Biogeographic inferences across spatial and evolutionary scales

Abstract

The field of biogeography unites landscape genetics and phylogeography under a common conceptual framework. Landscape genetics traditionally focuses on recent‐time, population‐based, spatial genetics processes at small geographical scales, while phylogeography typically investigates deep past, lineage‐ and species‐based processes at large geographical scales. Here, we evaluate the link between landscape genetics and phylogeographical methods using the western fence lizard (Sceloporus occidentalis) as a model species. First, we conducted replicated landscape genetics studies across several geographical scales to investigate how population genetics inferences change depending on the spatial extent of the study area. Then, we carried out a phylogeographical study of population structure at two evolutionary scales informed by inferences derived from landscape genetics results to identify concordance and conflict between these sets of methods. We found significant concordance in landscape genetics processes at all but the largest geographical scale. Phylogeographical results indicate major clades are restricted to distinct river drainages or distinct hydrological regions. At a more recent timescale, we find minor clades are restricted to single river canyons in the majority of cases, while the remainder of river canyons include samples from at most two clades. Overall, the broad‐scale pattern implicating stream and river valleys as key features linking populations in the landscape genetics results, and high degree of clade specificity within major topographic subdivisions in the phylogeographical results, is consistent. As landscape genetics and phylogeography share many of the same objectives, synthesizing theory, models and methods between these fields will help bring about a better understanding of ecological and evolutionary processes structuring genetic variation across space and time.

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

“…The species comprises 5 geographically structured subspecies, all of which occur in California, with 1 former subspecies ( S. o. becki ) recently elevated to species status ( S. becki ; Salerno et al 2023 ). S. occidentalis also exhibits fine-scale genetic structure ( Wishingrad and Thompson 2023 ) and a complex biogeographic history that includes divergence in a ring-like pattern as populations expanded northward across the Sierra Nevada and coast ranges ( Bouzid et al 2022 ).…”