When is a species not a species? Uncoupled phenotypic, karyotypic and genotypic divergence in two species of South African laminate-toothed rats (Murinae: Otomyini)

Diversification and evolutionary history of the African laminated-toothed rats (Rodentia, Otomyini)

The African continent was subjected to periodic climatic shifts during the Pliocene and Pleistocene. These habitat changes greatly affected the evolutionary processes and tempo of diversification in numerous, widely distributed mammals. The Otomyini (Family Muridae) comprises three African rodent genera, Parotomys, Otomys and Myotomys, characterized by unique laminated-shaped molars. Species within this tribe generally prefer open-habitat and show low dispersal capabilities, with previous studies suggesting that their diversification was closely associated with climatic oscillations over the last four million years. Our phylogenetic reconstructions, based on three mitochondrial (mtDNA) genes (Cytb, COI and 12S) and four nuclear introns (EF, SPTBN, MGF and THY), identified eight major genetic clades that are distributed across southern, eastern and western Africa. Our data permit the re-examination of the taxonomic status of the three genera as well as the previously proposed mesic-arid dichotomy of the 10 South African species. Moreover, multiple mtDNA species delimitation methods incorporating 168 specimens estimated the number of Otomyini species to be substantially higher than the ∼30 recognized, suggesting that the current taxonomy will necessitate an integrative approach to delimit extant species diversity within the Otomyini. The data suggests that the origin of the tribe can be dated back to ∼5.7 million years ago (Ma) in southern Africa. The distribution and phylogenetic associations among the eight major otomyine evolutionary lineages can best be explained by several waves of northward colonization from southern Africa, complemented by independent reversed dispersals from eastern back to southern Africa at different time periods. There is strong support for the hypothesis that the radiation, dispersion, and diversification of the otomyine rodents is closely linked to recent Plio-Pleistocene climatic oscillations.

Phylogeography of the mesic-adapted striped mouse, Rhabdomys dilectus chakae (Rodentia: Muridae) in forest margins of the Eastern Cape and southern KwaZulu-Natal provinces of South Africa

Rhabdomys is a genus that occupies a variety of habitats, including forest margins. Among the Rhabdomys taxa, Rhabdomys dilectus chakae has a distribution that covers the eastern seaboard of South Africa, with a poorly defined divergence date from its sister taxon Rhabdomys dilectus dilectus. Here, we study three mitochondrial markers (cytochrome b, cytochrome c oxidase I and partial control region) of R. d. chakae across the Eastern Cape and KwaZulu-Natal forests of South Africa, aiming to determine the cladogenesis (molecular dating) and effective population size of this subspecies through time, in addition to its cladogenesis in relationship to other species within the genus. A phylogenetic analysis revealed six clades within Rhabdomys, confirming that our study area is occupied solely by R. d. chakae, to the exclusion of other recognized sibling species. A fossil-calibrated Bayesian relaxed molecular clock estimated a recent split between R. d. chakae and R. d. dilectus ~1.4 ± 0.35 Mya and between two Rhabdomys pumilio groups, coastal A and B, at 1.16 ± 0.44 Mya. Coalescent Bayesian skyline plots revealed a stable population of R. d. chakae in the study area that was in slow decline until 2500 years ago, when there was an expansion in the late Holocene. Radiation within Rhabdomys dates as far back as 4.27 Mya, and subsequent demographic fluctuations primarily reflect palaeoclimatic changes.

The cryptic case of Otomys sloggetti (Sloggett’s vlei rat): Interpreting murid molar morphology in the fossil record

Vlei rats (Family: Muridae; Subfamily: Otomyinae) have a widespread distribution in southern Africa. They are favoured prey of barn and spotted eagle owls, and frequently become associated with archaeological deposits when the owls roost in cave sites. The phylogeny of several Otomyinae species is enigmatic, and Otomys sloggetti (Sloggett’s vlei rat) is no exception. This species has been referred to as the ‘ice rat’ and present distribution ranges are seemingly limited to mountainous areas, at high altitude, in Lesotho Drakensberg and the Karoo. It was thus surprising and unexpected when specimens closely resembling Otomys sloggetti (identification was based on molar morphology) were found in several archaeological sites on the south and west coasts of South Africa, and also in modern owl pellet assemblages – all extralimital to the current reported distribution. However, further examination of and comparison between these specimens, as well as extensive differences observed between comparative Otomys sloggetti specimens from museum collections, highlighted potential problems associated with the common practice of using tooth morphology to identify fossil murid species. We identified six molar morphotypes from the fossil and modern material, all of which bore a morphological resemblance to O. sloggetti. The material discussed in this paper suggests that cryptic, undescribed vlei rat species, or subspecies, have been in the past, and may yet be, co-occurring with modern populations of O. karoensis and O. irroratus. Phylogenetic studies need to be done in conjunction with morphological studies, as, currently, the relationship between the huge variation seen in interspecific morphology with genetics is little understood, different Otomys species are not always distinguishable morphologically, and considerable chromosomal polytypes have been found. Our findings highlight the need for extensive cladistic and genetic research on the Otomyinae.

