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The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo‐species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river‐refuge hypotheses on diversification in the arboreal sub‐Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo‐distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid‐Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river‐refuge hypotheses in favor of the river‐barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east‐central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions. [ABSTRACT FROM AUTHOR]

The African colubrid snake genus Crotaphopeltis currently comprises six species and occurs throughout sub‐Saharan Africa. The most widespread of these, Crotaphopeltis hotamboeia, inhabits most biomes, aside from rainforest and hyper‐arid regions, and its catholic niche has presumably facilitated substantial gene flow. Despite this, the geographical range is large enough that ecological or physical barriers might exist, facilitating allopatric diversification. In contrast, most of the other species are habitat specialists with limited distributions (e.g., Crotaphopeltis tornieri) and would be expected to show strong genetic structure. We therefore examined species boundaries within Crotaphopeltis in a phylogenetic context using five markers (16S, cyt b, ND4, c‐mos, and RAG‐1) for four of the six species. Species delimitation methods included two coalescent‐based and one barcoding approach. Widespread geographical sampling of C. hotamboeia allowed examination of genetic structuring across its range. The species status of Crotaphopeltis barotseensis, C. degeni, and C. hotamboeia was confirmed, whereas the Afromontane species C. tornieri comprised two candidate species. Crotaphopeltis hotamboeia did not show cryptic speciation, although its phylogeographic structure corresponded with the spatiotemporal pattern of the African savanna. Our results show how the heterogeneous African environment could influence genetic partitioning of habitat specialist and generalist species at broad geographical scales. [ABSTRACT FROM AUTHOR]

Aim: Species with wide distributions spanning the African Guinean and Congolian rain forests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rain forest species, the African foam‐nest treefrog Chiromantis rufescens. Location: Guinean and Congolian rain forests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA) and single‐nucleotide polymorphism (SNP) data for 130 samples of C. rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change and periods of isolation and secondary contact. Species distribution models were used to identify the regions of climatic stability that could have served as forest refugia since the last interglacial. Results: Population structure within C. rufescens resembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent‐based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene. Main conclusions: Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo–Congolian forest. Population demographic inferences help connect the patterns of genetic variation to diversification model predictions. The diversification history of C. rufescens was shaped by a variety of processes, including vicariance from river barriers, forest fragmentation and adaptive evolution along environmental gradients. [ABSTRACT FROM AUTHOR]

Psammophylax (Fitzinger 1843) is a widespread yet poorly studied genus of African grass snakes. A genetic phylogeny of six of the seven species was estimated using multiple phylogenetic and distance‐based methods. To support the genetic analyses, we conducted morphological analyses on the body (traditional morphology) and head (geometric morphometrics) separately. Phylogenetic analyses recovered a similar topology to past studies, but with better resolution and node support. We found substantial genetic structuring within the genus, supported by significantly different head shapes between P. a. acutus and other Psammophylax. Psammophylax a. acutus was recovered as sister to its congeners, and sequence divergence values and morphometrics supported its recognition as a new genus. Increased sampling in East Africa (Tanzania, Kenya, and Ethiopia) revealed that Psammophylax multisquamis is polyphyletic, necessitating the description of a new, morphologically cryptic species from northern Tanzania. The distribution of P. multisquamis sensu stricto is likely restricted to Kenya and Ethiopia. The study has further resolved multiple aspects of Psammophylax systematics, including the taxonomic validity of two central African subspecies, P. variabilis vanoyei (Laurent 1956) and P. tritaeniatus subniger (Laurent 1956). Inclusion of specimens from the more remote parts of Africa, in future analyses, may result in the recovery of additional diversity within Psammophylax. [ABSTRACT FROM AUTHOR]

Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a shared climatic and geological history. Our species-specific estimates of climatic suitability through time are consistent with temporal and spatial heterogeneity in diversification among the species complexes, indicating that differences in ecological breadth may partly explain these idiosyncratic patterns. Likewise, we demonstrated that fluctuating sea levels periodically exposed a land bridge connecting Bioko Island with the mainland Guineo-Congolian forest and that habitats across the exposed land bridge likely enabled dispersal in some species, but not in others. We did not find evidence that rivers are biogeographic barriers across any of the species complexes. Despite marked differences in the geographic extent of stable climates and temporal estimates of divergence among the species complexes, we recovered a shared pattern of intermittent climatic suitability with recent population connectivity and demographic expansion across the Congo Basin. This pattern supports the hypothesis that genetic exchange across the Congo Basin during humid periods, followed by vicariance during arid periods, has shaped regional diversity. Finally, we identified many distinct lineages among our focal taxa, some of which may reflect incipient or unrecognized species. [ABSTRACT FROM AUTHOR]

The African clawed frog Xenopus laevis has a large native distribution over much of sub-Saharan Africa and is a model organism for research, a proposed disease vector, and an invasive species. Despite its prominent role in research and abundance in nature, surprisingly little is known about the phylogeography and evolutionary history of this group. Here, we report an analysis of molecular variation of this clade based on 17 loci (one mitochondrial, 16 nuclear) in up to 159 individuals sampled throughout its native distribution. Phylogenetic relationships among mitochondrial DNA haplotypes were incongruent with those among alleles of the putatively female-specific sex-determining gene DM-W, in contrast to the expectation of strict matrilineal inheritance of both loci. Population structure and evolutionarily diverged lineages were evidenced by analyses of molecular variation in these data. These results further contextualize the chronology, and evolutionary relationships within this group, support the recognition of X. laevis sensu stricto, X. petersii, X. victorianus and herein revalidated X. poweri as separate species. We also propose that portions of the currently recognized distributions of X. laevis (north of the Congo Basin) and X. petersii (south of the Congo Basin) be reassigned to X. poweri. [ABSTRACT FROM AUTHOR]

