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Aim: The primary drivers of species and population extirpations have been habitat loss, overexploitation and invasive species, but human‐mediated climate change is expected to be a major driver in future. To minimise biodiversity loss, conservation managers should identify species vulnerable to climate change and prioritise their protection. Here, we estimate climatic suitability for two species‐rich taxonomic groups, then use phylogenetic analyses to assess vulnerability to climate change. Location: Aotearoa New Zealand (NZ). Taxa: NZ lizards: diplodactylid geckos and eugongylinae skinks. Methods: We built correlative species distribution models (SDMs) for NZ geckos and skinks to estimate climatic suitability under current climate and 2070 future climate scenarios. We then used Bayesian phylogenetic mixed models (BPMMs) to assess vulnerability for both groups with predictor variables for life‐history traits (body size and activity phase) and current distribution (elevation and latitude). We explored two scenarios: an unlimited dispersal scenario, where projections track climate, and a no‐dispersal scenario, where projections are restricted to areas currently identified as suitable. Results: SDMs projected vulnerability to climate change for most modelled lizards. For species' ranges projected to decline in climatically suitable areas, average decreases were between 42% and 46% for geckos and 33% and 52% for skinks, although area did increase or remain stable for a minority of species. For the no‐dispersal scenario, the average decrease for geckos was 37%–52% and for skinks was 33%–52%. Our BPMMs showed phylogenetic signal in climate change vulnerability for both groups, with elevation increasing vulnerability for geckos, and body size reducing vulnerability for skinks. Main conclusions: New Zealand lizards showed variable vulnerability to climate change, with most species' ranges predicted to decrease. For species whose suitable climatic space is projected to disappear from within their current range, managed relocation could be considered to establish populations in regions that will be suitable under future climates. [ABSTRACT FROM AUTHOR]

The African anuran genus Cardioglossa contains 19 described species, most of which are distinguished from one another by striking patterns and colors. We present a well-resolved phylogeny based on analyses of mitochondrial and nuclear loci for 18 species of Cardioglossa. This provides the basis for species-delimitation analyses and interpreting historical biogeography in the genus. Whereas much of the diversification within the genus occurred among Central African lineages during the Miocene following the origin of Cardioglossa in the latest Oligocene or earliest Miocene, most species-pairs in the genus diverged more recently during the Plio-Pleistocene. The two most geographically peripheral species--C. cyaneospila in the Albertine Rift Mountains and C. occidentalis in the Upper Guinean Forests of West Africa--both diverged from other lineages during the mid-late Miocene. Because our analyses do not support C. manengouba and C. oreas as distinct species, we recognize these geographically separate and phenotypically distinct populations as subspecies of C. oreas that diverged subsequent to the origin of Mount Manengouba during the past 1.5 million years. In contrast, we find that C. leucomystax likely represents two species found in the Lower Guinean and Congolian forests, respectively. We find recent divergences between several allopatric lineages (either species or populations) that differ in coloration and pattern, including in C. nigromaculata which varies in color across its range in Central Africa and Bioko Island. These recent divergences among allopatric lineages with distinctive coloration and pattern raise new questions about the significance of these traits in this genus for which little is known of its natural history and biology. [ABSTRACT FROM AUTHOR]

Abstract: Aim: To investigate models assessing the influence of geomorphology and climatic shifts on species diversification in sub‐Saharan Africa by reconstructing the pattern and timing of phylogenetic relationships of rain frogs (Brevicipitidae: Breviceps). Location: Sub‐Saharan Africa, south of the Congo Basin. Methods: Multilocus sequence data were generated for near complete species‐level sampling of the genus Breviceps. Phylogenetic relationships were inferred via Bayesian inference and maximum likelihood analyses on both concatenated and single‐gene datasets. Network analyses identified locus‐specific reticulate relationships among taxa. Bayesian methods were used to infer dates of divergence among Breviceps lineages, and niche modelling was used to identify possible adaptive divergence. Results: Breviceps is monophyletic and comprised of two major, largely allopatric subclades. Diversity within each subclade is concentrated in two areas with contrasting geologic and climatic histories: the arid/semiarid winter rainfall zone in the south‐western (SW) Cape, and the semitropical East Coast that receives predominantly summer rainfall. Recognized species diversity in the SW Cape based on phenotypic variation is consistent with observed genetic patterns whereas the East Coast is shown to harbour unexpectedly high genetic diversity and up to seven putative, cryptic species. Niche models show significant overlap between closely related species. Main conclusions: Dating analyses indicate that diversification of Breviceps occurred rapidly within the Miocene, with only a moderate decline over the Plio‐Pleistocene, suggesting that this process might be slowed but ongoing. Our findings suggest that a combination of two models, a landscape barrier model and climate fluctuation model, can explain patterns of diversification in Breviceps. This demonstrates that Miocene epeirogenic events and climatic shifts may have had a considerable influence on contemporary patterns of biodiversity. Topographic complexity and relative geoclimatic stability in the East have promoted cryptic diversification in allopatry, and this area clearly harbours numerous undescribed taxa and is in need of detailed biotic investigation. [ABSTRACT FROM AUTHOR]

