The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Böhme's sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we sequenced one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.

Agencia de Medio Ambiente y Agua de Andalucía C Johan G Gutenberg 1 41092 Seville Spain

Breeding Centre for Endangered Arabian Wildlife Environment and Protected Areas Authority Sharjah United Arab Emirates

CEFE CNRS Univ Montpellier EPHE IRD Montpellier France

CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Campus de Vairão Universidade do Porto 4485 661 Vairão Portugal

CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Campus de Vairão Universidade do Porto 4485 661 Vairão Portugal; BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Campus de Vairão 4485 661 Vairão Portugal

Department of Biology Faculty of Education Aden University Yemen

Department of Zoology Faculty of Science Charles University Vinicná 7 Prague Czech Republic

Institute of Evolutionary Biology Barcelona Spain

Institute of Evolutionary Biology Barcelona Spain; Department of Biodiversity Ecology and Evolution Faculty of Biology Universidad Complutense de Madrid 28040 Madrid Spain

Institute of Evolutionary Biology Barcelona Spain; Museu de Ciències Naturals de Barcelona P° Picasso s n Parc Ciutadella 08003 Barcelona Spain

National Center for Wildlife Prince Saud Al Faisal Wildlife Research Centre Taif Saudi Arabia

Universidad de Vigo Facultad de Biología Edificio de Ciencias Experimentales Bloque B Planta 2 Laboratorio 39 E 36310 Vigo Spain

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