In metropolitan regions, the change in the strength of "flows" between a core city and surrounding cities re-flects the range of the core city's influence, while the gravity between core city and other c...In metropolitan regions, the change in the strength of "flows" between a core city and surrounding cities re-flects the range of the core city's influence, while the gravity between core city and other cities reflects the strength of potential relation between them. This article firstly attempts to delimit the boundary of metropolitan regions with the two dimensions measure combining "flows" and gravitation. The former is measured through the flow of people be-tween the core city and surrounding cities, and the latter is measured through both population and gross domestic products (GDP) of the core city and surrounding cities. The hierarchy of the cities within a metropolitan region is classified in order to emphasize the roles of the cities belonging to the metropolitan regions, different from the general way through population scale and administrative level, and is typical in China. This paper uses the Shanghai metropolitan region as a research case, determining boundary of this metropolitan region clearly and classifying hierarchy of the cities within the region. The final results are significantly different to previous work, even overthrowing the traditional system of urban hierarchy partly. It is helpful to highlight the function of cities in organizing the regional economy, the level structure of metropolitan regions, and each city's relative importance in a metropolitan region, which can be taken as scientific basis for planning integrated regions or urban systems.展开更多
Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades.Debregeasia(Urticaceae),an economically important ge...Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades.Debregeasia(Urticaceae),an economically important genus,presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments.Here,we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia.We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia.Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter-and intra-specific levels.Three Debregeasia species were non-monophyletic and could not be discerned by any barcode;however,ultra-barcodes identified the remaining six(67%),outperforming standard barcodes(56%).Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia,although the placement between Debregeasia hekouensis and Debregeasia libera varied.There was extensive trait overlap in key morphologically diagnostic characters,with reticulation analysis showing potentially pervasive hybridization,likely influenced by speciation patterns and overlaps between species ranges.We inferred that Debregeasia crown diversification began at ca.12.82 Ma(95%HPD:11.54-14.63 Ma)in the mid-Miocene within Australia,followed by vicariance and later longdistance dispersal,mainly out of southern China.Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.展开更多
The Ashy-headed Laughingthrush (Argya cinereifrons), a species endemic to Sri Lanka, has been historically considered a laughingthrush in the genus Garrulax. However, based on phylogenetic evidence, recent studies hav...The Ashy-headed Laughingthrush (Argya cinereifrons), a species endemic to Sri Lanka, has been historically considered a laughingthrush in the genus Garrulax. However, based on phylogenetic evidence, recent studies have suggested a new classification for the species under the genus Argya (true babblers). Despite the genetic signal showing affinity to true babblers Argya, as its common name suggests, the Ashy-headed Laughingthrush (AHLT) shows remarkable morphological similarities to other laughingthrushes of the Indo-Himalayan region. Here we attempted to address this incongruence in phenotypic and phylogenetic signals in this species by reconstructing the molecular phylogeny of babblers and comparing that with the key morphological, plumage, and vocal features of the two concerned groups. We hypothesized that the convergence of phenotype and vocalization of Garrulax in the wet evergreen forests of the Indian mainland and AHLT in the wet tropical rainforests of southern Sri Lanka has historically confused the taxonomists. The phylogenetic relationships were reconstructed using Bayesian inference using four mitochondrial and seven nuclear gene regions. The molecular phylogenetic tree placed the AHLT with India's Large Grey Babbler (A. malcolmi) as the sister taxon within the genus Argya. The hierarchical clustering based on body size, shape, plumage colour, and vocal properties resulted in the inconsistent placement of ALTH with babblers or laughingthrushes. Therefore, an incongruence in phenotype and genotype is observed. Our findings show that the convergent patterns of phenotypic evolution can confuse both historic and recent taxonomic delimitations in highly divergent groups such as Asian babblers.展开更多
The seismic hazard of research area is evaluated by probabilistic analysis method for three different seismic statis-tical zone scenarios. The influence of uncertainty in seismic statistical zone delimiting on the eva...The seismic hazard of research area is evaluated by probabilistic analysis method for three different seismic statis-tical zone scenarios. The influence of uncertainty in seismic statistical zone delimiting on the evaluation result is discussed too. It can be seen that for those local sites along zone's border or within areas with vast change of upper bound magnitude among different scenarios the influence on seismic hazard result should not be neglected.展开更多
