Advances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive the formation of mountain biotas. These span from broad biogeographic patterns to population dynamics and adaptations to these environments. However, significant challenges remain in integrating large-scale and fine-scale findings to develop a comprehensive understanding of mountain biodiversity. One significant challenge is the lack of genomic data, especially in historically understudied arid regions where reptiles are a particularly diverse vertebrate group. In the present study, we assembled a de novo genome-wide SNP dataset for the complete endemic reptile fauna of a mountain range (19 described species with more than 600 specimens sequenced), and integrated state-of-the-art biogeographic analyses at the population, species, and community level. Thus, we provide a holistic integration of how a whole endemic reptile community has originated, diversified and dispersed through a mountain system. Our results show that reptiles independently colonized the Hajar Mountains of southeastern Arabia 11 times. After colonization, species delimitation methods suggest high levels of within-mountain diversification, supporting up to 49 deep lineages. This diversity is strongly structured following local topography, with the highest peaks acting as a broad barrier to gene flow among the entire community. Interestingly, orogenic events do not seem key drivers of the biogeographic history of reptiles in this system. Instead, past climatic events seem to have had a major role in this community assemblage. We observe an increase of vicariant events from Late Pliocene onwards, coinciding with an unstable climatic period of rapid shifts between hyper-arid and semiarid conditions that led to the ongoing desertification of Arabia. We conclude that paleoclimate, and particularly extreme aridification, acted as a main driver of diversification in arid mountain systems which is tangled with the generation of highly adapted endemicity. Overall, our study does not only provide a valuable contribution to understanding the evolution of mountain biodiversity, but also offers a flexible and scalable approach that can be reproduced into any taxonomic group and at any discrete environment.

BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Campus deVairão 4485 661 Vairão Portugal

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

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

Department of Biodiversity Ecology and Evolution Faculty of Biology Universidad Complutense de Madrid 28040 Madrid Spain

Department of Zoology Faculty of Science Charles University 128 00 Prague Czech Republic

Environment Authority Muscat Oman

Institute of Evolutionary Biology Passeig Marítim de la Barceloneta 37 49 08003 Barcelona Spain

Museo Nacional de Ciencias Naturales CSIC C José Gutiérrez Abascal 2 28006 Madrid Spain

Museu de Ciències Naturals de Barcelona P° Picasso s n Parc Ciutadella 08003 Barcelona Spain

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