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

Citation

Wu, Dongyi et al. (2022), Data from: Historical mitochondrial genome introgression confounds species delimitation—evidence from phylogenetic inference in the Odorrana grahami species complex, Dryad, Dataset, https://doi.org/10.5061/dryad.tmpg4f50v

Abstract

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.

Funding

Ministry of Science and Technology of the People's Republic of China, Award: 2021FY100203

Digitalization, Development and Application of Biotic Resource, Award: 202002AA100007

Science and Technology Bureau of Yunnan, Award: 02102AA310055

China Association for Science and Technology, Award: 2019-2021QNRC001

Second Tibetan Plateau Scientific Expedition and Research Program, Award: 2019QZKK0501

Science and Technology Bureau of Yunnan, Award: 202005AC160046

Science and Technology Bureau of Yunnan, Award: 202001AW070016