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.