Aim Conservation is often prioritized by identifying regional clusters of threatened or endemic species. Another approach is to assess the evolutionary distinctiveness of groups of taxa using phylodiversity measures. However, quantification of evolutionary history has traditionally not accounted for its uneven geographical distribution due to the variation in species ranges. We assess the efficacy of phylogenetic endemism ( PE) to predict high extinction risk in comparison to estimates of species range restriction (weighted endemism, WE) and phylogenetic diversity ( PD). PE measures the relative range restriction of evolutionary history (lineages), while WE concentrates on the tips of the tree of life, treating all such branches as being of equal length. Location/Methods Using New Zealand's endemic skinks and geckos, we mapped the geographical variation in their extinction risk, PE, WE and PD and measured the extent to which extinction risk exhibited phylogenetic clustering for each group. Correlations between geographical concentrations of high skink and gecko extinction risk with PE, WE and PD were calculated. Results PE was predictive of spatial clusters of high extinction risk for geckos ( r2 = 0.34, P < 0.001) while WE was markedly less so ( r2 = 0.19, P < 0.001). The reverse applied to skinks, with WE most predictive of high risk ( r2 = 0.26, P < 0.001). The phylogenetic signal of extinction risk was significantly conserved for geckos, but was weaker and non-significant for skinks. PE and WE were not predictive of low risk. PD was not predictive of risk. Main conclusions PE and related measures may be predictive of extinction risk when risk is phylogenetically conserved. Mapping the geographical variation in PE could be a useful first assessment of extinction risk for many groups because phylogenies are increasingly available, while full risk status categories are not. These findings might apply to other groups and locations and warrant further investigation. [ABSTRACT FROM AUTHOR]

Abstract: We used a multi-gene approach to assess the phylogenetic relationships of New Zealand diplodactylid geckos to their Australian and New Caledonian relatives and to one another. Data from nuclear (RAG-1, PDC) and mitochondrial (ND2, 16S) genes from >180 specimens representing all 19 recognized New Zealand taxa and all but two of 20 putatively new species suggested by previous studies were analyzed using Maximum Parsimony, Maximum Likelihood and Bayesian inference. All analyses retrieved a monophyletic New Zealand clade, most closely related to the Australian Diplodactylidae exclusive of Pseudothecadactylus. Hoplodactylus is paraphyletic and composed of two morphological groups: a broad-toed clade, consisting of the island-restricted, largest extant species, Hoplodactylus duvaucelii, and the species-rich, wide-ranging Hoplodactylus maculatus clade; and a narrow-toed clade, comprising five monophyletic subgroups: Naultinus, the Hoplodactylus pacificus and Hoplodactylus granulatus clades, and the distinctive species Hoplodactylus rakiurae and Hoplodactylus stephensi. Each of these lineages is here recognized at the generic level. Our data support recognition of 16 new species (36 total), and five new or resurrected genera (seven total). The New Zealand diplodactylid radiation split from its Australian relatives 40.2mya (95% highest posterior density estimate 28.9–53.5), after the opening of the Tasman Sea. Their distribution cannot, therefore, be regarded as derived as a result of Gondwanana vicariance. The age of the New Zealand crown group, 24.4mya (95% highest posterior density estimate 15.5–33.8), encompasses the period of the ‘Oligocene drowning’ of New Zealand and is consistent with the hypothesis that New Zealand was not completely inundated during this period. Major lineages within New Zealand geckos diverged chiefly during the mid- to late Miocene, probably in association with a suite of geological and climatological factors that have characterized the region’s complex history. [Copyright &y& Elsevier]

Summary For over 50 years, biologists have accepted that all extant snakes share the same ZW sex chromosomes derived from a common ancestor [ 1–3 ], with different species exhibiting sex chromosomes at varying stages of differentiation. Accordingly, snakes have been a well-studied model for sex chromosome evolution in animals [ 1, 4 ]. A review of the literature, however, reveals no compelling support that boas and pythons possess ZW sex chromosomes [ 2, 5 ]. Furthermore, phylogenetic patterns of facultative parthenogenesis in snakes and a sex-linked color mutation in the ball python ( Python regius ) are best explained by boas and pythons possessing an XY sex chromosome system [ 6, 7 ]. Here we demonstrate that a boa ( Boa imperator ) and python ( Python bivittatus ) indeed possess XY sex chromosomes, based on the discovery of male-specific genetic markers in both species. We use these markers, along with transcriptomic and genomic data, to identify distinct sex chromosomes in boas and pythons, demonstrating that XY systems evolved independently in each lineage. This discovery highlights the dynamic evolution of vertebrate sex chromosomes and further enhances the value of snakes as a model for studying sex chromosome evolution. [ABSTRACT FROM AUTHOR]

[Display omitted] • Multigene phylogeny of 56 Lygodactylus species reveals four well supported clades. • TIME calibrated analysis indicates multiple dispersal events between Madagascar and Continental Africa. • Morphological characters fail to reflect molecular phylogenetic results. • 15 New potential candidate sub-/species unveiled by this study double the number of undescribed Lygodactylus species. 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. [ABSTRACT FROM AUTHOR]