Hidden in the Arabian Mountains: Multilocus phylogeny reveals cryptic diversity in the endemicOmanosauralizards

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

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, spatial, and environmental processes that can obfuscate phylogenetic inference and bias 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 widespread, phenotypically conserved, and exhibits high levels of geographically-based 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 five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches 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. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

Dispersal beyond geographic barriers: a contribution to the phylogeny and demographic history of Pristurus rupestris Blanford, 1874 (Squamata: Sphaerodactylidae) from southern Iran

Pristurus rupestris is a member of Semaphore geckos with a wide distribution range. Recently, 14 candidate species of P. rupestris rupestris have been identified in the Hajar Mountains (Arabia), yet the knowledge on the Iranian counterparts is limited. The present study elucidates the phylogenetic position of the Iranian P. rupestris and investigates the hypothesis on its historical colonization from Oman to Iran and the associated islands. Therefore, 20 Iranian specimens along with 115 individuals from Oman were examined using two mitochondrial genes including the Cytochrome b and the 12S ribosomal RNA. The molecular phylogenetic analyses revealed that the individuals collected from Iran are well nested within the candidate Species 3 of P. r. rupestris, demonstrating a single population with high gene flow. Additionally, the molecular analyses showed that the genetic diversity within the Iranian Blanford's Semaphore geckos is low and that the candidate Species 3 experienced a recent expansion approximately 17 thousand years ago (Kya). The historical demographic analyses (BSP) showed a mild increase in the effective population size between 15-20 Kya. These time estimations coincide with the Last Glacial Maximum, when the Persian Gulf was almost dry, reinforcing the hypothesis that the species might have colonized southern Iran from Oman through the Persian Gulf. In addition, we propose P. r. iranicus to be synonymized with P. r. rupestris.