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The endemic South African velvet worm genus Peripatopsis currently contains eight recognized species described from variable morphological characters and the current taxonomy is unsatisfactory. In an attempt to investigate evolutionary relationships within Peripatopsis, we collected 137 individuals from 34 sample localities for six of the eight species. Sequence data derived from two partial mitochondrial (mt)DNA gene loci (COI and 12S rRNA), as well as partial sequence data from the ribosomal nuclear 18S rDNA locus in combination with gross morphological characters and scanning electron microscopy (SEM), was used to examine evolutionary relationships. Phylogenetic relationships were investigated using minimum evolution (ME) and Bayesian inferences (BI). Additionally, we also undertook a maximum likelihood (ML) analyses on the combined DNA sequence data set. The combined DNA evidence topologies derived from the ME, BI, and ML was highly congruent and was characterized by the presence of multiple lineages within recognized taxa. Peripatopsis clavigera, Peripatopsis moseleyi, and Peripatopsis sedgwicki each comprised two evolutionary lineages; Peripatopsis capensis comprised three; and Peripatopsis balfouri comprised six operational taxonomic units respectively. Genealogical exclusivity at both mtDNA and nuclear DNA among the geographically coherent groups coupled with pronounced sequence divergence suggested a two-fold increase in the number of species within Peripatopsis. Previously used gross morphological characters (such as the number of leg pairs and colour) were either highly variable within operational taxonomic units, or were invariant, suggesting that alternative morphological characters are necessary for species discrimination. SEM results revealed potentially useful diagnostic characters that can discriminate between at least discriminate some of the newly-identified lineages.

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.

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Aim The phylogeographic relationships among populations of the common Cape River crab, Potamonautes perlatus, are examined to investigate whether the contemporary population genetic structure is congruent with the hypothesized hydrographic evolution of drainage systems established during the Pliocene, or whether it reflects an older Miocene climatic amelioration.Location 139 samples of P. perlatus were collected from 31 populations distributed among the five major perennial drainage systems and a number of smaller catchments in the Western and Eastern Cape, South Africa.Methods Phylogeographic analysis using parsimony, maximum likelihood, minimum evolution and Bayesian inferences was employed for the 16S rRNA mtDNA gene region, while bootstrapping and posterior probabilities were used to assess the robustness of clades. In addition, nested clade analysis was performed in an attempt to disentangle the contemporary and historical factors that have sculpted genealogical relationships among conspecific populations of P. perlatus.Results Phylogenetic topologies were congruent irrespective of the evolutionary method employed. Two highly distinct reciprocally monophyletic clades characterized by marked levels of corrected sequence divergence were present, with no shared haplotypes between the two major phylogroups. Phylogroup one comprises the populations of the westward-flowing drainages (mainly the Berg and Olifants drainages), and phylogroup two comprises all of the southwardflowing drainages and can further be divided into two subclades -one containing the Breede River populations, and the other containing the Gamtoos and Gourits drainage systems. The nested clade analysis demonstrated restricted gene flow and long-distance dispersal for a number of higher clade levels. The higher-level groups and results for the total cladogram suggest either fragmentation or isolation by distance.Main conclusions Freshwater crabs are generally highly philopatric, and dispersal, although not common, has occurred historically. The westward-flowing drainages (Berg, Olifants, Eerste, Liesbeeck and Tokai) are isolated from the southward-flowing drainages by the Cape Fold Mountains, while the southwardflowing drainages have a number of tributaries that extend into the low-lying regions, allowing for gene flow between these three major drainages systems (Breede, Gamtoos and Gourits). Among the westward-flowing drainages, a more intensive sampling regime is required to understand evolutionary relationships. Our molecular results suggest that the observed patterns pre-date the formation of contemporary hydrographic patterns in the Cape. This suggests that an older Late Miocene event has severely impacted the contemporary population structure

A number of recent studies have shown the importance of the mammalian gut microbiome in host health. In the context of endangered species, a few studies have examined the relationship between the gut microbiome in wild versus captive populations due to digestive and other health issues. Unfortunately, the results seem to vary across taxa in terms of captive animals having higher, lower, or equivalent microbiome diversity relative to their wild counterparts. Here, we focus on the black rhinoceros as captive animals suffer from a number of potentially dietary related health effects. We compared gut microbiomes of wild and captive black rhinos to test for differences in taxonomic diversity (alpha and beta) and in functional diversity of the microbiome. We incorporated a more powerful metagenomic shotgun sequencing approach rather than a targeted amplification of the 16S gene for taxonomic assignment of the microbiome. Our results showed no significant differences in the alpha diversity levels between wild and captive black rhinos, but significant differences in beta diversity. We found that bacterial taxa traditionally associated with ruminant guts of domesticated animals had higher relative abundances in captive rhinos. Our metagenomic sequencing results suggest that unknown gut microbes of wild rhinos are being replaced by those found in conventional human-domesticated livestock. Wild rhinos have significantly different functional bacterial communities compared to their captive counterparts. Functional profiling results showed greater abundance of glycolysis and amino acid synthesis pathways in captive rhino microbiomes, representing an animal receiving sub-optimal nutrition with a readily available source of glucose but possibly an imbalance of necessary macro and micronutrients. Given the differences observed between wild and captive rhino gut microbiomes, we make a number of recommendations for potentially modifying captive gut microbiome to better reflect their wild counterparts and thereby hopefully improve overall rhino health in captivity.