Browsing by Author "Heideman, N"

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    Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa
    (BMC, 2020) Zhao, Z; Hofmeyr, D. M; Jordaan, A; Bester, P; Heideman, N
    Background: Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. Results: We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensifcation of the cold Benguela current, which caused western aridifcation and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fuctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by diferent climatic parameters, and that the niches difered substantially among the clades of the northern group but were similar among clades of the southern group. Conclusion: Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-A
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    Codon-based analysis of selection pressure and genetic structure in the Psammobates tentorius (Bell, 1828) species complex, and phylogeny inferred from both codons and amino acid sequences
    (John Wiley & Sons, 2021) Zhao, Z; Heideman, N; Hofmeyr, M. D.
    This study used codon analysis (dN/dS and Tv/Ti) to investigate selection pressure and genetic structure in the highly polymorphic Psammobates tentorius species complex, and amino acid sequences to construct a phylogeny tree for it. Our results revealed a strong selection signal at node ‘C2 + C3’, possibly driven by aridity intensification resulting from the development of the Benguela Current. A similar signal was noticed at C3, possibly due to the same driving force. These findings suggest that environmental selection pressure favoured those groups and that further cladogenic events were possible. Selection pressure was also found to be high at C1, C4 and C7, which may indicate that they are also favoured by the current selection pressure. The codon-based phylogeny did not retrieve any potentially undescribed species, but nonetheless provided support for the validity of the seven distinct clades retrieved with the DNA sequence data. The amino acid sequence-based phylogeny generally supported the seven lineages as valid putative species. Investigation at the genomic scale could, however, help to solve the issue. In general, we found the codon, dN, dS, Tv, Ti and amino acid sequence-based phylogenetic inferences useful in species delimitation and recommend their use in species delimitation studies.