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Data from: "RAD Sequencing for SNP Discovery in Two Populations of Bighorn Sheep (Ovis canadensis)" in Genomic Resources Notes accepted 1 April 2013 - 31 May 2013
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Miller, Joshua M.; Hogg, John T.; Coltman, David W. — 2013-07-19 In this work we present the development of a large set of single nucleotide polymorphisms (SNPs) discovered in two populations of bighorn sheep (Ovis canadensis). To do so we used restriction-site associated DNA (RAD) sequencing of four individuals from each population. Through alignment of reads to the domestic sheep (Ovis aries) genome we discovered >83,000 SNPs, of which >38,000 are suitable for assays such as an Illumina SNP chip. These loci will allow for fine-mapping of loci associated with horn size, and examination of the consequences of the genetic rescue including mapping genes underling differences in life-history characteristics.
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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.
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Data from: Genomic consequences of genetic rescue in an insular population of bighorn sheep (Ovis canadensis)
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Miller, Joshua M.; Poissant, Jocelyn; Hogg, John T.; Coltman, David W. — 2011-12-01 Genetic rescue is a management intervention whereby a small population is supplemented with individuals from other populations in an attempt to reverse the effects of inbreeding and increased genetic load. One such rescue was recently documented in the population of bighorn sheep (Ovis canadensis) within the National Bison Range wildlife refuge (Montana, USA). Here we examine the locus-specific effects of rescue in this population using a newly developed genome-wide set of 195 microsatellite loci and first-generation linkage map. We found that the rate of introgression varied among loci, and that 111 loci, 57% of those examined, deviated from patterns of neutral inheritance. The most common deviation was an excess of homozygous genotypes relative to neutral expectations, indicative of directional selection. As in previous study of this rescue, individuals with more introduced alleles had higher lifetime reproductive success and longevity. In addition, we found 30 loci, spread throughout the genome, which seem to have individual effects on these life history traits. Though the potential for outbreeding depression is a major concern when translocating individuals between populations, we found no evidence of such effects in this population.
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Data from: Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep
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Miller, Joshua M.; Poissant, Jocelyn; Malenfant, René M.; Hogg, John T.; Coltman, David W. — 2016-07-14 Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi-allelic LD, D′, and χ′2. We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross-sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible.

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(auteur : Hogg, John T.)

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