A species-level phylogeny of Trachylepis (Scincidae: Mabuyinae) provides insight into their reproductive mode evolution

Cycle of the sexual segment of the kidney: histological insights into the role of the urinary tract in the reproduction of male Notomabuya frenata (Squamata: Scincidae)

The kidneys of male Squamata have an important reproductive function as some portions of the nephron may undergo hypertrophy, characterizing the sexual segment of the kidney (SSK). Although its function is still not completely understood, it is believed that the secretions produced by the SSK may act in the maintenance of spermatozoa. In this study, we investigated the reproductive biology of males of Notomabuya frenata based on the seasonal variation of the SSK. We performed macroscopic and microscopic evaluations of the male reproductive tract of museum specimens to characterize the SSK cycle. The nephron portion in which hypertrophy was observed was the collecting duct with secretory granules accumulation in the apical portion. SSK hypertrophy was observed in all seasons, with the tubule diameter in autumn differing from spring and the epithelium height showing no variation. Alcian Blue reacted positively to acid mucopolysaccharides in all seasons. Periodic acid-Schiff's reacted positively to neutral mucopolysaccharides in all seasons, except autumn. Both stains reacted only in the collecting duct. In addition, spermatozoa were found in the lumen of the SSK of one specimen examined. Cycle of the SSK varied seasonally as does the chemical composition of the secretions produced by the collecting duct. The reflux of spermatozoa into SSK may indicate that (1) these secretions act in sperm maintenance, and (2) possibly there is communication between the seminal and urinary ducts.

Diversification of the African legless skinks in the subfamily Acontinae (Family Scincidae)

Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily's biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered "ghost introgression" in A. occidentalis. Our inferred species tree revealed a signal of gene flow, which implies possible cross-over in some groups. Fossil evidence calibration dating results showed that the divergence between Typhlosaurus and Acontias was likely influenced by cooling and increasing aridity along the southwest coast in the mid-Oligocene caused by the opening of the Drake Passage. Further cladogenesis observed in Typhlosaurus and Acontias was likely influenced by Miocene cooling, expansion of open habitat, uplifting of the eastern Great Escarpment (GE), and variation in rainfall patterns, together with the effect of the warm Agulhas Current since the early Miocene, the development of the cold Benguela Current since the late Miocene, and their co-effects. The biogeographic pattern of the Acontinae bears close resemblance to that of other herpetofauna (e.g., rain frogs and African vipers) in southern Africa.

Understanding the evolution of viviparity using intraspecific variation in reproductive mode and transitional forms of pregnancy

How innovations such as vision, flight and pregnancy evolve is a central question in evolutionary biology. Examination of transitional (intermediate) forms of these traits can help address this question, but these intermediate phenotypes are very rare in extant species. Here we explore the biology and evolution of transitional forms of pregnancy that are midway between the ancestral state of oviparity (egg‐laying) and the derived state, viviparity (live birth). Transitional forms of pregnancy occur in only three vertebrates, all of which are lizard species that also display intraspecific variation in reproductive phenotype. In these lizards (Lerista bougainvillii, Saiphos equalis, and Zootoca vivipara), geographic variation of three reproductive forms occurs within a single species: oviparity, viviparity, and a transitional form of pregnancy. This phenomenon offers the valuable prospect of watching ‘evolution in action’. In these species, it is possible to conduct comparative research using different reproductive forms that are not confounded by speciation, and are of relatively recent origin. We identify major proximate and ultimate questions that can be addressed in these species, and the genetic and genomic tools that can help us understand how transitional forms of pregnancy are produced, despite predicted fitness costs. We argue that these taxa represent an excellent prospect for understanding the major evolutionary shift between egg‐laying and live birth, which is a fundamental innovation in the history of animals.

A comprehensive phylogeny of dwarf geckos of the genus Lygodactylus, with insights into their systematics and morphological variation

