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 characteristic...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.展开更多
Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology.In this study,we generated a time-calibrated ph...Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology.In this study,we generated a time-calibrated phylogeny of Scutiger boulengeri,an endemic Xizang alpine toad occurring in mountain streams on the Qinghai-Xizang(Tibet)Plateau(QTP).Based on three mitochondrial DNA(mt DNA)genes,eight clades were assigned to three deeply divergent lineages.Analysis of nuclear DNA(nu DNA)genes revealed three distinct clusters without geographic structure,indicating significantly high rates of gene flow.Coalescent theory framework analysis(approximate Bayesian computation model DIYABC and Migrate-N)suggested that divergence of the main intraspecific clusters was the result of hybridization after secondary contact in the Holocene around 0.59 million years ago(Ma).The ratio of mt DNA FST(fixation index)to nu DNA FST was 2.3,thus failing to show male-biased dispersal.Geographic cline analysis showed that a wide hybrid zone was initially established in southwestern China,without significant reproductive isolation but with strong introgression in S.boulengeri,suggesting high hybrid fitness.Furthermore,mt DNA genes exhibited isolation by distance(IBD)while nu DNA genes exhibited significant isolation by environment(IBE).Results suggested that mitonuclear discordance may have initially been caused by geographic isolation,followed by precipitation-mediated hybridization,producing a wide hybrid zone and geographic structure confusion of nu DNA genes in S.boulengeri.This study indicated that complicated historical processes may have led to specific genetic patterns,with a specific climate factor facilitating gene flow in the system.展开更多
The Hengduan Mountains Region(HMR)is the largest“evolutionary frontier”of the northern temperate zone,and the origin and maintenance of species in this area is a research hotspot.Exploring species-specific responses...The Hengduan Mountains Region(HMR)is the largest“evolutionary frontier”of the northern temperate zone,and the origin and maintenance of species in this area is a research hotspot.Exploring species-specific responses to historical and contemporary environmental changes will improve our understanding of the role of this region in maintaining biodiversity.In this study,mitochondrial and microsatellite diversities were used to assess the contributions of paleogeological events,Pleistocene climatic oscillations,and contemporary landscape characteristics to the rapid intraspecific diversification of Liangshantriton taliangensis,a vulnerable amphibian species endemic to several sky-island mountains in the southeastern HMR.Divergence date estimations suggested that the East Asian monsoon,local uplifting events(Xigeda Formation strata),and Early-Middle Pleistocene transition(EMPT)promoted rapid divergence of L.taliangensis during the Pleistocene,yielding eight mitochondrial lineages and six nuclear genetic lineages.Moreover,population genetic structures were mainly fixed through isolation by resistance.Multiple in situ refugia were identified by ecological niche models and high genetic diversity,which played crucial roles in the persistence and divergence of L.taliangensis during glacial-interglacial cycles.Dramatic climatic fluctuations further promoted recurrent isolation and admixing of populations in scattered glacial refugia.The apparent mitonuclear discordance was likely the result of introgression by secondary contact and/or female-biased dispersal.Postglacial expansion generated two major secondary contact zones(Ganluo(GL)and Chuhongjue(CHJ)).Identification of conservation management units and dispersal corridors offers important recommendations for the conservation of this species.展开更多
基金supported by grants from the Ministry of Science and Technology of the People’s Republic of China(2022YFC2602500,2021FY100203)the DigitalizationDevelopment and Application of Biotic Resource(202002AA100007)+4 种基金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).
文摘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.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research Program(STEP,2019QZKK05010503)Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment,China(2019HJ2096001006)+1 种基金Construction of Basic Conditions Platform of Sichuan Science and Technology Department(2019JDPT0020)China Biodiversity Observation Networks(Sino BON)。
文摘Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology.In this study,we generated a time-calibrated phylogeny of Scutiger boulengeri,an endemic Xizang alpine toad occurring in mountain streams on the Qinghai-Xizang(Tibet)Plateau(QTP).Based on three mitochondrial DNA(mt DNA)genes,eight clades were assigned to three deeply divergent lineages.Analysis of nuclear DNA(nu DNA)genes revealed three distinct clusters without geographic structure,indicating significantly high rates of gene flow.Coalescent theory framework analysis(approximate Bayesian computation model DIYABC and Migrate-N)suggested that divergence of the main intraspecific clusters was the result of hybridization after secondary contact in the Holocene around 0.59 million years ago(Ma).The ratio of mt DNA FST(fixation index)to nu DNA FST was 2.3,thus failing to show male-biased dispersal.Geographic cline analysis showed that a wide hybrid zone was initially established in southwestern China,without significant reproductive isolation but with strong introgression in S.boulengeri,suggesting high hybrid fitness.Furthermore,mt DNA genes exhibited isolation by distance(IBD)while nu DNA genes exhibited significant isolation by environment(IBE).Results suggested that mitonuclear discordance may have initially been caused by geographic isolation,followed by precipitation-mediated hybridization,producing a wide hybrid zone and geographic structure confusion of nu DNA genes in S.boulengeri.This study indicated that complicated historical processes may have led to specific genetic patterns,with a specific climate factor facilitating gene flow in the system.
基金supported by the National Key Research and Development Programs of China(2017YFC0505202)Construction of Basic Conditions Platform of Sichuan Science and Technology Department(2019JDPT0020)Species Conservation Project of Liziping National Nature Reserve。
文摘The Hengduan Mountains Region(HMR)is the largest“evolutionary frontier”of the northern temperate zone,and the origin and maintenance of species in this area is a research hotspot.Exploring species-specific responses to historical and contemporary environmental changes will improve our understanding of the role of this region in maintaining biodiversity.In this study,mitochondrial and microsatellite diversities were used to assess the contributions of paleogeological events,Pleistocene climatic oscillations,and contemporary landscape characteristics to the rapid intraspecific diversification of Liangshantriton taliangensis,a vulnerable amphibian species endemic to several sky-island mountains in the southeastern HMR.Divergence date estimations suggested that the East Asian monsoon,local uplifting events(Xigeda Formation strata),and Early-Middle Pleistocene transition(EMPT)promoted rapid divergence of L.taliangensis during the Pleistocene,yielding eight mitochondrial lineages and six nuclear genetic lineages.Moreover,population genetic structures were mainly fixed through isolation by resistance.Multiple in situ refugia were identified by ecological niche models and high genetic diversity,which played crucial roles in the persistence and divergence of L.taliangensis during glacial-interglacial cycles.Dramatic climatic fluctuations further promoted recurrent isolation and admixing of populations in scattered glacial refugia.The apparent mitonuclear discordance was likely the result of introgression by secondary contact and/or female-biased dispersal.Postglacial expansion generated two major secondary contact zones(Ganluo(GL)and Chuhongjue(CHJ)).Identification of conservation management units and dispersal corridors offers important recommendations for the conservation of this species.
