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

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Current Zoology 2023年第1期69卷 82-90页

作者： Zhiyong Yuan Dongyi Wu Yang Wen Wei Xu Wei Gao Hollis A.Dahn Xiaolong Liu Jieqiong Jin Chuanxin Yu Heng Xiao Jing Che Key Laboratory of Freshwater Fish Reproduction and Development(Ministry of Education) School of Life SciencesSouthwest UniversityChongqing 400715China Key Laboratory for Conserving Wildlife with Small Populations in Yunnan Southwest Forestry UniversityKunming 650224China School of Life Sciences Yunnan UniversityKunming 650091China School of Ecology and Environment Sciences Yunnan UniversityKunming 650091China State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Department of Ecology and Evolutionary Biology University of TorontoTorontoOntarioCanada

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 mt genome introgression has occurred.Here,we illustrate how mt genome introgression among species of the Odorrana grahami complex confounds species delimitation using the combined evidence of morphological characters,mt 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 2 clades,with O.grahami and Odorrana junlianensis clustered together.In contrast,all nuclear evidence including gene trees,species trees,and genetic structure analyses based on GBS data support 3 species with distinct genetic clusters.These 3 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 mt 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 mt introgression.

关键词： gene flow ghost lineage integrative species delimitation mitonuclear concordance phylogenomic inference

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