Population genomics and phylogeography of South African Labeobarbus (Rüppel, 1835) species

Abstract

The hexaploid freshwater fish genus Labeobarbus are distributed across Africa. These large fish are renowned for their use in game and subsistence fishing. Recent taxonomic changes demonstrate the difficulty in delimiting species in this genus, primarily due to factors such as morphological plasticity, intraspecific variation and hybridisation between taxa. This is particularly true for several of the South African species. The KwaZulu-Natal yellowfish (L. natalensis) is renowned for intraspecific variation particularly in mouth morphotype. This wide range of variation has resulted in the species being described as up to 12 different species previously. Recent mitochondrial genetic analyses have suggested that there is substantial variation between populations of L. natalensis delimited by drainage system. Elsewhere, the Orange-Vaal smallmouth and largemouth yellowfishes (L. aeneus and L. kimberleyensis) occur sympatrically and are morphologically, ecologically and behaviourally distinct. However, a number of studies have reported hybrids occurring in the wild, particularly in artificial habitats such as dams. Some studies have even questioned the validity of these species due to their suspected propensity to hybridise and the inability for allozymes to distinguish the species. In this study I examine the phylogeography of these three South African species using a population genomics approach. I use a reduced-representation Next-Generation Sequencing (NGS) approach known as double-digest Restriction-site Associated DNA (ddRAD) sequencing to partially bypass some of the complications of working with a hexaploid genome. I investigate the genetic structure and phylogeographic patterns and processes influencing these populations. While exploring the phylogeography of L. natalensis I was able to delimit five populations using nuclear Single Nucleotide Polymorphisms (SNPs), contrary to previous studies that identified six geographically separate mitochondrial DNA (mtDNA) lineages. Discordance between these results was re-examined following the identification of a new approach to mine mitochondrial loci from Restriction-site Associated DNA (RAD) data which I showcase as a separate research chapter. My partial mitogenome reconstructions agreed with previous studies in identifying six mitochondrial lineages. This suggests that gene flow between populations together with local fixation of mitochondrial haplotypes may have resulted in the discrepancy between results, which points to a flaw in approaches such as DNA barcoding. I further focus on several methodological aspects, particularly for data filtering and SNP identification, where unexpected results were obtained. The mitogenome mining approach I have developed is highly useful for RAD studies which seek to verify their nuclear RAD results using mitochondrial markers. I demonstrate that there is no need to independently sequence mitochondrial genes as the marker merely needs to be extracted from the RAD data. Discordance between mitochondrial and nuclear results can suggest the presence of certain processes occurring such as introgression, as I show here. Finally, I examine the genetic differentiation of the two species of Orange-Vaal yellowfishes and determine that a few loci potentially under selection and the mitochondrial haplotype show genetic differentiation between the two species, against a background of relative homogeneity. Some evidence of hybridisation and bidirectional introgression was obtained between the two species, with one sample identified as a recent hybrid.