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

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