Phylogeographic patterning of three co-distributed forest-dwelling reptile species along the east coast of South Africa

Thesis (MSc)--Stellenbosch University, 2019.ENGLISH ABSTRACT: This study investigates the phylogeographic structure of three co-distributed forest-living reptile species, the Pondo flat gecko (Afroedura pondolia), the forest thread snake (Leptotyphlops sylvicolus) and the Natal black snake (Macrelaps microlepidotus), by sampling specimens from the Eastern Cape and KwaZulu-Natal provinces of South Africa. Phylogenetic results, using Bayesian inferences and maximum likelihood, from the combined mitochondrial sequence data (ND4 and cyt b), along with population genetic analyses suggest the presence of broadly congruent biogeographic breaks among the study taxa. Sequence divergence values suggest that A. pondolia and L. sylvicolus represent species complexes comprising several cryptic species while M. microlepidotus exhibits population level differentiation. Divergence-time estimates indicate that cladogenesis within the study taxa occurred during the late Miocene to the Plio/Pleistocene climatic shifts, suggesting that cladogenesis was driven by climatic oscillations and suitable habitat fragmentation. We further investigate the species level divergence within A. pondolia and L. sylvicolus by including two partial nuclear loci (PRLR and RAG1) and employing several species delimitation methods (ABGD, bGMYC, PTP and STACEY). The species delimitation results were generally incongruent, estimating between two and 14 species nested within A. pondolia and between ten and 12 species nested within L. sylvicolus. In both taxa, the species hypotheses retrieved by STACEY based on the total-evidence data were preferred and used to define groups in the morphological analyses. In A. pondolia the multivariate morphological analyses indicate statistically significant differences among the four putative species, corroborating the presence of four species. In L. sylvicolus the morphological analyses exhibit large overlap among the ten putative species but indicate differences between grassland and forest species. The narrow distributions of the putative species identified in the present study have further implications for the conservation status of A. pondolia and L. sylvicolus and suggest that the fragmented forest habitat along the east coast of South Africa may harbor significantly higher levels of diversity than currently recognized.Master