AbstractAimThe 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 and cladogenesis, but also promoted secondary contact and erosion of genetic divergence. Here we tested whether geographical diversification – or its lack thereof – in a complex of arboreal alligator lizards is explained by range shifts during Quaternary climatic oscillations.LocationPine–oak and cloud forests, central Mexico.TaxonAbronia taeniata–gramineaspecies complex (Squamata: Anguidae: Gerrhonotinae).MethodsWe generated genomic data (ddRADseq) to infer patterns of geographical diversification in the complex, 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).ResultsGenomic 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.Main ConclusionsThe geographical diversification of the complex has been moulded 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.
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