Phylogenomics of arboreal alligator lizards shed light on the geographical diversification of cloud forest-adapted biotas

The proximate ecological and evolutionary processes underlying the high biodiversity of neotropical montane cloud forests are still very poorly understood. Here we tested whether geographical diversification - or its lack thereof - in a complex of arboreal alligator lizards distributed in cloud forests from central Mexico is explained by range shifts during Quaternary climatic oscillations, which might have hypothetically contributed to vicariance and cladogenesis but also promoted secondary contact and erosion of genetic divergence. We generated genomic data (ddRADseq) to infer patterns of geographical diversification in the Abronia taeniata-graminea species complex (Squamata: Anguidae: Gerrhonotinae), reconstruct its demographic history, estimate the timing of lineage split, and test for the presence of contemporary and/or historical hybridization. We evaluated whether the tempo and mode of diversification (i.e., strict isolation vs. secondary contact with introgression) are explained by the contemporary distribution of suitable habitats and/or range shifts experienced by the complex since the Last Glacial Maximum (LGM), as inferred from environmental niche modelling (ENM). Genomic data supported a marked genetic structure within the complex, and phylogenomic and dating analyses revealed cryptic lineage diversification starting at the onset of the Pleistocene followed by secondary contact with limited introgression. ENM pointed to considerable range expansions of the complex during the LGM and a marked fragmentation and scarce connectivity among contemporary populations, which was supported by genomic-based demographic reconstructions. The geographical diversification of the complex has been molded by vicariant events promoted by Pleistocene geologic and climatic changes impacting the distribution of their pine-oak and cloud forest habitats. Our data supported a model of divergence with introgression, indicating that pulses of population fragmentation and expansion during the Quaternary have led to multiple opportunities for both allopatric isolation and secondary contact.