Data from: Historical mitochondrial genome introgression confounds species delimitation—evidence from phylogenetic inference in the Odorrana grahami species complex

Species delimitation is essential to informing conservation policy and
understanding ecological and evolutionary processes. Most of our recent
gains in knowledge on animal diversity rely on morphological
characteristics and mitochondrial (mt) DNA variation. Concordant results
based on both have led to an unprecedented acceleration in the
identification of new species and enriched the field of taxonomy. However,
discordances are also found commonly between morphological and mtDNA
evidence. This confounds species delimitation, especially when gene flow
or mitochondrial genome introgression has occurred. Here we illustrate how
mitochondrial genome introgression among species of the Odorrana grahami
complex confounds species delimitation using the combined evidence of
morphological characters, mitochondrial variation, and thousands of
nuclear single nucleotide polymorphisms (SNPs) from
genotyping-by-sequencing (GBS). Fifty-eight samples across the
distribution of the O. grahami complex were included. The mtDNA
matrilineal genealogy indicated two clades, with O. grahami and O.
junlianensis clustered together. In contrast, all nuclear evidence
including gene trees, species trees, and genetic structure analyses based
on GBS data support three species with distinct genetic clusters. These
three distinct genetic clusters also correspond to distinct morphological
characters. They affirm the distinct taxonomic entities of both O. grahami
and O. junlianensis, as well as a third clade distinct from either. Which
species the third clade belongs to remains unclear and will require
further testing. The nuclear genomic loci contradict the COI evidence,
with indications of rampant historical mitochondrial genome introgression
among the species of the O. grahami complex. These discordant signals
previously confused species delimitation efforts in this group. Based on
these findings, we recommend the integration of independent data,
especially nuclear genomic evidence, in species delimitation so as to be
robust against the pitfalls of mitochondrial introgression.