Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki).

In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.

Under the hood: Phylogenomics of hooded tick spiders (Arachnida, Ricinulei) uncovers discordance between morphology and molecules.

Ricinulei or hooded tick-spiders are a cryptic and ancient group of arachnids. The order consists of around 100 highly endemic extant species restricted to the Afrotropics and the Neotropics along with 22 fossil species. Their antiquity and low vagility make them an excellent group with which to interrogate biogeographic questions. To date, only four molecular analyses have been conducted on the group and they failed to resolve the relationships of the main lineages and even recovering the non-monophyly of the three genera. These studies were limited to a few Sanger loci or phylogenomic analyses with at most seven ingroup samples. To increase phylogenetic resolution in this little-understood and poorly studied group, we present the most comprehensive phylogenomic study of Ricinulei to date leveraging the Arachnida ultra-conserved element probe set. With a data set of 473 loci across 96 ingroup samples, analyses resolved a monophyletic Neotropical clade consisting of four main lineages. Two of them correspond to the current genera Cryptocellus and Pseudocellus while topology testing revealed one lineage to likely be a phylogenetic reconstruction artefact. The fourth lineage, restricted to Northwestern, Andean South America, is consistent with the Cryptocellus magnus group, likely corresponding to the historical genus Heteroricinoides. Since we did not sample the type species for this old genus, we do not formally re-erect Heteroricinoides but our data suggest the need for a thorough morphological re-examination of Neotropical Ricinulei.

Phylogenomic data reveal three new families of poorly studied Solifugae (camel spiders).

The systematics of the arachnid order Solifugae have been an enigma, owing to challenges in interpreting morphology, a paucity of molecular phylogenetic studies sampling across the group, and a dearth of taxonomic attention for many lineages. Recent work has suggested that solifuge families largely exhibit contiguous distributions and reflect patterns of vicariance, with the exception of three families: Melanoblossidae, Daesiidae and Gylippidae. Morphological studies have cast doubt on their existing circumscriptions and the present composition of these taxa renders their distributions as disjunct. We leveraged ultraconserved elements (UCEs) to test the phylogenetic placement of three key lineages of Solifugae that cause these anomalous distributions: Dinorhax rostrumpsittaci (putative melanoblossid), Namibesia (putative daesiid), and Trichotoma (putative gylippid). Phylogenetic placement of these three genera based on UCEs rendered the families that harbor them as para- or polyphyletic, recovering instead relationships that better accord with a biogeographic history driven by vicariance. Toward a stable and phylogenetically informed classification of Solifugae, we establish three new families, Dinorhaxidae new rank, Namibesiidae new rank and Lipophagidae new rank.

Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments.

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.

Climatic oscillations during the Mio/Pliocene epochs induced cladogenesis in the terrestrial snail genus Gittenedouardia (Mollusca: Gastropoda: Cerastidae) from South Africa.

In South Africa, the terrestrial snail genus Gittenedouardia is the most species-rich member of the Cerastidae, where it is primarily distributed in the highly fragmented Afrotemperate and Indian Ocean coastal belt (IOCB) forest biomes. Phylogenetic relationships and cladogenetic events within the genus remain unstudied. In this respect, we reconstructed a dated phylogeny for eight Gittenedouardia species, and two populations identified to genus level using a combined mitochondrial (16S rRNA and COI) DNA sequencing dataset analysed using Bayesian inference and Maximum Likelihood framework. Furthermore, we investigated the population genetic substructure of the three widely distributed species (Gittenedouardia spadicea, G. natalensis and G. arenicola) for the COI locus, while also subsampling these species using the nuclear DNA ITS-2 locus. Phylogenetic results based on the combined mtDNA dataset supported the monophyly of Gittenedouardia and revealed three major clades and deep genetic structure among the three widely distributed species. Divergence-time estimates suggest that diversification within Gittenedouardia occurred during the middle Miocene/late Pliocene, a period characterised by a decrease in precipitation and the contraction of the Afrotemperate and IOCB forest biomes. We used two species delimitation methods, (PTP and STACEY) to infer putative species in G. spadicea, G. natalensis and G. arenicola. The two methods recovered a large number of evolutionary distinct units, with minimal consensus in the exact number of lineages. Our findings suggest the presence of undescribed diversity, necessitating the need for taxonomic revisionary work on Gittenedouardia. We discuss the climatic factors which may have contributed to the observed cladogenesis and compare our results with other studies of forest dwelling faunal taxa.

