Cryptic species within the freshwater isopod Mesamphisopus capensis (Phreatoicidea: Amphisopodidae) in the Western Cape, South Africa: allozyme and 12S rRNA sequence data and morphometric evidence

Spatial genetic structure in the rock hyrax (Procavia capensis) across the Namaqualand and western Fynbos areas of South Africa — a mitochondrial and microsatellite perspective

The interplay between biotic and abiotic environments is increasingly recognized as a major determinant of spatial genetic patterns. Among spatial genetic studies, saxicolous or rock-dwelling species remain underrepresented in spite of their strict dependence on landscape structure. Here we investigated patterns and processes operating at different spatial (fine and regional scales) and time scales (using mitochondrial and microsatellite markers) in the rock hyrax (Procavia capensis (Pallas, 1766)). Our focus was on the western seaboard of South Africa and included two recognized biodiversity hotspots (Cape Floristic Region and Succulent Karoo). At fine spatial scale, significant genetic structure was present between four rocky outcrops in an isolated population, likely driven by the social system of this species. At a broader spatial scale, ecological dependence on rocky habitat and population-level processes, in conjunction with landscape structure, appeared to be the main drivers of genetic diversity and structure. Large areas devoid of suitable rocky habitat (e.g., the Knersvlakte, Sandveld, and Cape Flats, South Africa) represent barriers to gene flow in the species, although genetic clusters closely follow climatic, geological, and phytogeographic regions, possibly indicating ecological specialization or adaptation as contributing factors enforcing isolation. Taken together, our study highlights the need to consider both intrinsic and extrinsic factors when investigating spatial genetic structures within species.

Between an ocean and a high place: coastal drainage isolation generates endemic cryptic species in the Cape kurper Sandelia capensis (Anabantiformes: Anabantidae), Cape Region, South Africa

This study investigated the range-wide phylogenetics and biogeography of the Cape kurper Sandelia capensis, a primary freshwater fish endemic to and widespread within the Cape Floristic Region (CFR) of South Africa. Maximum likelihood, Bayesian phylogenetic and haplotype network analyses, based on two mitochondrial and two nuclear genes, revealed the existence of three reciprocally monophyletic, deeply divergent and allopatric clades that probably represent cryptic species. The West Coast Clade is largely confined to the Langvlei, Verlorenvlei, Berg and Diep Rivers, the Klein River Clade is endemic to the Klein River and the South Coast Clade is found everywhere else in the range of S. capensis sensu lato. It was hypothesised that divergences within S. capensis sensu lato probably occurred because of isolation of coastal drainages by persistent drainage divides or vicariance of current tributaries by the drowning of their confluences by high sea levels. The current distribution of lineages could be due to historical range expansion and gene flow via river capture or some other mode of transdivide dispersal or dispersal during periods of low sea level via palaeoriver confluences of currently isolated coastal rivers. Comparison of BEAST2 estimated divergence times with the timing of climatic, geological and geomorphological events supported long-term coastal drainage isolation, punctuated by rare transdivide dispersal events and limited palaeoriver dispersal, as the best explanation of current phylogeographic and divergence patterns in S. capensis. Hydrological barriers that block upstream passage in palaeotributaries could hypothetically explain why S. capensis failed to disperse through certain palaeoriver confluences. There were several sites where biogeographic patterns have likely been confounded by human translocation of S. capensis. Alien fish predators and water extraction may threaten the three cryptic species more severely than previously realised, due to their smaller population sizes and inhabitation of only a portion of the range previously ascribed to S. capensis sensu lato. The preponderance of cryptic diversity and endemism in the CFR suggests that additional undescribed cryptic species of obligate freshwater fishes may be found in short coastal river systems around the world, especially in regions with a history of geological stability and a narrow continental shelf.

