Range-wide genomic differentiation is driven by geography and climate in <i>Agave cerulata</i> Trel. (Asparagaceae), an endemic <i>Agav</i> e complex of the Baja California Peninsula

Abstract Identification of the spatial distribution of genetic variation is a central goal of evolutionary biology that can elucidate the mechanisms of evolution and speciation, shed light on the processes that affect geographical ranges, and locate populations of conservation concern. Genomic studies of species exhibiting high morphological variability adapted to heterogeneous landscapes may be particularly informative. Agave cerulata Trel. is one of the most abundant Agave species, represented by three subspecies and one variety, distributed along the latitudinal and climatic gradients of the Baja California Peninsula. By analysing over 50 000 single nucleotide polymorphisms from 39 populations sampled across the species’ distribution, we determined how selection and drift have shaped the genomic structure and diversity of A. cerulata. Moreover, we tested for concordance between genetic structure and morphological subspecies and answered long-standing questions regarding the subspecies/variety status of A. cerulata. Our data support the presence of two major regional genomic clusters, with the spatial distribution of genomic diversity driven by Holocene range expansion. Furthermore, the patterns of fine-scale genetic differentiation differed between the two regional clusters. In northern Baja California, neutral factors, such as isolation by distance and gene flow, have contributed to high admixture and low population divergence. In the southern group, differentiation was stronger and was associated with climate, particularly temperature extremes and precipitation seasonality. Finally, our data revealed a more complex pattern of population structuring than that suggested by morphological subspecies designations, with mixed support for the currently recognized taxonomic boundaries on the Baja California Peninsula.