Divergent evolutionary origins and biogeographic histories of two freshwater crabs (Brachyura: Potamonautes) on the West African conveyer belt islands of São Tomé and Príncipe.

We examined the colonization history and phylogeographic structure of the two endemic freshwater crab species (Potamonautes margaritarius and P. principe) inhabiting the volcanic islands of São Tomé and Príncipe, respectively, using mitochondrial and nuclear DNA sequence data. All samples were sequenced for the mtDNA COI locus and used in the phylogeographic analyses, while a single specimen per lineage was sequenced for the two remaining loci (16S rRNA and histone 3) and used in the phylogenetic reconstruction. Phylogenetic results reveal that P. principe diverged early within a clade of East/Southern African Potamonautes during the Miocene, while P. margaritarius diverged between the Late Eocene to Early Miocene. Furthermore, the two species are not sister taxa and are distantly related. These results corroborate previously hypothesised independent transoceanic dispersal events that resulted in the establishment of the endemic freshwater crab fauna of the two islands. Within P. margaritarius, we observed two reciprocally monophyletic clades on São Tomé Island. Clade one occurred in the southeast and southwest of the island, while clade two occurred in the northeast and the northwest; the divergence between the latter two clades was estimated to be of Pleistocene age. The two clades within P. margartarius are genetically highly structured and characterised by the absence of shared maternal haplotypes, suggesting possible speciation within P. margartarius. In contrast P. principe exhibits a shallow population genetic structure. Possible mechanisms of colonization and cladogenesis in the two freshwater crabs are discussed.

Multilocus Phylogeny of the Afrotropical Freshwater Crab Fauna Reveals Historical Drainage Connectivity and Transoceanic Dispersal Since the Eocene.

Phylogenetic reconstruction, divergence time estimations and ancestral range estimation were undertaken for 66% of the Afrotropical freshwater crab fauna (Potamonautidae) based on four partial DNA loci (12S rRNA, 16S rRNA, cytochrome oxidase one [COI], and histone 3). The present study represents the most comprehensive taxonomic sampling of any freshwater crab family globally, and explores the impact of paleodrainage interconnectivity on cladogenesis among freshwater crabs. Phylogenetic analyses of the total evidence data using maximum-likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) produced a robust statistically well-supported tree topology that reaffirmed the monophyly of the Afrotropical freshwater crab fauna. The estimated divergence times suggest that the Afrotropical Potamonautidae diverged during the Eocene. Cladogenesis within and among several genera occurred predominantly during the Miocene, which was associated with major tectonic and climatic ameliorations throughout the region. Paleodrainage connectivity was observed with specimens from the Nilo-Sudan and East African coast proving to be sister to specimens from the Upper Guinea Forests in West Africa. In addition, we observed strong sister taxon affinity between specimens from East Africa and the Congo basin, including specimens from Lake Tanganyika, while the southern African fauna was retrieved as sister to the Angolan taxa. Within the East African clade we observed two independent transoceanic dispersal events, one to the Seychelles Archipelago and a second to Madagascar, while we observe a single transoceanic dispersal event from West Africa to São Tomé. The ancestral area estimation suggested a West African/East African ancestral range for the family with multiple dispersal events between southern Africa and East Africa, and between East Africa and Central Africa The taxonomic implications of our results are discussed in light of the widespread paraphyly evident among a number of genera.

Unmasking alpha diversity, cladogenesis and biogeographical patterning in an ancient panarthropod lineage (Onychophora: Peripatopsidae: Opisthopatus cinctipes) with the description of five novel species.

