Genomic data now permit investigations into speciation that yield unprecedented detail on processes of diversification. In herpetology, this has helped cement broad understanding of relationships within amphibians and major reptile groups (Burbrink et al. 2020; Milián-Garcia et al. 2020; Singhal et al. 2020; Hime et al. 2021), as well as revealing that hybridization and introgression are common at both deep and shallow phylogenetic scales (O’Connell et al. 2017; Portik et al. 2017; Leaché et al. 2020; Myers et al. 2020; Reyes-Velasco et al. 2020). Furthermore, phylogeographic studies since the naming of the field (Avise et al. 1987) have increasingly shown that many wideranging species are composed of multiple geographic lineages, and that these evolutionarily lineages often conflict with traditional, taxonomic arrangements that are typically based on a few morphological characters (Leaché et al. 2002; Lemmon et al. 2007; Burbrink et al. 2008; Myers et al. 2013; Burbrink and Guiher 2015; Weinell and Austin 2017; Cox et al. 2018).
Many studies have demonstrated that divergence with gene flow either in primary or secondary contact is a common part of the speciation process, and that strict reproductive isolation is often not observed across the genome. Differential isolation across the genomes of geographic lineages is possible, with some chromosomal regions showing low levels of introgression and others showing considerable admixture (Canestrelli et al. 2015; Martin et al. 2019; Burbrink et al. 2021). Nevertheless, it is possible for ancient lineages to persist in the face of ongoing gene flow dating back as early as the Miocene (e.g., Barth et al. 2020). Additionally, migration may not be equal for all loci, as some alleles are adapted to particular environments and resist introgression. This differential level of migration among loci is expected under a process of speciation with ecological adaptation via natural selection (Mayr 1963; Van Valen 1976; Coyne and Orr 2004; Nosil 2008, 2012; Feder et al. 2012; Harrison and Larson 2014; Ravinet et al. 2017).