A hidden world beneath the sand : testing phylogeographic and biogeographic patterns of Southern African sandy beach species

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Stellenbosch : Stellenbosch University
ENGLISH ABSTRACT: South Africa‟s sandy shores are listed as some of the best studied in the world, however, most of these studies have focused on documenting biodiversity and the classification of beach type and there is a distinct lack of genetic data. This has led to a poor understanding of biogeographic and phylogeographic patterns of southern African sandy beach species. Thus, in order to contribute towards plugging the phylogeography knowledge gap, the objectice of this study is to determine levels of genetic differentiation in isopods of the genera Tylos and Excirolana in the South African coast to understand their genetic diversity, connectivity and diversification processes. Individuals (n = 214) of T. granulatus were sampled from nine locations along the west coast of South Africa and Namibia, almost covering the full distribution range of the species. Sequence data was obtained using the mitochondrial genes, COI and 16S. A total of ten sampling locations were covered for E. latipes (n = 140) and nine for E. natalensis (n = 171). For both species, sequence data was obtained with the mtDNA COI gene. Sequences from the COI gene of T. granulatus yielded 44 haplotypes and 91% singletons. Overall, results indicated high haplotype diversity (h = 0.25 - 1.00) and low nucleotide diversity (π = 0.00 - 0.13). Further analyses revealed a strong pattern of genetic divergence characterized by two deeply divergent lineages of T. granulatus, with pairwise comparisons (Φst) ranging from 0.01 to 0.98 (P < 0.05). The genetic pattern is influenced by a phylogeographic break located between Hondeklip Bay and Kleinzee. Dating this divergence reveals a link to the Plio-Pleistocene transition that was characterized by low ocean temperatures and rapid climate and oceanographic oscillations, that also had major impacts on biogeographic and phylogeographic patterns of marine species elsewhere. Results indicated that E. latipes and E. natalensis are sister species with monophyletic groupings. Excirolana latipes was characterized by a strong genetic structure across Cape Point, that appears to act as a barrier to gene flow between the western and southern lineages. Similarly, mtDNA COI revealed two distinct lineages within E.natalensis, although Cape Point did not appear as a significant barrier to gene flow for this species. This provides evidence that although both species have similar life-history patterns and are sympatric; their phylogeographic patterns are driven by different phylogeographic breaks. The estimates of the divergence within lineages of both Excirolana species (140 000 - 1.23 Ma) suggest a strong link with the Pleistocene period. In addition, both Excirolana species were characterised by deeply divergent lineages, potentially indicating cryptic species. This study revealed unknown diversities and possibilities of cryptic speciation. All three isopods were characterized by distinct lineages that should be regarded at least as Management Units (MUs) until nuclear markers and further samples are added. These MUs should be considered separately in conservation and management aims of sandy beaches. Most importantly, the outcome of this study shows the importance of integrating genetic approaches into marine conservation in South Africa.
AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar
Thesis (MSc)--Stellenbosch University, 2018.
Phylogeographic breaks, Biogeographic patterns, Sandy beach species of Southern Africa, Tylos -- Genetics, Excirolana -- Genetics, UCTD