten Nygaard; Loeschcke, Volker; Gregersen, Vivi Raundahl; Coltman, David W.; Wilson, Gregory; Randi, Ettore; Henryon, Mark; Berthou, Christian

doi:10.1007/s10592-009-9977-y

Cited by 48 publications

(51 citation statements)

References 24 publications

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“…The level of polymorphism, however, is unexpectedly high and could result from historically high population sizes of mule deer, black-tailed deer and white-tailed deer in North America [24]. In contrast, the bison species analyzed by Pertoldi et al [18] have undergone several severe population bottlenecks, while the wild sheep species investigated by Miller et al [17] live in relatively small, isolated populations. The identification of 1068 novel, polymorphic SNPs in this study demonstrates that commercial SNP chip technology is a viable and potentially underutilized means of discovering SNP loci in non-model species, even when used between highly divergent lineages.…”

Section: Discussionmentioning

confidence: 98%

Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

Haynes

Latch

2012

PLoS ONE

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Single nucleotide polymorphisms (SNPs) are growing in popularity as a genetic marker for investigating evolutionary processes. A panel of SNPs is often developed by comparing large quantities of DNA sequence data across multiple individuals to identify polymorphic sites. For non-model species, this is particularly difficult, as performing the necessary large-scale genomic sequencing often exceeds the resources available for the project. In this study, we trial the Bovine SNP50 BeadChip developed in cattle (Bos taurus) for identifying polymorphic SNPs in cervids Odocoileus hemionus (mule deer and black-tailed deer) and O. virginianus (white-tailed deer) in the Pacific Northwest. We found that 38.7% of loci could be genotyped, of which 5% (n = 1068) were polymorphic. Of these 1068 polymorphic SNPs, a mixture of putatively neutral loci (n = 878) and loci under selection (n = 190) were identified with the FST-outlier method. A range of population genetic analyses were implemented using these SNPs and a panel of 10 microsatellite loci. The three types of deer could readily be distinguished with both the SNP and microsatellite datasets. This study demonstrates that commercially developed SNP chips are a viable means of SNP discovery for non-model organisms, even when used between very distantly related species (the Bovidae and Cervidae families diverged some 25.1−30.1 million years before present).

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Section: Discussionmentioning

confidence: 98%

Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

Haynes

Latch

2012

PLoS ONE

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“…Moreover, although assisted translocation of entire species may be difficult, translocation of genotypes adapted to different conditions is likely to be much more feasible and might provide an insurance policy against future change (Broadhurst et al 2008, Hedrick & Fredrickson 2010, but see Bijlsma et al 2010. In this regard, assessments of movements of individuals into areas perhaps already occupied by other populations of the species may have to move away from the consideration of neutral markers only (which will show differences based mostly on time of isolation) and consider genes that are likely to have significance in the context of environmental responses (Demontis et al 2009, Pertoldi et al 2010. Genome-based evolutionary physiology has much to offer here too.…”

Section: Conservation Implicationsmentioning

confidence: 99%

“…Genome-based evolutionary physiology has much to offer here too. For example, genome-wide breeding strategies can be used on captive populations of endangered species before translocation into the wild to optimize genetic variability in physiologically important parts of the genome (Pertoldi et al 2010).…”

Section: Conservation Implicationsmentioning

confidence: 99%

Adapting to climate change: a perspective from evolutionary physiology

et al. 2010

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Much attention has been given to forecasting the likely effects of ongoing climate change on biodiversity. A large and often contentious literature has developed about how changes in species' ranges should be modelled and how additional biological mechanisms might be incorporated to improve their utility. Nonetheless, 2 areas stand out as relatively underappreciated: the importance of understanding a species' physiological capacities when forecasting its response to climate change, and the likely influence that capacities for genetic change across generations and changes in plastic responses, or the lack thereof, will have on a species' response. Although perhaps not as well developed as correlative approaches to understanding species responses to change, mechanistic approaches are advancing rapidly. In this review, we explore several of the key messages emerging from the mechanistic approach, embodied in evolutionary physiology, to understanding and forecasting species responses to climate change.

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“…One means of SNP discovery that does not require extensive sequencing is to use commercially available SNP chips developed for a related, well-studied model species (Haynes and Latch, 2012). In the last period have been used SNP chips from livestock to identify SNPs in closely related species to non-model species (Miller et al, 2011;Pertoldi et al, 2010), including deer. Bixley et al (2009) have produced a reduced representational sequence of >160 million base pairs (Mbp), of which they mapped 44 Mbp to unique positions on the bovine genome.…”

Section: Utilization Of Snps In Deer As Non-model Speciesmentioning

confidence: 99%