Laurent Chirio

A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for Agama, and their close relatives, using a hybrid phylogenetic-phylogenomic approach that combines traditional Sanger sequence data from five loci for 57 species (146 samples) with anchored phylogenomic data from 215 nuclear genes for 23 species. The Sanger data are analyzed using coalescent-based species tree inference using (*)BEAST, and the resulting posterior distribution of species trees is attenuated using the phylogenomic tree as a backbone constraint. The result is a time-calibrated species tree for Agama that includes 95% of all species, multiple samples for most species, strong support for the major clades, and strong support for most of the initial divergence events. Diversification within Agama began approximately 23 million years ago (Ma), and separate radiations in Southern, East, West, and Northern Africa have been diversifying for >10Myr. A suite of traits (morphological, coloration, and sociality) are tightly correlated and show a strong signal of high morphological disparity within clades, whereby the subsequent evolution of convergent phenotypes has accompanied diversification into new biogeographic areas.

The global distribution of tetrapods reveals a need for targeted reptile conservation

The distributions of amphibians, birds and mammals have underpinned global and local conservation priorities, and have been fundamental to our understanding of the determinants of global biodiversity. In contrast, the global distributions of reptiles, representing a third of terrestrial vertebrate diversity, have been unavailable. This prevented the incorporation of reptiles into conservation planning and biased our understanding of the underlying processes governing global vertebrate biodiversity. Here, we present and analyse the global distribution of 10,064 reptile species (99% of extant terrestrial species). We show that richness patterns of the other three tetrapod classes are good spatial surrogates for species richness of all reptiles combined and of snakes, but characterize diversity patterns of lizards and turtles poorly. Hotspots of total and endemic lizard richness overlap very little with those of other taxa. Moreover, existing protected areas, sites of biodiversity significance and global conservation schemes represent birds and mammals better than reptiles. We show that additional conservation actions are needed to effectively protect reptiles, particularly lizards and turtles. Adding reptile knowledge to a global complementarity conservation priority scheme identifies many locations that consequently become important. Notably, investing resources in some of the world’s arid, grassland and savannah habitats might be necessary to represent all terrestrial vertebrates efficiently.The global distribution of nearly all extant reptile species reveals richness patterns that differ spatially from that of other taxa. Conservation prioritization should specifically consider reptile distributions, particularly lizards and turtles.

Modeling the effects of anthropogenic habitat change on savanna snake invasions into African rainforest.

We used a species-distribution modeling approach, ground-based climate data sets, and newly available remote-sensing data on vegetation from the MODIS and Quick Scatterometer sensors to investigate the combined effects of human-caused habitat alterations and climate on potential invasions of rainforest by 3 savanna snake species in Cameroon, Central Africa: the night adder (Causus maculatus), olympic lined snake (Dromophis lineatus), and African house snake (Lamprophis fuliginosus). Models with contemporary climate variables and localities from native savanna habitats showed that the current climate in undisturbed rainforest was unsuitable for any of the snake species due to high precipitation. Limited availability of thermally suitable nest sites and mismatches between important life-history events and prey availability are a likely explanation for the predicted exclusion from undisturbed rainforest. Models with only MODIS-derived vegetation variables and savanna localities predicted invasion in disturbed areas within the rainforest zone, which suggests that human removal of forest cover creates suitable microhabitats that facilitate invasions into rainforest. Models with a combination of contemporary climate, MODIS- and Quick Scatterometer-derived vegetation variables, and forest and savanna localities predicted extensive invasion into rainforest caused by rainforest loss. In contrast, a projection of the present-day species-climate envelope on future climate suggested a reduction in invasion potential within the rainforest zone as a consequence of predicted increases in precipitation. These results emphasize that the combined responses of deforestation and climate change will likely be complex in tropical rainforest systems.

Biogeography of the reptiles of the central African republic

Abstract A large number of reptiles from the Central African Republic (CAR) were collected during recent surveys conducted over six years (October 1990 to June 1996) and deposited at the Paris Natural History Museum (MNHN). This large collection of 4873 specimens comprises 86 terrapins and tortoises, five crocodiles, 1814 lizards, 38 amphisbaenids and 2930 snakes, totalling 183 species from 78 localities within the CAR. A total of 62 taxa were recorded for the first time in the CAR, the occurrence of numerous others was confirmed, and the known distribution of several taxa is greatly extended. Based on this material and an additional six species known to occur in, or immediately adjacent to, the country from other sources, we present a biogeographical analysis of the 189 species of reptiles in the CAR.

