Admixture Underlies Cryptic Diversity in Philippine Puddle-frogs (Occidozyga laevis). Occidozyga

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, which has been shown to obfuscate phylogenetic inference and species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle-frogs, a group that is phenotypically cryptic and exhibits high levels of genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of four distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the four groups and explicate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. Furthermore, the relationship between mitochondrial and nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and consequently, species diversity. Overall, we showed that the high levels of genetic diversity in Philippine Puddle-frogs predominantly comprises metapopulation lineages that arose through complex patterns of admixture as opposed to species divergence. Our findings call into question the prevalence of hidden cryptic diversity throughout the tree of life, indicating that a paradigm shift in the way we conceptualize cryptic species diversity is warranted.