Abstract
The KwaZulu‐Natal yellowfish (Labeobarbus natalensis) is an abundant cyprinid, endemic to KwaZulu‐Natal Province, South Africa. In this study, we developed a single‐nucleotide polymorphism (SNP) dataset from double‐digest restriction site‐associated DNA (ddRAD) sequencing of samples across the distribution. We addressed several hidden challenges, primarily focusing on proper filtering of RAD data and selecting optimal parameters for data processing in polyploid lineages. We used the resulting high‐quality SNP dataset to investigate the population genetic structure of L. natalensis. A small number of mitochondrial markers present in these data had disproportionate influence on the recovered genetic structure. The presence of singleton SNPs also confounded genetic structure. We found a well‐supported division into northern and southern lineages, with further subdivision into five populations, one of which reflects north–south admixture. Approximate Bayesian Computation scenario testing supported a scenario where an ancestral population diverged into northern and southern lineages, which then diverged to yield the current five populations. All river systems showed similar levels of genetic diversity, which appears unrelated to drainage system size. Nucleotide diversity was highest in the smallest river system, the Mbokodweni, which, together with adjacent small coastal systems, should be considered as a key catchment for conservation.
Highlights
The Cyprinidae is the largest freshwater fish family, comprising approximately 80% of all freshwater fish species in temperate zones (Naran, Skelton, & Villet, 2007) and including over 2,400 species
The average GC content of the reads obtained through restriction site-associated DNA (RAD) sequencing, between 38.5% and 40.8%, was similar to that reported for the zebrafish, Danio rerio, genome (38.6%) (Zhou, Bizzaro, & Marx, 2004) giving confidence that these data were not biased by our choice of AT-rich restriction sites
We found that some signal of finer-scale structure was being driven by mitochondrial single- nucleotide polymorphism (SNP)
Summary
The Cyprinidae is the largest freshwater fish family, comprising approximately 80% of all freshwater fish species in temperate zones (Naran, Skelton, & Villet, 2007) and including over 2,400 species (de Graaf, Nagelkerke, Palstra, & Sibbing, 2010; Swartz, Mwale, & Hanner, 2008). RAD sequencing has been used, 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 suited to phylogeographic studies as the inference power from large numbers of markers may identify patterns that are not visible in traditional analyses based on relatively few loci (Davey et al, 2011). 23 high-quality samples were selected for analysis (Table S1)
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