Heinicke, M. P., Greenbaum, E., Jackman, T. R. & Bauer, A. M. Phylogeny of a trans-Wallacean radiation (Squamata, Gekkonidae, Gehyra) supports a single early colonization of Australia. - Zoologica Scripta, 40, 584-602. The genus Gehyra (34 species) is rare among squamate reptile radiations in spanning continents, extending from southeast Asia to Australia and Polynesia. Among the family Gekkonidae sensu stricto, Gehyra is the only genus that is species rich in Australia. We performed molecular phylogenetic, divergence timing, and ancestral area analyses to investigate the evolutionary and biogeographic history of Gehyra. Phylogenetic analyses resolve Hemiphyllodactylus as the closest relative of Gehyra. Some data also link Perochirus to this group, but previously suggested relationships with other morphologically similar genera of geckos are not supported. Within Gehyra, three geographically discrete clades are recovered, respectively, concentrated in Asia, the Pacific islands and Australia. Ancestral area analyses suggest that Gehyra originated in Asia, with a single colonization of Australia occurring in the mid-Cenozoic. This date places the time of Gehyra colonization prior to those of other Australian gekkonid geckos, but after the near-endemic pygopodoid geckos, a Gondwanan relictual group. Based on these dates, times of origin may best explain relative differences in species diversity among Australian gekkotans. In contrast, although originating earlier, Gehyra is less diverse in Asia than in Australia. This pattern may be explained by the long-term presence of many competing, ecologically similar genera in Asia (e.g. Gekko, Hemidactylus, Lepidodactylus), whereas nearly all pygopodoids in Australia (the only gekkotans present at the time of colonization of Australia by Gehyra) are ecologically distinct. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships among gekkotan lizards were estimated from five nuclear protein-coding genes in separate and combined analyses using maximum parsimony, maximum likelihood and Bayesian analyses. All analyses recovered a monophyletic trans-Atlantic gecko clade (Phyllodactylidae) consisting of the genera Asaccus, Haemodracon, Homonota, Phyllodactylus, Phyllopezus, Ptyodactylus, Tarentola and Thecadactylus. No other phylogenetic or taxonomic hypotheses have proposed linking these genera, which have been consistently grouped with other taxa outside of the clade. In this paper, we determine the relationships of this new clade to other major gekkotan groups, evaluate previous phylogenetic hypotheses regarding constituent members of this novel clade, and critically examine the use of historically important morphological characters in gekkotan systematics as they relate to this novel clade, specifically — phalangeal formulae, hyoid morphology and external structure of the toe-pads. [ABSTRACT FROM AUTHOR]

Aim Geckos (Reptilia: Squamata), due to their great age and global distribution, are excellent candidates to test hypotheses of Gondwanan vicariance against post-Gondwanan dispersal. Our aims are: to generate a phylogeny of the sphaerodactyl geckos and their closest relatives; evaluate previous phylogenetic hypotheses of the sphaerodactyl geckos with regard to the other major gecko lineages; and to use divergence date estimates to inform a biogeographical scenario regarding Gondwanan relationships and assess the roles of vicariance and dispersal in shaping the current distributions of the New World sphaerodactyl geckos and their closest Old World relatives. Location Africa, Asia, Europe, South America, Atlantic Ocean. Methods We used parsimony and partitioned Bayesian methods to analyse data from five nuclear genes to generate a phylogeny for the New World sphaerodactyl geckos and their close Old World relatives. We used dispersal–vicariance analysis to determine ancestral area relationships among clades, and divergence times were estimated from the phylogeny using nonparametric rate smoothing. Results We recovered a monophyletic group containing the New World sphaerodactyl genera, Coleodactylus, Gonatodes, Lepidoblepharis, Pseudogonatodes and Sphaerodactylus, and the Old World Gekkotan genera Aristelliger, Euleptes, Quedenfeldtia, Pristurus, Saurodactylus and Teratoscincus. The dispersal–vicariance analysis indicated that the ancestral area for this clade was North Africa and surrounding regions. The divergence between the New World spaherodactyl geckos and their closest Old World relative was estimated to have occurred c. 96 Myrbp. Main conclusions Here we provide the first molecular genetic phylogenetic hypothesis of the New World sphaerodactyl geckos and their closest Old World relatives. A combination of divergence date estimates and dispersal–vicariance analysis informed a biogeographical scenario indicating that the split between the sphaerodactyl geckos and their African relatives coincided with the Africa/South America split and the opening of the Atlantic Ocean. We resurrect the family name Sphaerodactylidae to represent the expanded sphaerodactyl clade. [ABSTRACT FROM AUTHOR]

Patterns of formation and sequence of ossification of the entire skeleton are described for the snapping turtle Chelydra serpentina based on new and previously published data. Differences in the sequences of ossification events are described and demonstrate considerable intraspecific variation in these developmental data. The chondrocranium of a late developmental-stage specimen is described and illustrated as baseline data for comparative studies. Patterns of formation and chondrification of forelimb and hind limb elements are generally consistent with those of previous studies; however, conspicuous differences in the patterns of ossification are observed among metapodial and phalangeal elements. In the cranium, patterns of ossification of dermal elements are generally more variable than are those of endochondral elements of the braincase, and as in previous studies, endochondral elements ossify after dermal elements. Documented intraspecific variation in sequence and timing of formation, chondrification, and ossification of skeletal elements should serve as a caveat for those conducting studies of phylogeny, heterochrony, and evolution with these data. Causes of natural and induced variation are discussed briefly. [ABSTRACT FROM AUTHOR]