Phylogeography of the endemic grasshopper genus Betiscoides (Lentulidae) in the South African Cape Floristic Region

Vicariance and dispersal are two important processes shaping biodiversity patterns. The South African Cape Floristic Region (CFR) is known for its high biotic diversity and endemism. However, studies on the phylogeography of endemic invertebrates in this biodiversity hotspot are still scarce. Here, we present a phylogenetic study of the flightless grasshopper genus Betiscoides, which is endemic to the CFR and strongly associated with restio plants (Restionaceae). We hypothesized that the genus originated in the southwestern part of the CFR, that differentiation within the genus is mainly an effect of vicariance and that the three known species only represent a minor fraction of the real genetic diversity of the genus. We inferred the phylogeny based on sequences of three mitochondrial and two nuclear genes from 99 Betiscoides specimens collected across the CFR. Furthermore, we conducted a SDIVA analysis to detect distributions of ancestral nodes and the possible spatial origin of these lineages. Strong differentiation among genetic lineages was shown. The ancestor of this genus was most likely distributed in the southwestern CFR. Five major lineages were detected, three of which were ancestrally distributed in the southwestern CFR. The ancestors of the two other lineages were distributed in the northern and eastern margins of the CFR. A total of 24 divergent evolutionary lineages were found, reflecting the geographical isolation of restio-dominated fynbos habitats. Dispersal played a more prominent role than expected in differentiation of Betiscoides. While the five main lineages were separated during a first phase via dispersal, differentiation occurred later and on smaller spatial scale, predominantly driven by isolation in montane refugia (i.e. vicariance). Our study also suggests that flightless insect taxa likely show high levels of differentiation in biodiversity hotspots with their taxonomy often being incomplete.

Multilocus coalescent species delimitation reveals widespread cryptic differentiation among Drakensberg mountain-living freshwater crabs (Decapoda : Potamonautes)

Cryptic lineages present major challenges for evolutionary and conservation studies, particularly where these lineages remain undiscovered. Freshwater crabs are known to harbour cryptic diversity, in most cases with limited morphological differences. During the present study, we used a multilocus (12S rRNA, 16S rRNA, COI, 28S rRNA, DecapANT and PEPCK) Bayesian species delimitation to examine cryptic diversity within a freshwater crab species complex (Potamonautes clarus/P. depressus). We sampled 25 highland rivers in the Tugela and uMkomazi River drainage systems of the Drakensberg Mountain range, in the KwaZulu–Natal province of South Africa. Our results showed there to be at least eight lineages: six novel potamonautid freshwater crabs, and two described taxa P. clarus and P. depressus. Divergence from the most recent common ancestor occurred between the mid- and late Miocene (12.1 Mya), while divergence within the species complex occurred ~10.3 Mya up until the Holocene (0.11 Mya). The discovery of six novel lineages of freshwater crabs from a seemingly restricted distribution range has conservation implications, but to date most conservation planning strategies have focussed on freshwater vertebrates. By conducting a fine-scale phylogenetic survey using invertebrates, this study provides a platform for the inclusion of freshwater invertebrates in future conservation assessments.

Genetic and morphological evidence for a new mountain-living freshwater crab species (Decapoda : Potamonautidae : Potamonautes) from the Western Cape province of South Africa

Recent studies in southern Africa have revealed a wealth of novel freshwater crab species in high mountainous regions. In the present study, phylogeographic affinities between two sister mountain-living freshwater crab species (Potamonautes brincki and P. parvicorpus) were examined for novel lineages. Seventy-six crab specimens were collected throughout the Western Cape Province of South Africa and sequenced for the COI locus. Evolutionary relationships were analysed using Bayesian inference, maximum likelihood and maximum parsimony, a haplotype network and analyses of molecular variance (AMOVA). Results revealed three divergent clades. Clade A comprised specimens of P. brincki restricted to the Hottentots Holland; sister to which was Clade B from the Overberg, while Clade C comprised specimens of P. parvicorpus from the Cape Peninsula and adjacent interior. Haplotype networks and AMOVA provide evidence for the absence of gene flow whilst morphology of the male gonopods and the mandibular palp revealed subtle but consistent differences between the three clades. Since Clades A and C represent two described species, P. brincki and P. parvicorpus, respectively, Clade B is herein described as a new species, P. tuerkayi, sp. nov. These results highlight the importance of continued sampling of mountain habitats to document aquatic invertebrate diversity.

