Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

Abstract

Caviar-producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta-samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data focused on the identification of SNPs in the paired-end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population-wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping-by-sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools.

Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

“…This method is popular and has been used in many studies since its inception (Figure S1). RAD sequencing has been used, particularly in fish, to identify population divergence (Boehm, Waldman, Robinson, & Hickerson, 2015; Ferchaud & Hansen, 2016; Larson et al., 2014), for SNP identification in polyploid fish (Hohenlohe, Amish, Catchen, Allendorf, & Luikart, 2011; Ogden et al., 2013; Palti et al., 2014), in phylogeographic studies (Macher et al., 2015; Reitzel, Herrera, Layden, Martindale, & Shank, 2013), for QTL analysis (Gagnaire, Normandeau, Pavey, & Bernatchez, 2013; Houston et al., 2012; Yoshizawa et al., 2015), for linkage mapping (Brieuc, Waters, Seeb, & Naish, 2014; Henning, Lee, Franchini, & Meyer, 2014), in hybridization studies (Hand et al., 2015; Lamer et al., 2014; Pujolar et al., 2014), for exploration of genome architecture and evolution (Brawand et al., 2014; Kai et al., 2014; Waples, Seeb, & Seeb, 2016), and in phylogenetic analyses (Gonen, Bishop, & Houston, 2015; Wagner et al., 2013). This methodology should be particularly suited to phylogeographic studies as the inference power from large numbers of markers may identify patterns that are not easily visible in traditional analyses based on relatively few loci (Davey et al., 2011).…”

Using Mendelian Inheritance To Improve High-Throughput SNP Discovery

“…To date, only a handful of GBS studies have used Mendelian inheritance as an additional filter. Most of these studies simply discarded any loci with extreme segregation distortion (Miller et al 2012) or non-Mendelian inheritance patterns (Gagnaire et al 2013;Ogden et al 2013). Senn et al (2013) used an estimate of Mendelian error rate to set a threshold for genotype confidence scores, but they considered only two cases of Mendelian error and did not incorporate genotype probabilities or sex linkage into their estimates.…”

Genetic Applications in the Conservation of Neotropical Freshwater Fish

“…However, alongside transcriptome analysis, the ability to identify true SNPs is hampered by the occurrence of errors caused by high-throughput sequencing. To mitigate this problem, a sufficient sequence read depth is necessary for both techniques [154].…”