Speciation and biogeographical patterning in the velvet worm Opisthopatus cinctipes was examined under a null hypothesis that numerous discrete lineages are nested within the species. A total of 184 O. cinctipes specimens, together with a single specimen of each of the two congeneric point endemic sister species (O. roseus and O. herbertorum), were collected throughout the forest archipelago in the Eastern Cape, KwaZulu-Natal and Mpumalanga provinces of South Africa. All specimens were sequenced for two partial mitochondrial DNA loci (COI and 12S rRNA), while a single specimen from each locality was sequenced for the nuclear 18S rRNA locus. Evolutionary relationships were assessed using maximum-likelihood and Bayesian inferences, while divergence time estimations were conducted using BEAST. A Bayesian species delimitation approach was undertaken to explore the number of possible novel lineages nested within Opisthopatus, while population genetic structure was examined for the COI locus using ARLEQUIN. Phylogenetic results revealed that O. cinctipes is a species complex comprising seven geographically discrete and statistically well-supported clades. An independent statistical approach to species delimitations circumscribed ca. 67 species. Results from divergence time estimation and rate constancy tests revealed near constant net diversification occurring throughout the Eocene and Oligocene with subdivision of ranges during the Miocene. Gross morphological characters such as leg pair number within O. cinctipes were invariant, while dorsal and ventral integument colour was highly polymorphic. However, scanning electron microscopy revealed considerable differences both between and within clades. The caveats associated with both morphological and algorithmic delineation of species boundaries are discussed. The five novel Opisthopatus species are described.

Exploring the Impact of Habitat Size on Phylogeographic Patterning in the Overberg Velvet Worm Peripatopsis overbergiensis (Onychophora: Peripatopsidae).

Evolutionary relationships in the velvet worm species, Peripatopsis overbergiensis, were examined in 3 forest areas in the Overberg region of South Africa to explore the impact of historical habitat fragmentation on the population genetic structure of the species. We collected 84 P. overbergiensis specimens from Grootvadersbosch, Koppie Alleen, and Marloth Nature Reserves and sequenced all these specimens for the cytochrome c oxidase subunit I (COI) locus, whereas a subset of 13 specimens were also sequenced for the 18S rRNA locus. Phylogenetic analyses of the 20 unique COI haplotypes revealed 4 genetically distinct clades, a result that is corroborated by the haplotype network. A hierarchical analysis of genetic variation was performed on the COI haplotype data within the 2 large forested areas, Grootvadersbosch and Marloth Nature Reserves, and across all 3 of the sample localities. These results revealed low haplotypic and nucleotide diversity within the largest Grootvadersbosch Nature Reserve forest and high haplotypic and nucleotide diversity within the fragmented Marloth Nature Reserve forest, whereas Koppie Alleen had the lowest haplotypic and nucleotide diversity. Across all 3 main localities statistically significant F ST values were found, together with the absence of shared haplotypes indicating the absence of maternal gene flow. Divergence time estimations based on the 20 COI haplotypes calculated in BEAST suggest a Pleistocene/Holocene divergence between the 4 clades as a result of habitat fragmentation and the aridification of the region. Our results indicate that conservation efforts should also prioritize linked, smaller fragmented habitats together with continuous habitats to maximize the genetic diversity of saproxylic fauna.

Genetic and Morphological Characterization of Freshwater Shrimps (Caridina africana Kingsley, 1882) Reveals the Presence of Alien Shrimps in the Cape Floristic Region, South Africa.

Morphological identification and molecular data (mtDNA COI) were used to resolve the taxonomic identity of a non-native freshwater shrimp in the Cape Floristic Region (CFR) of South Africa and to evaluate levels of genetic diversity and differentiation in the species' core natural distribution. The species was morphologically and genetically identified as Caridina africana Kingsley, 1882, whose main natural distribution is in the KwaZulu-Natal (KZN) Province, more than 1200 km from the point of new discovery. Subsequently, sequence data from natural populations occurring in seven rivers throughout KZN showed the presence of nuclear copies of the mtDNA COI gene (NUMTs) in 46 out of 140 individuals. Upon removal of sequences containing NUMTs, levels of genetic diversity were low in the alien population (possibly as a consequence of a bottleneck event), while varying levels of genetic diversity and differentiation were found in natural populations, indicating habitat heterogeneity, fragmentation and restricted gene flow between rivers. Following the present study, the alien shrimp has survived the Western Cape's winter and dispersed into a nearby tributary of the Eerste River System, hence posing an additional potential threat to endangered endemics. Understanding the biology of this alien species will aid detection and eradication procedures.

A living fossil tale of Pangaean biogeography.

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.

Ain't no mountain high enough, ain't no valley low enough? Phylogeography of the rupicolous Cape girdled lizard (Cordylus cordylus) reveals a generalist pattern.

