Abstract
BackgroundThe Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so far have been based on 36 STRs, but their limited variability and the more complex situation of current populations demand more efficient molecular markers. The recent characterization of the Iberian lynx genome identified more than 1.6 million SNPs, of which 1536 were selected and genotyped in an extended Iberian lynx sample.MethodsWe validated 1492 SNPs and analysed their heterozygosity, Hardy-Weinberg equilibrium, and linkage disequilibrium. We then selected a panel of 343 minimally linked autosomal SNPs from which we extracted subsets optimized for four different typical tasks in conservation applications: individual identification, parentage assignment, relatedness estimation, and admixture classification, and compared their power to currently used STR panels.ResultsWe ascribed 21 SNPs to chromosome X based on their segregation patterns, and identified one additional marker that showed significant differentiation between sexes. For all applications considered, panels of autosomal SNPs showed higher power than the currently used STR set with only a very modest increase in the number of markers.ConclusionsThese novel panels of highly informative genome-wide SNPs provide more powerful, efficient, and flexible tools for the genetic management and non-invasive monitoring of Iberian lynx populations. This example highlights an important outcome of whole-genome studies in genetically threatened species.
Highlights
The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world
Single-nucleotide polymorphism (SNP) selection, samples, and genotyping Out of >1.6 million SNPs identified through whole genome sequencing of 11 Iberian lynx males [31], a total of 1536 SNPs were selected based on their global Minor Allele Frequency (MAF ≥ 0.4), inter-SNP distance (d > 0.6 Mb), and genotyping quality score predicted by the Illumina’s Assay Design Tool algorithm (ADT > 0.9)
SNP selection, samples and genotyping In order to identify highly informative SNP panels for genetic monitoring and management, we analysed SNPs which were previously selected from a whole genome variation scan and were genotyped using Illumina GoldenDate technology [31]
Summary
The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. They provide valuable insights into population sizes, mating systems, relatedness, population structure, and dispersal rates [1, 2], which can be effectively integrated into management and monitoring programmes of wildlife populations Such programmes typically involve one or several of the following tasks: (i) individual identification, which allows for the estimation of census sizes, the identification of Kleinman-Ruiz et al BMC Genomics (2017) 18:556 size, genetic diversity, gene flow, and to infer demographic changes. SNPs are single base nucleotide variants which make up a stable polymorphism in a species [12], and represent the most abundant and widespread source of sequence variation within genomes [13] Their appeal with respect to STRs builds on: (i) their lower mutation rates [14], which in turn imply less homoplasy [3], (ii) their lower expected error rates both in genotyping and allele calling Their biallelic nature often implies lower resolution and statistical power per marker compared to the multiallelic STRs, but this can be counterbalanced by increasing the number of SNPs [18]
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