Delimiting phylogeographic diversity in the genomic era: application to an Iberian endemic frog

The rich genetic and phenotypic diversity of species complexes is best recognized through formal taxonomic naming, but one must first assess the evolutionary history of phylogeographic lineages to identify and delimit candidate taxa. Using genomic markers, mitochondrial DNA barcoding, and morphometric analyses, we examined lineage diversity and distribution in the Iberian endemic frog Rana parvipalmata. We confirmed two deep phylogeographic lineages, one relatively homogenous genetically, found in Asturias and adjacent areas (T2), and one more fragmented and locally genetically impoverished, restricted to Galicia (T1). Analyses of their hybrid zone suggested a shallow transition characterized by far-ranging admixture, which was modelled by a wide geographic cline (similar to 60 km for the genome average) and no obvious barrier loci (i.e. loci showing disproportionally restricted introgression). The relatively young T1 and T2 have thus remained reproductively compatible, which argues against their distinction as biological species, and we accordingly describe T2 as a new subspecies, Rana parvipalmata asturiensis ssp. nov. Remarkably, we highlight striking discordances between mitochondrial and nuclear distributions across their hybrid zones, as well as between their genetic and morphological differentiation. Our study illustrates how genomic-based phylogeographic frameworks can help decipher the high genetic and phenotypic variation of species complexes and substantiate the taxonomic assessment of candidate lineages.

Automated summary

Using genomic markers, mitochondrial DNA barcoding, and morphometric analyses, this study examined the lineage diversity and distribution of the Iberian endemic frog, Rana parvipalmata. Two distinct lineages were identified, one genetically homogenous in Asturias and adjacent areas (T2), and one more fragmented and genetically impoverished in Galicia (T1). Analysis of their hybrid zone suggested a shallow transition characterized by far-reaching admixture, without obvious barrier loci. The study highlights the importance of genomic-based phylogeographic frameworks in understanding genetic and phenotypic variation and supporting taxonomic assessment.