New Species of Cnemaspis (Squamata: Gekkonidae) from Northern Cameroon, a Neglected Biodiversity Hotspot

Abstract A new species of diurnal gecko of the genus Cnemaspis is described from granite boulder habitats in gallery forests in the Monts Alantika and Hosséré Vokré, north of the Adamaoua Plateau in north Cameroon. The new species is most similar to the widespread species Cnemaspis spinicollis but differs from this and all other congeners in details of both scalation (single enlarged scale beneath the penultimate interphalangeal joint of digit IV of pes, absence of an enlarged, flattened preaxial metatarsal scale, absence of tubercles on the crown and beneath the ear) and coloration (pale, with little contrast between background color and series of distinct whitish dorsal markings, throat markings weakly developed). The discovery of several new reptile species from the Adamaoua Plateau and its outliers highlights the potential importance of the northern Cameroonian highlands as a center of endemism.

New Species of Leptosiaphos (Scincidae) from Adamaoua Massif, Central-Northern Province, Cameroon

Abstract A small skink of the genus Leptosiaphos from the Adamaoua Massif in Central-Northern Province of Cameroon is described. The new species is most similar to the East African Leptosiaphos kilimensis from which it differs in coloration and in having 22 scales around midbody.

Bayesian inference of species diffusion in the West African Agama agama species group (Reptilia, Agamidae)

The savannah and tropical forest biomes of Africa have a long history of expansion and contraction, and the recent and rapid spread of dry savannah habitats has influenced the spatial and temporal diversification of vertebrate taxa across this region. We used a combination of species tree and phylogeographic methods to describe the spatio-temporal changes through time and across space (= species diffusion) in a clade of seven West African lizard species in the Agama agama species group. A Bayesian species tree diffusion approach was used to compare the relative rates at which species ranges changed across the landscape. We found that some species have high diffusion rates characterized by significant movement in their range location and minor changes to their overall range size, whereas other species show little movement in their range centre with an exponential increase in range size. This discrepancy between the rates that range locations shift versus change in their relative area could be linked to populations tracking their preferred habitats through time. A continuous Bayesian phylogeography approach using a relaxed random walk model was used to estimate the timing and rate of population size change and geographic diffusion in A. picticauda, the single species in the group with an extensive African distribution from Mauritania to Ethiopia. The mean dispersal rate of A. picticauda increased dramatically throughout the Pleistocene, and a Bayesian skyride analysis supports exponential population growth over this same time period. A comparison of genetic diversity across different loci and species suggests that A. lebretoni experienced a mitochondrial selective sweep that has caused a deficit of variation at this locus in relation to nuclear loci.

New species of Hemidactylus (Squamata: Gekkonidae) from Cameroon

Abstract A new large (100 mm SVL) species of forest‐dwelling gecko of the genus Hemidactylus is described from the Furu‐Awa area in the Northwest Province of Cameroon. The species is distinguished from other equatorial West African members of the genus by its large size, 18–20 rows of small dorsal tubercles, 45 precloacal‐femoral pores in males, transversely enlarged median subcaudal plates, reduced tail tuberculation and distinctive purplish colour pattern.

Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra ( Naja melanoleuca ) species complex in Central and West Africa (Serpentes: Elapidae)

Cobras are among the most widely known venomous snakes, and yet their taxonomy remains incompletely understood, particularly in Africa. Here, we use a combination of mitochondrial and nuclear gene sequences and morphological data to diagnose species limits within the African forest cobra, Naja (Boulengerina) melanoleuca. Mitochondrial DNA sequences reveal deep divergences within this taxon. Congruent patterns of variation in mtDNA, nuclear genes and morphology support the recognition of five separate species, confirming the species status of N. subfulva and N. peroescobari, and revealing two previously unnamed West African species, which are described as new: Naja (Boulengerina) guineensis sp. nov. Broadley, Trape, Chirio, Ineich Wüster, from the Upper Guinea forest of West Africa, and Naja (Boulengerina) savannula sp. nov. Broadley, Trape, Chirio Wüster, a banded form from the savanna-forest mosaic of the Guinea and Sudanian savannas of West Africa. The discovery of cryptic diversity in this iconic group highlights our limited understanding of tropical African biodiversity, hindering our ability to conserve it effectively.

Author Correction: The global distribution of tetrapods reveals a need for targeted reptile conservation

In the version of this Article originally published, grant no. 2015/20215-7 for C.N. was omitted from the Acknowledgements section. This has now been corrected in all versions of the Article.