Duarte V. Gonçalves

Unravelling biodiversity, evolution and threats to conservation in the Sahara‐Sahel

Deserts and arid regions are generally perceived as bare and rather homogeneous areas of low diversity. The Sahara is the largest warm desert in the world and together with the arid Sahel displays high topographical and climatic heterogeneity, and has experienced recent and strong climatic oscillations that have greatly shifted biodiversity distribution and community composition. The large size, remoteness and long‐term political instability of the Sahara‐Sahel, have limited knowledge on its biodiversity. However, over the last decade, there have been an increasing number of published scientific studies based on modern geomatic and molecular tools, and broad sampling of taxa of these regions. This review tracks trends in knowledge about biodiversity patterns, processes and threats across the Sahara‐Sahel, and anticipates needs for biodiversity research and conservation. Recent studies are changing completely the perception of regional biodiversity patterns. Instead of relatively low species diversity with distribution covering most of the region, studies now suggest a high rate of endemism and larger number of species, with much narrower and fragmented ranges, frequently limited to micro‐hotspots of biodiversity. Molecular‐based studies are also unravelling cryptic diversity associated with mountains, which together with recent distribution atlases, allows identifying integrative biogeographic patterns in biodiversity distribution. Mapping of multivariate environmental variation (at 1 km × 1 km resolution) of the region illustrates main biogeographical features of the Sahara‐Sahel and supports recently hypothesised dispersal corridors and refugia. Micro‐scale water‐features present mostly in mountains have been associated with local biodiversity hotspots. However, the distribution of available data on vertebrates highlights current knowledge gaps that still apply to a large proportion of the Sahara‐Sahel. Current research is providing insights into key evolutionary and ecological processes, including causes and timing of radiation and divergence for multiple taxa, and associating the onset of the Sahara with diversification processes for low‐mobility vertebrates. Examples of phylogeographic patterns are showing the importance of allopatric speciation in the Sahara‐Sahel, and this review presents a synthetic overview of the most commonly hypothesised diversification mechanisms. Studies are also stressing that biodiversity is threatened by increasing human activities in the region, including overhunting and natural resources prospection, and in the future by predicted global warming. A representation of areas of conflict, landmines, and natural resources extraction illustrates how human activities and regional insecurity are hampering biodiversity research and conservation. Although there are still numerous knowledge gaps for the optimised conservation of biodiversity in the region, a set of research priorities is provided to identify the framework data needed to support regional conservation planning.

Phylogeny of North African Agama lizards (Reptilia: Agamidae) and the role of the Sahara desert in vertebrate speciation

The origin of Saharan biodiversity is poorly understood, in part because the geological and paleoclimatic events that presumably shaped species diversity are still controversial, but also because few studies have explored causal explanations for the origin of Saharan diversity using a phylogenetic framework. Here, we use mtDNA (16S and ND4 genes) and nDNA (MC1R and CMOS genes) to infer the relationships and biogeographic history of North African agamas (genus Agama). Agamas are conspicuous, diverse and abundant African lizards that also occur in the Saharan xeric and mesic environments. Our results revealed the presence of three Agama lineages in North Africa: one Afrotropical, one Sahelo-Saharan, and one broadly distributed in North Africa and mainly Saharan. Southern Mauritania contains the highest known diversity, with all three lineages present. Results suggest that agamas colonized the Sahara twice, but only one lineage was able to radiate and diversify there. Species in the Saharan lineage are mostly allopatric, and their splitting, genetic diversity and distribution are greatly explained by mountain ranges. One species in this lineage has colonized the Mediterranean climatic zone (A. impalearis), and another one the Sahel savannah (A. boueti). The other lineage to colonize the Sahara corresponds to A. boulengeri, an eminently Sahelian species that also inhabits Saharan mountain ranges in Mauritania and Mali. Phylogenetic analyses indicate that allopatric montane populations within some currently recognized species are also genetically divergent. Our study therefore concludes that vicariant speciation is a leading motor of species diversification in the area: Inside the Sahara, associated to mountain-ranges isolated by dune seas and bare plains; outside, associated to less harsh climates to the North and South. Paleoclimatic oscillations are suggested as causal explanations of the vicariant distribution and origin of species. Agamas are thought to have colonized northern Africa during wet periods, with subsequent dry periods fragmenting species distribution and leading to allopatric populations associated to milder and wetter climates in the Mediterranean, Sahel, and in Saharan mountains, in an island-model fashion. Finally, our results support the synonymization of A. castroviejoi with A. boueti, the reciprocal monophyly of all other North African agamas, and suggest one candidate species within A. boulengeri.

