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

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 

机构地区：[1]Key Laboratory of Freshwater Fish Reproduction and Development(Ministry of Education),School of Life Sciences,Southwest University,Chongqing 400715,China [2]Key Laboratory for Conserving Wildlife with Small Populations in Yunnan,Southwest Forestry University,Kunming 650224,China [3]School of Life Sciences,Yunnan University,Kunming 650091,China [4]School of Ecology and Environment Sciences,Yunnan University,Kunming 650091,China [5]State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming 650223,China [6]Department of Ecology and Evolutionary Biology,University of Toronto,Toronto,Ontario,Canada

出　　处：《Current Zoology》2023年第1期82-90,共9页动物学报（英文版）

基　　金：supported by grants from the Ministry of Science and Technology of the People’s Republic of China(2022YFC2602500,2021FY100203)the Digitalization;Development and Application of Biotic Resource(202002AA100007);programs from the Science and Technology Bureau of Yunnan(02102AA310055,202001AW070016,and 202005AC160046);Young talent project of China Association for Science and Technology(2019-2021QNRC001);the Second Tibetan Plateau Scientific Expedition and Research Program(2019QZKK0501);China’s Biodiversity Observation Network(Sino-BON);the Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(the Large Research Infrastructure Funding).

摘　　要：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 

分 类 号：Q95[生物学—动物学]