Biogeographic inferences across spatial and evolutionary scales

The field of biogeography unites landscape genetics and phylogeography under a common conceptual framework. Landscape genetics traditionally focuses on recent-time, population-based, small geographic scale, spatial genetics processes, while phylogeography typically investigates deep past, lineage- and species-based processes at large geographic scales. Here, we evaluate the link between landscape genetics and phylogeographic methods using the Western Fence lizard (Sceloporus occidentalis) as a model species. First, we conducted replicated landscape genetics studies across several geographic scales to investigate how population genetics inferences change depending on the spatial extent of the study area. Then, we carried out a phylogeographic 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 proces..., ddRAD LIBRARY PREPARATION AND GENOMIC SEQUENCING
We followed Peterson et al.'s (2012) method for genomic library preparation, with some modifications. For each individual, we extracted high-molecular-weight genomic DNA using a standard phenol-chloroform extraction protocol (Tsai et al. 2019). We measured DNA concentrations using a Qubit fluorometer, and for each sample, we digested 0.5 μg of DNA for 3 hours with SbfI and NIaIII restriction enzymes. We then purified these fragments with Agencourt AMPure beads before ligation of barcoded Illumina adaptors onto the fragment ends. All barcodes differed by at least two base pairs to reduce duplexing error rates. We then pooled equimolar amounts of each sample before conducting size selection using a Pippin Prep to select fragments between 400 and 550 bp in length. We used proofreading Taq and Illumina’s index primers for final library amplification for 8-10 cycles to reduce PCR bias. We quantified the final library concentration using a Qubi...,