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During the present study, we re‐examined species boundaries in three mountain‐dwelling velvet worm species complexes (Peripatopsis balfouri s.l., P. bolandi s.l. and P. purpureus s.l.) along the Cape Fold Mountains of South Africa. We obtained DNA sequence data for both the mitochondrial cytochrome c oxidase subunit one (COI) and the nuclear 18S rRNA loci. Phylogenetic inferences were derived with the use of maximum likelihood and Bayesian inference coupled with a divergence time estimation. Four species delimitation methods (ASAP, bPTP, bGYMC and STACEY) together with gross morphological analyses and scanning electron microscopy (SEM) were used to validate the diagnosis of novel species. Combined phylogenetic results demonstrated the presence of three geographically discrete clades (A‐C). Corroborative evidence for the novel lineages could be derived from the dorsal integument colour of live specimens and fixed dorsal and ventral papilla scales rank counts. The four species delimitation methods produced variable results. Divergence time estimations indicated that the Miocene epochs was a major period of cladogenesis. The seven novel velvet worm species, P. barnardi sp. nov., P. fernkloofi sp. nov., P. jonkershoeki sp. nov., P. kogelbergi sp. nov., P. landroskoppie sp. nov., P. limietbergi sp. nov., and P. palmeri sp. nov., are herein described. Molecular systematic studies revealed seven novel velvet worm species from the Cape Fold Mountains in the Western Cape, South Africa suggest high levels of endemism for forest‐dwelling species such a velvet worms (Peripatopsis). Photographic images of five of the new species (B‐F).

During the present study, DNA sequence and morphological data were used to delineate species boundaries in the velvet worm, Peripatopsis sedgwicki species complex. The combined mitochondrial cytochrome c oxidase subunit one (COI) and the nuclear 18S rRNA loci were phylogenetically analyzed using Bayesian inference and maximum likelihood platforms that both demonstrated the presence of four, statistically well-supported clades (A–D). In addition, five species delimitation methods (ASAP, bPTP, bGMYC, STACEY and iBPP) were used on the combined DNA sequence data to identify possible novel lineages. All five species delimitation methods supported the distinction of the Fort Fordyce Nature Reserve specimens in the Eastern Cape province, however, in the main P. sedgwicki s.l. species complex, the species delimitation methods revealed a variable number of novel operational taxonomic units. Gross morphological characters were of limited utility, with only the leg pair number in the Fort Fordyce Nature Reserve specimens and the white head-collar of the Van Stadens Wildflower Nature Reserve specimens being diagnostic. The RADseq results from the earlier study of P. sedgwicki s.l. provided highly congruent results with the four clades observed in the present study. The distribution of P. sedgwicki s.s. (clade B) is restricted to the western portions of its distribution in the Afrotemperate forested regions of the Western Cape Province, South Africa. Three novel species, P. collarium sp. nov., (clade C) P. margaritarius sp. nov., (clade A) and P. orientalis sp. nov., (clade D) are described, of which the first two species are narrow range endemics. The present study, along with several recent systematic studies of velvet worms affirms the importance of fine-scale sampling to detect and document the alpha taxonomic diversity of Onychophora.

During the present study, the evolutionary relationship within a clade of mountain clade of freshwater crabs (Potamonautes) was examined using mtDNA sequence data for species from the Cape Fold Mountain (CFM) and Great Escarpment (Drakensberg Mountain range). We undertook phylogenetic analyses, divergence time estimation, and an ancestral area reconstruction to explore the period of cladogenesis and understand the biogeographic history in this high‐altitude clade. Furthermore, we applied four species delimitation methods using ASAP, bPTP, bGMYC, and STACEY on the latter clade. Bayesian phylogenetic analyses retrieved a monophyletic freshwater crab clade comprised of two major sister clades, one comprised of the Cape Fold (clade A) and two comprised of Drakensberg Mountains (clade B) species. Divergence time estimation indicated that the two clades underwent Mio/Pliocene cladogenesis. Within the CFM clade (A), P. amathole (Amathola Mountains) was sister to P. parvispina (Cederberg and Kouebokkeveld Mountains) and the latter species were sister to P. parvicorpus (Cape Peninsula, Jonkershoek, and Helderberg Mountains) sister to P. tuerkayi (Overberg Mountains) and P. brincki (Hottentots Holland Mountains). Within the Drakensberg Mountain clade (B), we observed in situ diversification. Specimens from the southcentral Drakensberg Mountains (Dargle Forest, Injasuti, Karkloof, and Impendle) represent a new undescribed lineage Potamonautes sp. nov. 1. The second clade from the northern Drakensberg, representing P. clarus, was sister to a central Drakensberg Mountain clade that comprised P. depressus that was in turn sister to P. baziya from the Eastern Cape Province. The application of species delimitation methods generally overestimated the number of species. The biogeographic analyses indicated that the Eastern Cape Province is the most likely ancestral range area. Ecological niche modelling of representative species in clades A (Cape Fold Mountains) and B (Drakensberg Mountains) demonstrated that temperature and rainfall were the major abiotic drivers that differentiated the two clades. Our data favours the mountain gradient speciation hypothesis. BioGeoBears analyses of the biogeographic analyses in a endemic clade of freshwater crabs in South Africa. The figure includes the tree topology and a picture of the Cape Fold Mountains and the Drakensberg Mountains.