The 71 currently known species of dwarf geckos of the genus Lygodactylus are a clade of biogeographic interest due to their occurrence in continental Africa, Madagascar, and South America. Furthermore, because many species are morphologically cryptic, our knowledge of species-level diversity within this genus is incomplete, as indicated by numerous unnamed genetic lineages revealed in previous molecular studies. Here we provide an extensive multigene phylogeny covering 56 of the named Lygodactylus species, four named subspecies, and 34 candidate species of which 19 are newly identified in this study. Phylogenetic analyses, based on ∼10.1 kbp concatenated sequences of eight nuclear-encoded and five mitochondrial gene fragments, confirm the monophyly of 14 Lygodactylus species groups, arranged in four major clades. We recover two clades splitting from basal nodes, one comprising exclusively Malagasy species groups, and the other containing three clades. In the latter, there is a clade with only Madagascar species, which is followed by a clade containing three African and one South American species groups, and its sister clade containing six African and two Malagasy species groups. Relationships among species groups within these latter clades remain weakly supported. We reconstruct a Lygodactylus timetree based on a novel fossil-dated phylotranscriptomic tree of squamates, in which we included data from two newly sequenced Lygodactylus transcriptomes. We estimate the crown diversification of Lygodactylus started at 46 mya, and the dispersal of Lygodactylus among the main landmasses in the Oligocene and Miocene, 35-22 mya, but emphasize the wide confidence intervals of these estimates. The phylogeny suggests an initial out-of-Madagascar dispersal as most parsimonious, but accounting for poorly resolved nodes, an out-of-Africa scenario may only require one extra dispersal step. More accurate inferences into the biogeographic history of these geckos will likely require broader sampling of related genera and phylogenomic approaches to provide better topological support. A survey of morphological characters revealed that most of the major clades and species groups within Lygodactylus cannot be unambiguously characterized by external morphology alone, neither by unique character states nor by a diagnostic combination of character states. Thus, any future taxonomic work will likely benefit from integrative, phylogenomic approaches.

Herpetological results of Francisco Newtons Zoological Expedition to Angola (19031906): a taxonomic revision and new records of a forgotten collection

Francisco Newtons zoological expedition to Angola undertaken between 1903 and 1906 is one of the least studied of the naturalists life. Only three major papers regarding the herpetofauna collected in this expedition have been published, and a significant part of the specimens remains unstudied since the 1900s. Here we review the extant herpetological specimens of this expedition, present an updated taxonomic revision, and provide new insights on their taxonomic status. The extant collection is constituted by 329 specimens (155 amphibians and 174 reptiles), corresponding to 73 species, 39 genera and 22 families, and it is presently housed in the Museu de Histria Natural e da Cincia da Universidade do Porto (MHNC-UP).

Ansorge’s cusimanse in Angola: 100 years apart, new records contribute to the species known range

Ansorge’s cusimanse, Crossarchus ansorgei Thomas, 1910, has until recently been known in Angola only from a single specimen collected in 1908, the holotype. During a camera trap survey conducted in Quiçama National Park (Angola) in 2017, we recorded the presence of the species 115 km south-west of the type locality – 40 km from the edge of the current known distribution range, – extending it south of the Cuanza river and possibly following the woodlands along the Angolan Escarpment. We combine our records of Ansorge’s cusimanse with the available published and unpublished records from Angola and compare with other vertebrate taxa that follow a similar pattern, in which Central African species extend their southern distribution into Angola, through the more forested areas in northwestern Angola and further south along the Escarpment. Furthermore, we discuss the urgent need for more research on this species and the impact bushmeat harvesting may have on its conservation.

Molecular phylogenetics of sub-Saharan African natricine snakes, and the biogeographic origins of the Seychelles endemic Lycognathophis seychellensis

Phylogenetic relationships of sub-Saharan African natricine snakes are understudied and poorly understood, which in turn has precluded analyses of the historical biogeography of the Seychelles endemic Lycognathophis seychellensis. We inferred the phylogenetic relationships of Seychelles and mainland sub-Saharan natricines by analysing a multilocus DNA sequence dataset for three mitochondrial (mt) and four nuclear (nu) genes. The mainland sub-Saharan natricines and L. seychellensis comprise a well-supported clade. Two maximally supported sets of relationships within this clade are (Limnophis,Natriciteres) and (Afronatrix,(Hydraethiops,Helophis)). The relationships of L. seychellensis with respect to these two lineages are not clearly resolved by analysing concatenated mt and nu data. Analysed separately, nu data best support a sister relationship of L. seychellensis with (Afronatrix,(Hydraethiops,Helophis)) and mt data best support a sister relationship with all mainland sub-Saharan natricines. Methods designed to cope with incomplete lineage sorting strongly favour the former hypothesis. Genetic variation among up to 33 L. seychellensis from five Seychelles islands is low. Fossil calibrated divergence time estimates support an overseas dispersal of the L. seychellensis lineage to the Seychelles from mainland Africa ca. 43-25 million years before present (Ma), rather than this taxon being a Gondwanan relic.

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

BACKGROUND

Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world's tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa.

RESULTS

We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63-5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group.

CONCLUSION

Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B-Ptr, Ptt-A and Pv-A.