In the present study we examined the phylogeography of the rupicolous Cape girdled lizard, Cordylus cordylus. Samples were collected from 63 localities across the species distribution range in the Eastern and Western Cape and Free State provinces of South Africa, yielding a total sample size of 207 specimens. Four partial DNA loci, two mitochondrial (16S rRNA and ND2) and two nuclear (PRLR and PTPN12), were sequenced. Bayesian inference, maximum likelihood and maximum parsimony methods were employed to test evolutionary relationships among populations, followed by population structure analyses, divergence time estimations and niche modelling. Our results confirm the species monophyly and revealed the presence of two distinct clades. Clade 1 comprised specimens from the western and southern portions of the Western Cape coast, while clade 2 comprised specimens from the southern and eastern Cape coast and adjacent interior of the Eastern and Western Cape and Free State provinces. An area of sympatry between the two clades was observed in the Breede river valley. The divergence time estimates revealed an Early Pliocene (4.31 Ma), Late Miocene (6.01 Ma) divergence for each of the two clades retrieved. Phylogeographic data suggest that clade 1 coalesced more recently (lower haplotypic and nucleotide diversity), when compared to clade 2. Furthermore, the niche modelling shows that C. cordylus occupies a wide range of unfavourable habitats, though slight niche differentiation was observed for each clade. The absence of marked phylogeographic patterning within clades is very uncharacteristic for a rupicolous vertebrate species. The ecological pliability and generalist nature of C. cordylus presumably contributed to the observed phylogeographic pattern and have facilitated the absence of within clade differentiation. Moreover, we suggest that microclimatic variables, rather than geographic barriers influence the genetic structuring of C. cordylus.

Sample design in biodiversity studies matters: a fine-scale study of Lawrence's velvet worm, Peripatopsis lawrencei (Onychophora: Peripatopsidae), reveals hidden diversity.

A fine-scale phylogenetic and phylogeographic analysis of Peripatopsis lawrencei s.l. was conducted with both mitochondrial and nuclear DNA sequence data, using both external morphology and scanning electron microscopy of taxonomically important characters. A total of 119 sequences were used for the mitochondrial cytochrome c oxidase subunit I (COI ) whereas a single representative specimen from each locality was sequenced for the nuclear 18S rRNA locus. Phylogenetic analyses were conducted on the total COI data set and the combined COI + 18S rRNA data set using a Bayesian analysis and maximum likelihood analyses. For the combined DNA sequence data set, a divergence time estimation was further undertaken in BEAST and specimens placed in a phylogenetic framework including all the described Peripatopsis species from South Africa. In addition, a phylogeographic study was conducted exclusively on P. lawrencei s.s. (clade A) using an analysis of molecular variance and haplotype network. Phylogenetic results indicated that, at the Oubos sample locality, two highly distinct genetic lineages were present (clades A and B), whereas a divergence time estimation suggests a Miocene cladogenesis of the novel Oubos lineage. Marked phylogeographic structure was observed for P. lawrencei s.s. (restricted to clade A) across the distribution range with limited maternal dispersal. Morphologically, the two sympatric lineages at Oubos A and B differed in leg pair number, ventral colour and dorsal scale rank counts, as evident from scanning electron microscopy. Our results support the recognition of a distinct species that occurs in sympatry with P. lawrencei s.s. The new species, P. aereus sp. nov. (clade B) is described and the implication for fine-scale taxonomic studies on saproxylic taxa is discussed. ZooBank: urn:lsid:zoobank.org:pub:AB6E0BDA-7B5F-4FD3-A863-BA7C814E278C.

Let's get high: Cladogenesis in freshwater crabs (Decapoda: Potamonautidae: Potamonautes) supports the mountain gradient speciation hypothesis in the Cape Fold and Drakensberg Mountains, South Africa.

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.

A biogeographical appraisal of the threatened South East Africa Montane Archipelago ecoregion.

