Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

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.

Finding stories in noise: Mitochondrial portraits from RAD data

“…The 665 nuclear SNPs for KwaZulu‐Natal yellowfish and 984 SNPs for Orange‐Vaal yellowfish were used to produce a pair of phylogenetic trees (Supporting Information Figure S6). These trees demonstrated very similar results to those obtained using the mined mitochondrial data, but with several key differences—namely that the Umzimkhulu lineage of KwaZulu‐Natal yellowfish was subsumed within the Mkomaas lineage and is no longer distinct as has also been shown elsewhere (Stobie et al, ), and only one sample of Orange‐Vaal yellowfish now appears to be introgressed. All other samples which had been identified to have an incongruent mitochondrial assignment compared to their morphological assignment seem to have a nuclear genotype supporting the morphological assignment.…”

“…Yellowfish from the Umzimkhulu system carry a distinct mitochondrial lineage, as suggested in a previous study of mitochondrial control region sequences (Bloomer et al, ). These individuals were not distinguished from the Mkomaas population using nuclear RAD SNPs either here or in a previous study (Stobie et al, ). This may be indicative of a recent divergence that is not yet evident from sorting of nuclear polymorphisms, or irregular gene flow between populations which has allowed fixation of mitochondrial haplotypes despite sharing of nuclear alleles (Stobie et al, ).…”

Adaptive radiation of barbs of the genus Labeobarbus (Cyprinidae) in an East African river

“…The genus Labeobarbus provides an Ancient introgressions have also been detected in Arctic charr (Salvelinus; Lecaudey et al, 2018), which are classic examples of sympatric divergence in high latitudes (Alekseyev et al, 2002;Hindar & Jonsson, 1982;Knudsen, Klemetsen, Amundsen, & Hermansen, 2006;Taylor, 2016). Application of advanced molecular technologies to investigations of hexaploids can contribute deeper insights into the evolutionary history of Labeobarbus (Stobie, Oosthuizen, Cunningham, & Bloomer, 2018).…”

Adaptive radiation of barbs of the genusLabeobarbus(Cyprinidae) in the East African river

“…Ancient introgressions have also been detected in Arctic charr (Salvelinus; Lecaudey et al 2018) which are classic examples of sympatric divergence in high altitudes (Hindar and Jonsson 1982;Alekseyev et al 2002;Knudsen et al 2006;Taylor 2016). Application of advanced molecular technologies to investigations of hexaploids can contribute deeper insights into the evolutionary history of Labeobarbus (Stobie et al 2018).…”