Abstract
For conservation genetic studies using non-invasively collected samples, genome-wide data may be hard to acquire. Until now, such studies have instead mostly relied on analyses of traditional genetic markers such as microsatellites (SSRs). Recently, high throughput genotyping of single nucleotide polymorphisms (SNPs) has become available, expanding the use of genomic methods to include non-model species of conservation concern. We have developed a 96-marker SNP array for use in applied conservation monitoring of the Scandinavian wolverine (Gulo gulo) population. By genotyping more than a thousand non-invasively collected samples, we were able to obtain precise estimates of different types of genotyping errors and sample dropout rates. The SNP panel significantly outperforms the SSR markers (and DBY intron markers for sexing) both in terms of precision in genotyping, sex assignment and individual identification, as well as in the proportion of samples successfully genotyped. Furthermore, SNP genotyping offers a simplified laboratory and analysis pipeline with fewer samples needed to be repeatedly genotyped in order to obtain reliable consensus data. In addition, we utilised a unique opportunity to successfully demonstrate the application of SNP genotype data for reconstructing pedigrees in wild populations, by validating the method with samples from wild individuals with known relatedness. By offering a simplified workflow with improved performance, we anticipate this methodology will facilitate the use of non-invasive samples to improve genetic management of many different types of populations that have previously been challenging to survey.
Highlights
Management and conservation of wide-ranging, elusive species occurring at low densities is challenging due to their hard-to-survey nature
We describe the development and benchmarking of a single nucleotide polymorphisms (SNPs) genotyping pipeline implemented in the conservation-monitoring program for wolverines in Scandinavia
Our study provides an extensive empirical validation of the use of SNP markers for conservation genetics with non-invasively collected samples that is applicable to many other systems facing similar management challenges
Summary
Management and conservation of wide-ranging, elusive species occurring at low densities is challenging due to their hard-to-survey nature. The main limitations for non-invasively collected genetic samples are that they often contain low-quality and quantity of DNA, limiting the use of high-throughput genomic analysis methods (Carroll et al 2018; but see Khan et al 2020), and high cost of sequencing large number of samples. Many genetic studies have been restricted to more traditional low-throughput genetic markers such as microsatellites (SSRs), hampering the uptake of genomics applications in practical conservation projects, and creating the so called “conservation genomics gap” (Shafer et al 2015). Practical limitations in the form of restricted financial and technical resources often lead to a need to reduce the amount of SNP markers, while maximizing the genomic resolution to render manageable and cost effective methods for genetic monitoring of wildlife
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