Molecular species boundaries in the phreatoicidean genus Amphisopus (Isopoda : Amphisopidae) and evidence for a new freshwater isopod species from Western Australia

The freshwater isopod genus Amphisopus is one of only two phreatoicidean genera in Western Australia with wide distributions and containing multiple described species. Two species (Amphisopus annectans and A. lintoni) are known from the south-western part of the state. With recent sampling extending the known range of Amphisopus and the recorded possibility of an undescribed species, this study aimed to examine genetic species boundaries and to detect additional species diversity. Isopods were sampled from across the range, and genetic structure was examined using mtDNA sequence data from a COI fragment and data from ten polymorphic allozyme loci. While allozyme data supported the clear separation of the known species, phylogenetic analyses presented three divergent monophyletic, geographically restricted clades occurring in the western, eastern and central parts of the Amphisopus distribution. These corresponded to A. annectans, A. lintoni and an undescribed species, respectively. The latter’s status was supported by its phylogenetic position relative to the known species and by the extent of differentiation observed among other phreatoicidean taxa. As with other taxa from the region, divergence times among these three species supported aridity in the Miocene–Pliocene as a driver of diversification, and suggested the existence of wetter refugial areas in south-western Australia.

Phylogeography of the Cape velvet worm (Onychophora: Peripatopsis capensis) reveals the impact of Pliocene/Pleistocene climatic oscillations on Afromontane forest in the Western Cape, South Africa

Habitat specialists such as soft-bodied invertebrates characterized by low dispersal capability and sensitivity to dehydration can be employed to examine biome histories. In this study, the Cape velvet worm (Peripatopsis capensis) was used to examine the impacts of climatic oscillations on historical Afromontane forest in the Western Cape, South Africa. Divergence time estimates suggest that the P. capensis species complex diverged during the Pliocene epoch. This period was characterized by dramatic climatic and topographical change. Subsequently, forest expansion and contraction cycles led to diversification within P. capensis. Increased levels of genetic differentiation were observed along a west-to-south-easterly trajectory because the south-eastern parts of the Cape Fold Mountain chain harbour larger, more stable fragments of forest patches, have more pronounced habitat heterogeneity and have historically received higher levels of rainfall. These results suggest the presence of three putative species within P. capensis, which are geographically discreet and genetically distinct.

Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae) in southern Africa

BACKGROUND

Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9-10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa.

RESULTS

Four gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S]) and two nuclear (elongation factor 1 alpha [EF1α] and phosphoenolpyruvate carboxykinase [PEPCK]). Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC) model. Results from the EF1α gene were significantly incongruent with both mitochondrial and nuclear (PEPCK) results, possibly due to incomplete lineage sorting of the EF1α gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD) between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4-11.5 mya).

CONCLUSIONS

The distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from neutral-to-alkaline streams found within eastern South Africa, Malawi and Zambia. The results of this study suggest that B. harrisoni as it is currently recognised is not a single species with a wide geographic range and pH-tolerance, but may comprise up to five species under the phylogenetic species concept, each with limited pH-tolerances, and that the B. harrisoni species group is thus in need of taxonomic review.

The potential for predicted climate shifts to impact genetic landscapes of lizards in the South African Cape Floristic Region

The Cape Floristic Region (CFR) is well-known for its floral diversity, yet also contains a rich herpetofauna with >180 species, 28% of which are endemic. Recent studies conducted on CFR lizards indicated that phylogeographic patterns show some congruency, and that the western CFR shows higher overall diversity in the form of population and/or clade turnover. Here, we combine mitochondrial sequence data from two published (Bradypodion spp. and Agama atra) and one new dataset (Pedioplanis burchelli) to investigate whether geographic patterns of genetic diversity could be influenced by predicted climatic changes. We utilised Bayesian methodology and spatial genetic landscapes to establish broad-scale patterns and show that the western CFR is a contact zone for several clades in all three taxa, supporting the hypothesis of phylogeographic congruence. Current levels of gene flow are virtually zero between the western and eastern CFR. In the east, gene flow between populations is negligible at present but was probably stronger in the past given the present lack of strong genetic structure. Bioclimatic modelling predicted that climatically suitable areas within the CFR will decline for Bradypodion spp. and P. burchelli, with areas high in clade turnover loosing more climatically suitable areas than areas with low clade turnover. The models also predict that loss of climatic suitability may result in highly fragmented and patchy distributions, resulting in a greater loss of connectivity. In contrast, A. atra does not show significant climatic suitability losses overall, although it may experience localised losses (and gains). This species is not predicted to loose suitability in areas of high clade turnover. Thus, the incorporation of genetic data into climatic models has extended our knowledge on the vulnerability of these species given the predicted threat of landscape change.