Recent biological surveys of ancient inselbergs in southern Malawi and northern Mozambique have led to the discovery and description of many species new to science, and overlapping centres of endemism across multiple taxa. Combining these endemic taxa with data on geology and climate, we propose the 'South East Africa Montane Archipelago' (SEAMA) as a distinct ecoregion of global biological importance. The ecoregion encompasses 30 granitic inselbergs reaching > 1000 m above sea level, hosting the largest (Mt Mabu) and smallest (Mt Lico) mid-elevation rainforests in southern Africa, as well as biologically unique montane grasslands. Endemic taxa include 127 plants, 45 vertebrates (amphibians, reptiles, birds, mammals) and 45 invertebrate species (butterflies, freshwater crabs), and two endemic genera of plants and reptiles. Existing dated phylogenies of endemic animal lineages suggests this endemism arose from divergence events coinciding with repeated isolation of these mountains from the pan-African forests, together with the mountains' great age and relative climatic stability. Since 2000, the SEAMA has lost 18% of its primary humid forest cover (up to 43% in some sites)-one of the highest deforestation rates in Africa. Urgently rectifying this situation, while addressing the resource needs of local communities, is a global priority for biodiversity conservation.

Reconstructing the colonisation and diversification history of the endemic freshwater crab (Seychellum alluaudi) in the granitic and volcanic Seychelles Archipelago.

The endemic, monotypic freshwater crab species Seychellum alluaudi was used as a template to examine the initial colonisation and evolutionary history among the major islands in the Seychelles Archipelago. Five of the "inner" islands in the Seychelles Archipelago including Mahé, Praslin, Silhouette, La Digue and Frégate were sampled. Two partial mtDNA fragments, 16S rRNA and cytochrome oxidase subunit I (COI) was sequenced for 83 specimens of S. alluaudi. Evolutionary relationships between populations were inferred from the combined mtDNA dataset using maximum parsimony, maximum likelihood and Bayesian inferences. Analyses of molecular variance (AMOVA) were used to examine genetic variation among and within clades. A haplotype network was constructed using TCS while BEAST was employed to date the colonisation and divergence of lineages on the islands. Phylogenetic analyses of the combined mtDNA data set of 1103 base pairs retrieved a monophyletic S. alluaudi group comprised three statistically well-supported monophyletic clades. Clade one was exclusive to Silhouette; clade two included samples from Praslin sister to La Digue, while clade three comprised samples from Mahé sister to Frégate. The haplotype network corresponded to the three clades. Within Mahé, substantial phylogeographic substructure was evident. AMOVA results revealed limited genetic variation within localities with most variation occurring among localities. Divergence time estimations predated the Holocene sea level regressions and indicated a Pliocene/Pleistocene divergence between the three clades evident within S. alluaudi. The monophyly of each clade suggests that transoceanic dispersal is rare. The absence of shared haplotypes between the three clades, coupled with marked sequence divergence values suggests the presence of three allospecies within S. alluaudi.

Cryptic diversity and morphological convergence in threatened species of fossorial skinks in the genus Scelotes (Squamata: Scincidae) from the Western Cape Coast of South Africa: implications for species boundaries, digit reduction and conservation.

We investigated the evolutionary relationships among populations of two threatened Red Data Book fossorial skinks, Scelotes gronovii and Scelotes kasneri, along the Western Cape Coast of South Africa. The genus Scelotes shows considerable variation in limb and digit reduction. We sampled four localities purported to contain S. gronovii and seven of S. kasneri, encompassing all of each species' limited distribution. Each of these species lack forelimbs, and differ by the number of digits on the hind limbs, among other morphological characters; S. gronovii bears a single digit and S. kasneri bears two digits on the hind limbs. Sequence data obtained from three mtDNA (16S ribosomal RNA, cytochrome b, and nicotinamide adenine dinucleotide dehydrogenase 1 unit; 2035 bp ttl.) and two nuclear (dynein axonemal heavy chain 3 and the natural killer tumor recognition; 1848 bp ttl.) gene regions were used to reconstruct the evolutionary relationships among the two focal species and several other co-distributed species (Scelotes bipes, Scelotes montispectus, and Scelotes sexlineatus). Phylogenetic results (Bayesian and parsimony) revealed that several populations previously considered S. kasneri actually belong to other species, and others are paraphyletic with respect to one another. Additionally, populations of S. gronovii were also found to be paraphyletic, with populations south of the Berg River supported as sister to S. bipes, and populations north of the Berg River sister the remaining sampled species. Our results require a redefinition of S. sexlineatus to encompass populations morphologically convergent with S. kasneri and restrict the ranges of the already threatened S. kasneri and S. gronovii even further. The paraphyly of S. gronovii and the placement of each clade as sister to clades of species bearing two digits on the hind limbs suggests that digit loss has occurred at least twice in this group.