Phylogeny, phylogeography, and evolution in the Mediterranean region: news from a freshwater mussel (Potomida, Unionida)

The Potomida genus (Bivalvia, Unionida) has a Circum-Mediterranean distribution and like other freshwater mussel species, its populations have suffered dramatic declines. Although this genus is currently considered as monotypic, it has a long history of taxonomic revisions and presently many aspects of its systematics and evolutionary history are unclear. We sampled a total of 323 individuals from 39 different sites across the Potomida genus distribution, and sequenced two mitochondrial (16S rDNA and Cytochrome c Oxidase Subunit I) and one nuclear (28S rDNA) genes to clarify its phylogeny and phylogeographic history. Our results show that the genus includes two well-supported clades, one comprising solely the western Mediterranean species Potomida littoralis, and the other including two eastern Mediterranean species, the Greek endemic P. acarnanica and the Anatolian and Middle Eastern P. semirugata. We suggest that Potomida started radiating during the upper Miocene, and that both vicariance and dispersal events shaped the diversification and distribution of the genus along the Mediterranean region. P. littoralis is further divided in two mitochondrial lineages, one restricted to Europe and the other occurring mostly in North Africa. Moreover, some European basins present both lineages in sympatry. The conservation status of the three recognized species should be reevaluated, particularly P. acarnanica, since it is restricted to two Greek river basins presenting a high risk of extinction. Overall, our results clarify some important gaps in knowledge concerning the phylogeny, phylogeography and evolution of the Potomida genus in the Mediterranean region with important taxonomical, ecological and conservational implications.

Nuclear and mitochondrial markers reveal the existence of several geographically concordant lineages within a Sahelian gecko species, Ptyodactylus ragazzii

The genetic diversity within Ptyodactylus ragazzii was analysed for the first time across the Western part of its range. We have used two mitochondrial (12s rRNA and 16s rRNA) and one nuclear (Cmos) marker to compare results directly with other related Ptyodactylus species, P. oudrii and P. hasselquistii. Results show high levels of intraspecific variability, with at least three divergent mtDNA lineages that have different haplotypes for Cmos and that are geographically concordant. P. ragazzii from Mauritania is probably a distinct species and possibly other lineages too, such as those from the Air Mountains in Niger, although more nuclear markers are needed to confirm this. All analysed Ptyodactylus species appear to be cryptic species complexes containing multiple deeply divergent forms, highlighting the need for a careful reassessment of the taxonomy of the whole genus.

The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa

Highlands, hydrographic systems and coastal areas have been hypothesised to form corridors across the hyperarid Sahara desert in North Africa, allowing dispersal and gene flow for non-xeric species. Here we aim to provide a genetic test for the trans-Saharan corridor model, and predict the location and stability of ecological-corridors, by combining phylogeography and palaeoclimatic modelling. The model was the Psammophis schokari (Schokari sand racer) group, fast-moving and widely distributed generalist colubrids occurring mostly in arid and semiarid scrublands. We combined dated phylogenies of mitochondrial and nuclear markers with palaeoclimatic modelling. For the phylogeographic analysis, we used 75 samples of P. schokari and P. aegyptius, and Bayesian and Maximum-Likelihood methods. For the ecological models, we used Maxent over the distribution of P. schokari and West African lineages. Models were projected to past conditions (mid Holocene, Last Glacial Maximum and Last Inter-Glacial) to infer climatic stable areas. Climatic stability was predicted to be mostly restricted to coastal areas and not spatially continuous. A putative temporary trans-Saharan corridor was identified in Eastern Sahara, with a more stable one along the Atlantic coast. Six parapatric lineages were identified within P. schokari, four occurring in North Africa. These likely diverged during the Pliocene. The Tamanraset River might have been a vicariant agent. African lineages may have experienced further subsequent diversification during the late Pleistocene. The main P. schokari refugia were probably located along the northern margins of the Sahara, allowing its North-to-South colonization. Trans-Saharan corridors seem to have played a role in P. schokari biogeography, allowing colonization of central Saharan mountains and Sahel. Some might have worked as refugia, and even the most stable corridors may have sections working as filters, depending on each climatic phase. We expect the use of trans-Saharan corridors to decrease for more mesic species or with less dispersal capabilities.

Distribution, suitable areas and conservation status of the Boulenger’s agama (Agama boulengeri, Lataste 1886)

Agama boulengeri is a West African endemic lizard. It occurs in arid rocky areas in the Mauritanian mountains and Kayes region of Mali. Data on the distribution of Agama boulengeri is however very coarse, and the contribution of climatic and habitat factors for population isolation are unknown. Using Maxent, GLM, and high-resolution data, we generated environmental niche models, and quantified suitable areas for species occurrence. Field observations and predicted suitable areas were used to evaluate the conservation status of Agama boulengeri. Results revealed the species occurs preferentially close to gueltas, bare areas, and rocky deserts and in areas of increasing rainfall. Suitable cells were mostly located in Mauritania, and four potentially fragmented subpopulations were identified. The conservation status of Agama boulengeri was determined to be of Least Concern.