Aim: To investigate models assessing the influence of geomorphology and climatic shifts on species diversification in sub-Saharan Africa by reconstructing the pattern and timing of phylogenetic relationships of rain frogs (Brevicipitidae: Breviceps). Location: Sub-Saharan Africa, south of the Congo Basin. Methods: Multilocus sequence data were generated for near complete species-level sampling of the genus Breviceps. Phylogenetic relationships were inferred via Bayesian inference and maximum likelihood analyses on both concatenated and singlegene datasets. Network analyses identified locus-specific reticulate relationships among taxa. Bayesian methods were used to infer dates of divergence among Breviceps lineages, and niche modelling was used to identify possible adaptive divergence. Results: Breviceps is monophyletic and comprised of two major, largely allopatric subclades. Diversity within each subclade is concentrated in two areas with contrasting geologic and climatic histories: the arid/semiarid winter rainfall zone in the south-western (SW) Cape, and the semitropical East Coast that receives predominantly summer rainfall. Recognized species diversity in the SW Cape based on phenotypic variation is consistent with observed genetic patterns whereas the East Coast is shown to harbour unexpectedly high genetic diversity and up to seven putative, cryptic species. Niche models show significant overlap between closely related species. Main conclusions: Dating analyses indicate that diversification of Breviceps occurred rapidly within the Miocene, with only a moderate decline over the Plio-Pleistocene, suggesting that this process might be slowed but ongoing. Our findings suggest that a combination of two models, a landscape barrier model and climate fluctuation model, can explain patterns of diversification in Breviceps. This demonstrates that Miocene epeirogenic events and climatic shifts may have had a considerable influence on contemporary patterns of biodiversity. Topographic complexity and relative geoclimatic stability in the East have promoted cryptic diversification in allopatry, and this area clearly harbours numerous undescribed taxa and is in need of detailed biotic investigation.

During the present study, the phylogeography of the wetland specialist, freshwater crab, Potamonautes flavusjo, was investigated and compared to that of the ubiquitous, generalist, P. sidneyi, using DNA sequence data from the mitochondrial cytochrome oxidase subunit one (COI). We inferred the evolutionary history of each species and compared their population‐level genetic structure by constructing haplotype networks and using an analysis of molecular variation. Additionally, we explored the evolutionary relationship between southern African lentic and lotic freshwater crab species by examining the usefulness of carapace attributes in relation to genetic indices and a species' assumed dispersal capacity. In the lentic species, P. flavusjo, a single interconnected haplocluster characterized by shared haplotypes was observed, suggesting marked maternal dispersal, a result corroborated by the low FST values. In contrast, for the lotic species, P. sidneyi two distinct haploclusters and marked genetic differentiation was observed indicating the absence of maternal dispersal, a result corroborated by the high FST values. The phylogenetic relationship in P. sidneyi was further investigated using a maximum likelihood and Bayesian inference analyses with the addition of sequence data from the mitochondrial 16S rRNA locus to estimate divergence times. Three species delimitation methods (ASAP, PTP, and bGMYC) were used to explore the presence of distinct lineages in P. sidneyi. The phylogenetic results indicated that within P. sidneyi two clades were present, while divergence time estimates suggest cladogenesis during the middle to late Pleistocene. The species delimitation methods used showed moderate congruence, however all oversplit the number of putative lineages. Our results indicated that P. sidneyi is a species complex comprised of two cryptic lineages, occurring in sympatry contemporarily possibly alluding to secondary contact. Carapace height was found to have no discernible influence on the genetic indices and presumed dispersal capabilities of mainland southern African freshwater crab species. The importance of our results are discussed in terms of conservation of freshwater habitats. The study investigated the phylogeography of two freshwater crab species, Potamonautes flavusjo and P. sidneyi, comparing their evolutionary history and population genetic structure using DNA sequencing. While P. flavusjo showed evidence of marked maternal dispersal and low genetic differentiation, P. sidneyi exhibited significant genetic divergence and absence of maternal dispersal. Additionally, the study explored the relationship between carapace attributes and genetic indices, finding no significant influence on dispersal capabilities. These findings have implications for the conservation of freshwater habitats.