Redescriptions of three species of freshwater crabs from Angola, southern Africa (Brachyura: Potamoidea: Potamonautidae).

The taxonomy of three species of freshwater crabs from Angola, Potamonautes adeleae Bott, 1968, P. macrobrachii Bott, 1953, and P. kensleyi Cumberlidge Tavares, 2006, is revised based on examination of the paratypes and new material. Updated diagnoses, illustrations, and distribution maps are provided for these three species, and their conservation status is discussed.

The mitochondrial genome of the onychophoran Opisthopatus cinctipes (Peripatopsidae) reflects the ancestral mitochondrial gene arrangement of Panarthropoda and Ecdysozoa.

The ancestral genome composition in Onychophora (velvet worms) is unknown since only a single species of Peripatidae has been studied thus far, which shows a highly derived gene order with numerous translocated genes. Due to this lack of information from Onychophora, it is difficult to infer the ancestral mitochondrial gene arrangement patterns for Panarthropoda and Ecdysozoa. Hence, we analyzed the complete mitochondrial genome of the onychophoran Opisthopatus cinctipes, a representative of Peripatopsidae. Our data show that O. cinctipes possesses a highly conserved gene order, similar to that found in various arthropods. By comparing our results to those from different outgroups, we reconstruct the ancestral gene arrangement in Panarthropoda and Ecdysozoa. Our phylogenetic analysis of protein-coding gene sequences from 60 protostome species (including outgroups) provides some support for the sister group relationship of Onychophora and Arthropoda, which was not recovered by using a single species of Peripatidae, Epiperipatus biolleyi, in a previous study. A comparison of the strand-specific bias between onychophorans, arthropods, and a priapulid suggests that the peripatid E. biolleyi is less suitable for phylogenetic analyses of Ecdysozoa using mitochondrial genomic data than the peripatopsid O. cinctipes.

Deep genealogical lineages in the widely distributed African helmeted terrapin: evidence from mitochondrial and nuclear DNA (Testudines: Pelomedusidae: Pelomedusa subrufa).

We investigated the phylogeographic differentiation of the widely distributed African helmeted terrapin Pelomedusa subrufa based on 1503 base pairs of mitochondrial DNA (partial cyt b and ND4 genes with adjacent tRNAs) and 1937 bp of nuclear DNA (partial Rag1, Rag2, R35 genes). Congruent among different analyses, nine strongly divergent mitochondrial clades were found, representing three major geographical groupings: (1) A northern group which includes clades I from Cameroon, II from Ghana and Ivory Coast, III from Benin, Burkina Faso and Niger, IV from the Central African Republic, and V from Kenya, (2) a northeastern group consisting of clades VI from Somalia, and VII from Saudi Arabia and Yemen, and (3) a southern group comprising clade VIII from Botswana, the Democratic Republic of Congo, Madagascar and Malawi, and clade IX from South Africa. Malagasy and continental African populations were not clearly differentiated, indicating very recent arrival or introduction of Pelomedusa in Madagascar. The southern group was in some phylogenetic analyses sister to Pelusios, rendering Pelomedusa paraphyletic with respect to that genus. However, using partitioned Bayesian analyses and sequence data of the three nuclear genes, Pelomedusa was monophyletic, suggesting that its mitochondrial paraphyly is due to either ancient introgressive hybridization or phylogenetic noise. Otherwise, nuclear sequence data recovered a lower level of divergence, but corroborated the general differentiation pattern of Pelomedusa as revealed by mtDNA. This, and the depth of the divergences between clades, indicates ancient differentiation. The divergences observed fall within, and in part exceed considerably, the differentiation typically occurring among chelonian species. To test whether Pelomedusa is best considered a single species composed of deep genealogical lineages, or a complex of up to nine distinct species, we suggest a future taxonomic revision that should (1) extend the geographical sampling of molecular data, specifically focusing on contact zones and the possible sympatric occurrence of lineages without admixture, and (2) evaluate the morphology of the various genealogical lineages using the type specimens or topotypical material of the numerous junior synonyms of P. subrufa.