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Climate shifts during the Quaternary Period have driven changes in regional range dynamics for many species, influencing population structure of species and in some cases promoting speciation. Within southern Africa, the psammophine snakes Psammophis trinasalis and P. namibensis were historically considered subspecies of P. leightoni but were elevated to species rank based on ecological differences. Preliminary phylogenetic analyses suggested intraspecific, not interspecific genetic variation between these taxa, but this finding was based on very limited data and could not be confirmed. To assess the level of genetic differentiation within the P. leightoni species complex, we explored the evolutionary history of these snakes by combining phylogenetic analyses, species distribution modelling and an examination of morphology. We generated a comprehensive, multi‐gene phylogeny for Psammophis that included wider geographic sampling of the three species in the complex. Using this phylogeny, Bayesian and distance‐based species delimitation analyses showed intraspecific, not interspecific divergences between taxa in the complex, suggesting that they collectively represent a single taxon. Furthermore, non‐metric multidimensional scaling analysis of scalation characters showed no differences between the species. Moreover, palaeo‐modelling at three time periods since the last interglacial period suggest that there have been varying levels of connectivity between these taxa, which has likely facilitated gene flow between them. Given the evidence, we propose that the P. leightoni complex represents a single species and therefore formally synonymise the three species. [ABSTRACT FROM AUTHOR]

The Great Karoo and Namaqualand of South Africa are home to a species complex of morphologically conserved lizards that occur in allopatry (Karoo: Cordylus aridus , Cordylus cloetei , Cordylus minor ; Namaqualand: Cordylus imkeae). However, there are negligible morphological differences and a lack of obvious physical or climatic barriers, particularly among the three Karoo species. We hypothesized that poor geographic coverage in previous studies and lack of an explicit species concept has caused taxonomic inflation. We therefore tested species boundaries by examining multiple criteria: multi-gene phylogenetics, niche distribution modelling and re-examination of diagnostic morphological features with a larger sample size. We found that C. aridus , C. cloetei and C. minor lack diagnosable differences for both genetics and morphology. Distribution modelling, ranging from present day to the last interglacial period, show connectivity has been maintained especially during cooler periods. Conversely, C. imkeae is morphologically diagnosable, genetically distinct and lacks connectivity with the other taxa. By evaluating multiple operational criteria, we conclude that the C. minor species complex comprises only two species, C. minor (with C. aridus and C. cloetei as junior synonyms) and C. imkeae , demonstrating that species defined from inadequate data and lack of an explicit species concept can lead to taxonomic inflation. [ABSTRACT FROM AUTHOR]

The Karoo boasts a wide variety of unique flora and fauna yet the region is still currently poorly surveyed for biodiversity. This lack of knowledge is true for all taxonomic groups, but none more so than reptiles. For example, only 3.5% of South Africa's reptile records have been obtained from the Karoo despite the region making up more than 30% of the country's total land mass and offering exceptional habitat for many of our reptile species. The Karoo has also been identified as an important development area for South Africa. Large scale international development projects such as shale gas drilling, uranium mining and the Square Kilometre Array, in conjunction with renewable energy infrastructure and continued farming will require responsible and informed planning. Here we present a detailed account of the herpetological surveys conducted by SANBI as part of the Karoo Biogaps Project made possible by a grant from the Foundational Biodiversity Information Programme (FBIP), and offer preliminary investigations into the herpetological diversity of this unique region. [ABSTRACT FROM AUTHOR]

Over 50% of South African reptile species are endemic, with at least 35% of these species found in the semi-arid Karoo region. The research attraction of the Karoo however, has been eclipsed by megadiverse areas within South Arica, resulting in a lack of baseline biodiversity data for the region. Shale gas development (fracking) in the Karoo has been proposed as a benefit for South Africa in terms of economy, job creation and the current energy crisis. However, the potential impacts on biodiversity could be substantial. Without sufficient biodiversity data, decisions relating to infrastructure development will be poorly informed, and monitoring future impacts on species diversity and ecosystem function will not be possible. Here we discuss the outcomes of the Karoo BioGaps Project, with particular interest in the contributions to reptiles in the region. From 2016-2018, 36 sites were surveyed in the Karoo, where over 2,000 new records were collected for 84 reptile species. Our surveys have doubled the number of individual records from the region. At some survey sites, we validated the presence of a large percentage of expected species, but we also found a number of unexpected species at several sites. DNA barcoding was an integral part of the project, and results suggests that some taxa are in need of revision. These findings demonstrate that biodiversity patterns can shift and change given improved survey data. Poor data therefore, can result in poor land use management decisions and emphasis should be placed on improving data in data deficient areas. [ABSTRACT FROM AUTHOR]

The Pachydactylus mariquensis species complex is comprised of four species, namely P. mariquensis, P. latirostris, P. macrolepis, and P. amoenus that occur in Northern, Western Cape and Free State provinces of South Africa. Pachydactylus mariquensis and P. latirostris are both widespread, while P. macrolepis and P. amoenus have small distributions. The former two species have a substantial geographic overlap zone in the Great Karoo, while the latter two probably have overlapping geographic ranges in the northwest, but locality data are sparse making it difficult to understand their ranges. Recent phylogenetic work shows all these species to be genetically well differentiated, with some specimens having been misidentified, calling into question the validity of the geographic overlap zones and the distribution of these species. We examined the extent of these species distributions and associated overlap zones by combining phylogenetic, taxonomic and species distribution modelling (SDM) approaches using comprehensive geographic sampling. Bayesian and maximum likelihood analyses were run using two mitochondrial markers (16S and ND2) for 37 samples. The SDMs were run in MaxEnt using a dataset of 132 locality records for P. mariquensis and P. latirostris. The phylogenetic analysis highlighted several misidentifications between P. latirostris, P. mariquensis and P. macrolepis. The large overlap zone previously shown on distribution maps for P. mariquensis and P. latirostris in the Great Karoo was not as apparent once the phylogenetic analysis was used to assign individuals. Indeed, the distributions of the two species overlap in a very narrow region below the Great Escarpment. Moreover, the distribution of P. macrolepis extends farther south along the west coast, possibly overlapping with P. mariquensis. Thus, our previous understanding of the distributions and overlap within this species complex is likely due to misidentifications. [ABSTRACT FROM AUTHOR]