We compare the genetic structuring and demographic history of two sympatric caridean shrimp species with distinct life history traits, one amphidromous species Palaemon capensis and one marine/estuarine species Palaemon peringueyi, in the historical biogeographical context of South Africa. A total of 103 specimens of P. capensis collected from 12 localities and 217 specimens of P. peringueyi collected from 24 localities were sequenced for the mitochondrial cytochrome oxidase one (CO1) locus. Results from analyses of molecular variance (AMOVA), pairwise ΦST comparisons and haplotype networks demonstrate weak to moderate genetic differentiation in P. capensis and P. peringueyi respectively. P. peringueyi exhibits partial isolation between populations associated with distinct biogeographic regions, likely driven by the region's oceanography. However, there is minimal evidence for the occurrence of discrete regional evolutionary lineages. This demonstrated lack of genetic differentiation is consistent with a marine, highly dispersive planktonic phase in both the amphidromous P. capensis and the marine/estuarine P. peringueyi. Bayesian skyline plots, mismatch expansions and time since expansion indicate that both species maintained stable populations during the Last Glacial Maximum (LGM), unlike other southern African aquatic species.

An assessment of the global freshwater crab diversity is presented. A total of 1,476 species in 14 families are currently known from all zoogeographical regions (except Antarctica), including 1,306 species in eight exclusively freshwater families (Pseudothelphusidae, Trichodactylidae, Potamonautidae, Deckeniidae, Platythelphusidae, Potamidae, Gecarcinucidae and Parathelphusidae). Estimates of true freshwater crab diversity including likely numbers of undescribed taxa suggest that the field remains largely in a “discovery” phase. Main ideas on the origins, diversification, and phylogeny of true freshwater crabs are briefly discussed. The economic importance of freshwater crabs is also highlighted.

The current distributions of widespread groups of terrestrial animals and plants are supposedly the result of a mixture of either vicariance owing to continental split or more recent trans-oceanic dispersal. For organisms exhibiting a vicariant biogeographic pattern—achieving their current distribution by riding on the plates of former supercontinents—this view is largely inspired by the belief that Pangaea lacked geographical or ecological barriers, or that extinctions and dispersal would have erased any biogeographic signal since the early Mesozoic. We here present a time-calibrated molecular phylogeny of Onychophora (velvet worms), an ancient and exclusively terrestrial panarthropod group distributed throughout former Pangaean landmasses. Our data not only demonstrate that trans-oceanic dispersal does not need be invoked to explain contemporary distributions, but also reveal that the early diversification of the group pre-dates the break-up of Pangaea, maintaining regionalization even in landmasses that have remained contiguous throughout the history of the group. These results corroborate a growing body of evidence from palaeontology, palaeogeography and palaeoclimatic modelling depicting ancient biogeographic regionalization over the continuous landmass of Pangaea.

CITATION: Kulenkampff, K., et al. 2019. Molecular evidence for cryptic species in the common slug eating snake Duberria lutrix lutrix (Squamata, Lamprophiidae) from South Africa. ZooKeys, 838:133-154, doi:10.3897/zookeys.838.32022.

A new pearl white freshwater crab was collected in sympatry with Potamonautes sidneyi (Rathbun, 1904) in the Indian Ocean coastal belt forest at Mbotyi on the Wild Coast of the Eastern Cape Province, South Africa. Specimens of the two sympatric congeneric species were subjected to DNA sequencing of three partial mitochondrial loci (COI, 12S rRNA and 16S rRNA) together with morphological examination. Phylogenetic analyses of the new species were undertaken to determine its evolutionary relationship with the other east and southern African species of freshwater crabs. Results revealed that, Potamonautes mhlophe sp. nov. is sister to P. dentatus (Stewart & Cook, 1995) and distantly related to the sympatric P. sidneyi. The two congeneric sympatric species were characterised by the absence of shared COI haplotypes and marked sequence divergence value for the latter locus. Furthermore, Potamonautes mhlophe sp. nov. is morphologically distinct from P. sidneyi based on the structure of the first and second gonopods. Considering the congruence between the mtDNA and morphology, the new species is herein described.