Biomes, geology and past climate drive speciation of laminate-toothed rats on South African mountains (Murinae: Otomys)

Mitochondrial DNA sequences (1137 bp) of the cytochrome b gene and craniodental and craniometric data were used to investigate the evolutionary relationships of six putative rodent taxa of Otomys (family Muridae: subfamily Murinae: tribe Otomyini) co-occurring in the Western Cape and Eastern Cape provinces of South Africa. Phylogenetic analysis of 20 new sequences together with craniodental and craniometric characters of 94 adult skulls reveal the existence of a unique lineage of Otomys cf. karoensis (named herein Otomys willani sp. nov.) from the Sneeuberg Centre of Floristic Endemism in the southern Drakensberg Mountain Range. Craniometric analysis distinguished O. karoensis from O. willani and identified a further four localities in the range of the latter species. We document southern range extensions of both Sloggett’s ice rat, Otomys sloggetti, and the vlei rat Otomys auratus to the Sneeuberg Mountain Range, in addition to appreciable genetic divergence between Sneeuberg and southern and central Drakensberg populations of O. sloggetti. Our results demonstrate parallel patterns of cryptic speciation in two co-occurring species complexes (Otomys irroratus s.l. and O. karoensis s.l.) associated closely with the boundaries of biomes (fynbos vs. grassland biomes) and geological formations (Cape Fold Belt vs. Great Escarpment).

Taxonomic anarchy or an inconvenient truth for conservation? Accelerated species discovery reveals evolutionary patterns and heightened extinction threat in Afro-Malagasy small mammals

We respond to recent criticisms of supposed “taxonomic anarchy” which is said to hamper conservation efforts. Using examples from African small mammals, we document recent increases of 13% (rodents) and 18% (bats) over the past three decades in the number of recognized species of Afro-Malagasy rodents and bats. By reference to a number of case studies involving Afro-Malagasy taxa (predominantly from montane habitats), and a suggested four-criterion approach to delimiting species accurately, we show that these increases are a genuine reflection of speciation in cryptic species complexes. Moreover, we show that some of these cryptic species are subject to increased extinction risks due to small population size and anthropogenic changes (habitat degradation and climate change). These changes were captured accurately in a recent Mammal Red List of South Africa, Lesotho and Swaziland, indicating that taxonomists and conservationists can work together to assess the Red List status of cryptic species based on robust taxonomic revisions.

Past, present, and future distribution of Afromontane rodents (Muridae: Otomys) reflect climate-change predicted biome changes

Climate change constitutes a potential threat to montane biodiversity, particularly in low-altitude, tropical mountains; however, few data exist for the Afromontane taxa. In South Africa, the temperate grassland and fynbos biomes are mostly associated with the Great Escarpment and the high-lying central plateau. Varying contractions of the grassland and fynbos biomes are predicted under different climate scenarios by 2050. Animal taxa adapted to these biomes should suffer similar range declines and can be used to independently test the vegetation models. We constructed MaxEnt models from 271 unique locality records for three species of montane and submontane vlei rats that are closely associated with grassland (

Afromontane small mammals do not follow the hump-shaped rule: altitudinal variation in the Soutpansberg Mountains, South Africa

Altitudinal transects of biodiversity are important to understanding macro-ecological patterns. Hump-shaped altitudinal profiles in species richness are a common pattern in terrestrial small-mammal communities studied previously mostly in New World mountain ranges. Based on capture–mark–recapture live-trapping conducted over four seasons (four nights per session) along an altitudinal transect from 1000 to 1747 m asl on the southern slopes of the Soutpansberg Mountains of northern South Africa, we recorded 12 species of small mammal, including nine rodents, two shrews and one elephant shrew (sengi). Three species of rodent and the sengi dominated the communities whilst six species were recorded with three or fewer captures. Although we found no effect of season, we found a significant linear increase in terrestrial small-mammal richness (but not Simpson's diversity, D) with altitude in the Soutpansberg Mountains located just north of the Tropic of Capricorn in South Africa. This trend could best be explained by an increase in the proportion of rocky cover and a change in vegetation from savanna to grassland. Peak densities of three common rodent species and one common insectivore varied from 10 ha−1 (Elephantulus myurus) to 54 ha−1 (Micaelamys namaquensis) and density showed no significant variation with season. However, density either declined (Aethomys ineptus) or increased (Rhabdomys dilectus and Elephantulus myurus) significantly with altitude; this variation was best explained by the proportion of rocky cover. Seasonal variation had a significant effect on body mass of two rodent species. A review of small-mammal studies from major mountain ranges in Africa and Madagascar found that the hump-shaped pattern is not common. Declines in richness with increasing altitude as well as cases of no significant altitudinal change were the most common patterns noted. Tropical African mountains (including the Soutpansberg with 27 species) have far higher small-mammal diversity than temperate African mountains.

Chromosomal polymorphisms in African vlei rats, Otomys irroratus (Muridae: Otomyini), detected by banding techniques and chromosome painting: inversions, centromeric shifts and diploid number variation

Pericentric inversions are important for evolutionary biology because of their potential role in speciation. They may result in reproductive isolation due to illegitimate pairing of homologues at meiosis which leads to the production of aneuploid gametes (containing deletions or duplications of chromosomal segments), and consequently mediate chromosomal divergence. In this study, we describe the prevalence of pericentric inversions in the African vlei rat, Otomys irroratus (OIR). The species is characterized by intraspecific chromosomal variation (2n = 23-32) across its distribution in southern Africa. Here, we analyzed 55 individuals collected from 7 localities in South Africa by G- and C-banding and chromosome painting with flow sorts of Myotomys unisulcatus. Of the 55 specimens that were analyzed, 47% contained inversions or centromeric shifts on 4 autosomes (OIR1, 4, 6 and 10) which were present singly in specimens (i.e. none of the specimens contained all 4 inversions concurrently). These inversions were found in both homozygous and heterozygous state over a wide geographic range suggesting that they are floating polymorphisms. Given the potential role of inversions in post-mating isolation (through production of aneuploid gametes), the prevalence of inversions as floating polymorphisms in the vlei rats suggests that they are probably retained in the population through suppression of recombination in the inverted regions of the chromosomes.