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Diet diversity and overlap was investigated in the sympatric skinks Trachylepis punctatissima and Trachylepis varia from central South Africa using stomach and intestinal contents of museum specimens. Simpson's Index and the Shannon–Wiener Index were used to determine their food niche breadths and Pianka's Index to determine the extent to which they shared the food resource. Food items were identified from head capsules, mouthparts and appendages to order level. The two species contained similar prey types with T. varia having the wider niche breadth. Females also had wider niche breadths than males and isopterans were present in significantly higher quantities than the rest of the food items in both species. Larvae were found in both, but arachnids only in T. varia. Trophic niche overlap between the two was fairly high (Pianka's Index, 0.6915) and therefore did not support the hypothesis that similar species sharing a food resource should have well differentiated diets to reduce competition. This finding however requires further verification as the two species may consume different species of the corresponding orders identified. Intraspecifically trophic niche overlap between the sexes was low (T. punctatissima, 0.3889; T. varia, 0.4633) suggesting strong competition for the food resource. Notably lower niche breadth in males compared to females may be due to morphological and behavioural differences and should be further investigated. [ABSTRACT FROM AUTHOR]

We examined morphometric differentiation in the highly polymorphic and taxonomically confusing Psammobates tentorius (tent tortoise) species complex in southern Africa, using morphological data together with previously published DNA sequence and microsatellite DNA data. We used the approximate Bayesian computation‐based simulation analysis to test alternative phylogenetic hypotheses supported by different markers, using a total evidence dataset for the tent tortoise species complex. The results supported a scenario, which is better and more inclusive in explaining its genealogical history. Our total evidence‐based Bayesian BPP species delimitation analysis (mtDNA + nDNA + morphology) suggested a seven species scheme should be applied to the P. tentorius species complex. Nonetheless, based on comparative results obtained from sequence, microsatellite, ecological niche, and morphological data, a four‐species scheme (among the seven mtDNA clades) appears to be the best taxonomic solution for the systematic puzzle of the P. tentorius species complex, namely, "C1 + C4 + C5 + C7," "C3," "C2," and "C6." We detected several possible hybridizations between C1 and C2 in their intergradation zone that confirmed the possible cross‐over between them. Lastly, we provide a summarized flow chart of the analyses carried out for determining the optimal taxonomic solution for this phenotypically difficult group, as it may also be useful for resolving complex taxonomic issues in other species groups. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed 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. [ABSTRACT FROM AUTHOR]

The high level of phenotypic diversity in southern African tent tortoises (Psammobates tentorius complex) has for decades prevented systematists from developing a stable taxonomy for the group. Here, we used a comprehensive DNA sequence dataset (mtDNA: Cytb, ND4, ND4 adjacent tRNA‐His, and tRNA‐Ser, 12S, 16S; and nDNA: PRLR gene) of 455 specimens, and the latest phylogenetic and species delimitation analytical procedures, to unravel the long‐standing P. tentorius complex systematic puzzle. Our results for mtDNA and nDNA were incongruent, with the poorly supported nDNA phylogeny differentiating the three recognized subspecies, and showing potential hybridization in some regions. In contrast, the concatenated mtDNA phylogeny identified seven operational taxonomic units, with strong support. Clades 1, 4, 5, and 7 corresponded to tortoises identified as P. t. tentorius, clade 3 to P. t. trimeni, and clades 2 and 6 to P. t. verroxii. Our analyses showed conflicting topologies for the placement of C6 (P. t. verroxii north of the Orange River), with stronger support for it being sister to C2 + C3 than to the other clades. Clades 1, 2, and 6 had significantly higher genetic diversity than clades 3, 4, 5, and 7, perhaps because these clades inhabit substantially larger areas. The potential for future cladogenic radiations seems high in C1 and C6, particularly in C6 for which the within‐clade diversification level was highest. Further research involving microsatellite DNA, phylogeographic evaluations, and morphological variation among clades is crucial for understanding the adaptive radiation of the P. tentorius complex and for modifying their taxonomy. [ABSTRACT FROM AUTHOR]

Acontias plumbeus has traditionally been considered a monotypic, invariable species, a fact that highly contrasts with documented examples of high phylogenetic complexity and phenotypic diversity in other members of the Acontinae. We employed mitochondrial and nuclear DNA markers to investigate genetic structuring among A. plumbeus populations and the relationship between A. plumbeus and the closely related A. poecilus. Molecular genetic analyses revealed three clades with non‐overlapping distributions: an Eastern clade, a widely distributed Northern clade, and a Southern clade that includes topotypical A. poecilus. Morphometric analyses of preserved specimens showed that Southern clade populations are comprised of individuals with absolute and proportionally smaller body sizes than their Northern and Eastern relatives. Phylogenetic affinities within A. plumbeus indicate a complex biogeographic scenario within South Africa and suggest that A. poecilus should be considered a junior synonym of A. plumbeus instead of a truly valid species. Acontias plumbeus consists of allopatric Northern, Eastern, and Southern clades, with the Northern and Southern groups being sister taxa. Populations of the Southern clade, which includes Acontias poecilus, are formed by smaller individuals than those of the Northern and Eastern clades. Both phylogenetic and morphological analyses suggest that A. poecilus should not be considered a valid species, but a junior synonym of A. plumbeus instead. [ABSTRACT FROM AUTHOR]

Acontias plumbeus has traditionally been considered a monotypic, invariable species, a fact that highly contrasts with documented examples of high phylogenetic complexity and phenotypic diversity in other members of the Acontinae. We employed mitochondrial and nuclear DNA markers to investigate genetic structuring among A. plumbeus populations and the relationship between A. plumbeus and the closely related A. poecilus. Molecular genetic analyses revealed three clades with non-overlapping distributions: an Eastern clade, a widely distributed Northern clade, and a Southern clade that includes topotypical A. poecilus. Morphometric analyses of preserved specimens showed that Southern clade populations are comprised of individuals with absolute and proportionally smaller body sizes than their Northern and Eastern relatives. Phylogenetic affinities within A. plumbeus indicate a complex biogeographic scenario within South Africa and suggest that A. poecilus should be considered a junior synonym of A. plumbeus instead of a truly valid species. [ABSTRACT FROM AUTHOR]