Patterns and processes underlying evolutionary significant units in the Platypleura stridula L. species complex (Hemiptera: Cicadidae) in the Cape Floristic Region, South Africa

Cicadas have been shown to be useful organisms for examining the effects of distribution, plant association and geographical barriers on gene flow between populations. The cicadas of the Platypleura stridula species complex are restricted to the biologically diverse Cape Floristic Region (CFR) of South Africa. They are thus an excellent study group for elucidating the mechanisms by which hemipteran diversity is generated and maintained in the CFR. Phylogeographical analysis of this species complex using mitochondrial DNA Cytochrome Oxidase I (COI) and ribosomal 16S sequence data, coupled with preliminary morphological and acoustic data, resolves six clades, each of which has specific host-plant associations and distinct geographical ranges. The phylogeographical structure implies simultaneous or near-simultaneous radiation events, coupled with shifts in host-plant associations. When calibrated using published COI and 16S substitution rates typical for related insects, these lineages date back to the late Pliocene - early Pleistocene, coincident with vegetation change, altered drainage patterns and accelerated erosion in response to neotectonic crustal uplift and cyclic Pleistocene climate change, and glaciation-associated changes in climate and sea level.

Gondwanan groundwater: subterranean connections of Australian phreatoicidean isopods (Crustacea) to India and New Zealand

Phreatoicidea Stebbing, 1893 live in freshwaters of Gondwana: Australia, South Africa, India and New Zealand. Many of these isopods have a subterranean lifestyle. Parsimony analysis of morphological data of generic exemplars and a Triassic fossil was used to explore the timing of this habitat adaption. The monophyly of the Hypsimetopidae Nicholls, 1943, including blind taxa Hyperoedesipus Nicholls & Milner, 1923 (Western Australia), Nichollsia Chopra and Tiwari, 1950 (Ganges Plain, India) and Phreatoicoides Sayce, 1900 (Tasmania and Victoria) was strongly supported. Crenisopus Wilson and Keable, 1999 (Kimberleys, Western Australia) and the PonderellidaeWilson & Keable, 2004 (Queensland mound springs) may be sister to hypsimetopids. Blind Phreatoicidae found only in south-eastern Australia and in New Zealand were also monophyletic. The hypogean habitat, blindness, fossil and plate tectonic evidence were mapped on the cladogram to estimate timing of this adaptation. A subterranean adaptation before 130 million years ago was supported for hypsimetopids. Phreatoicus Chilton, 1891 and Neophreatoicus Nicholls, 1944 (hypogean in New Zealand) were in a monophyletic clade with epigean Phreatoicidae, Crenoicus Nicholls, 1944 (south-eastern Australia) and Notamphisopus Nicholls, 1943 (New Zealand). Blindness in epigean taxa is consistent with recolonisation of surface waters from underground refuges. Because Crenoicus is sister-group to the New Zealand clade, and because overseas dispersal between Australia and New Zealand is unlikely, the minimum age for these blind phreatoicids is ~80 million years. This evidence is consistent with a subterranean freshwater fauna surviving the presumed Oligocene inundation of New Zealand.

Lack of taxonomic differentiation in an apparently widespread freshwater isopod morphotype (Phreatoicidea: Mesamphisopidae: Mesamphisopus) from South Africa

The unambiguous identification of phreatoicidean isopods occurring in the mountainous southwestern region of South Africa is problematic, as the most recent key is based on morphological characters showing continuous variation among two species: Mesamphisopus abbreviatus and M. depressus. This study uses variation at 12 allozyme loci, phylogenetic analyses of 600 bp of a COI (cytochrome c oxidase subunit I) mtDNA fragment and morphometric comparisons to determine whether 15 populations are conspecific, and, if not, to elucidate their evolutionary relationships. Molecular evidence suggested that the most easterly population, collected from the Tsitsikamma Forest, was representative of a yet undescribed species. Patterns of differentiation and evolutionary relationships among the remaining populations were unrelated to geographic proximity or drainage system. Patterns of isolation by distance were also absent. An apparent disparity among the extent of genetic differentiation was also revealed by the two molecular marker sets. Mitochondrial sequence divergences among individuals were comparable to currently recognized intraspecific divergences. Surprisingly, nuclear markers revealed more extensive differentiation, more characteristic of interspecific divergences. This disparity and the mosaic pattern of differentiation may be driven by stochastic population crashes and genetic bottlenecks (caused by seasonal habitat fluctuations), coupled with genetic drift.