This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five n...This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny （A00）, species tree estimation when the assignment and species delimitation are fixed （A01）, species delimitation using a fixed guide tree （A10）, and joint species delimitation and species-tree estimation or unguided species delimitation （A11）. For the joint analysis （A11）, two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis [Current Zoology 61 （5）： 854-865, 2015].展开更多
DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, par...DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, partly driven by the new sequencing technologies, the focus has shifted to multi-locus sequence data and the identification of species within the frame-work of the multi-species coalescent （MSC）. In this paper, I discuss model-based Bayesian methods for species delimitation that have been developed in recent years using the MSC. Several approximate methods for species delimitation （and their limitations） are also discussed. Explicit species delimitation models have the advantage of clarifying more precisely what is being delimited and what assumptions we are making in doing so. Moreover, the methods can be very powerful when applied to large multi-locus datasets and thus take full advantage of data generated using today＇s technologies [Current Zoology 61 （5）： 846-853,2015].展开更多
Geological anomaly is a geological body or geological body combination different from its surroundings in composition, structure, or genetic sequence. If there is a value (value interval ) that works as a valve repres...Geological anomaly is a geological body or geological body combination different from its surroundings in composition, structure, or genetic sequence. If there is a value (value interval ) that works as a valve representing the background field, exceeding or lower than the valve value,it is called a geological anomaly. Geological anomalies can be divided into high geological anomaly and low geological anomaly .The former shows the area that is more complex in composition, Structure or genetic sequence than its surroundings; while the latter just gives an opposite indication, i. e. much simpler. According to their distribution and delimitation markers, geological anomalies can be classified into (1)global geological anomaly; (2)regional geological anomaly; (3) local geological anomaly; (4) minor geological anomaly and (5)micro-geological anomaly .The methods for delimiting geological anomalies include (1)crustal elevation-subsidence coefficieat (G value ) determination; (2) geological complex coefficient (C value ) determination; (3) entropy (H value ) determination; (4) geological similarity coefficient (S value ) determination and (5 ) geological correlation coefficient (R value ) determination. As the result of the movements of Eurasian, Pacific and Indian Plates, the Chinese geological anomalies, including 11 regional ones and 32 main local ones, most Paleozoic in age, are distributed in strip on the margin or the outer and inner folded zones in the east and west arcs of the block symmetric arc tectonic system (BSATS), which controls the distribution of various minerals in China. Thus, geological anomaly theory is of great significance in searching for large, super-large and very large ore deposits.展开更多
Objective:To examine and study the morphology,epidemiology,and molecular phylogeny of Anisakis larvae in blue mackerel[Scomber australasicus(Cuvier,1832)]and Indian mackerel[Rastrelliger kanagurta(Cuvier,1816)]using l...Objective:To examine and study the morphology,epidemiology,and molecular phylogeny of Anisakis larvae in blue mackerel[Scomber australasicus(Cuvier,1832)]and Indian mackerel[Rastrelliger kanagurta(Cuvier,1816)]using light microscope,scanning electron microscope,molecular phylogeny,and species delimitation methods for confirmation and investigation of Anisakis species and their evolutionary relationship.Methods:A total of 90 fish(45 per species)were purchased from a department store in Chiang Mai,Thailand.Anisakis samples were investigated for morphological characteristics using light and scanning electron microscopes.Molecular phylogeny and species delimitation methods based on the cox2 gene were performed.Results:The prevalence,mean intensity(Mean±SEM),and mean abundance of Anisakis larvae(Mean±SEM)in blue mackerel were 77.78%,6.74±1.320,and 5.24±1.107,respectively,and in Indian mackerel,these values were 13.33%,2.50±0.764,and 0.33±0.159,respectively.Scanning electron microscopy showed the detail of morphological characteristics and provided the different shapes of mucron and excretory pores in Anisakis larvae congruent with the phylogenetic tree.The species tree was congruent with the phylogenetic tree.Conclusions:The prevalence,mean intensity,and mean abundance of Anisakis larvae were higher in blue mackerel.To the best of our knowledge,this is the first time that Anisakis pegreffii was found in blue mackerel in Thailand.The phylogenetic tree also supported the morphological data of Anisakis larvae.However,species delimitation based on cox2 revealed 1-3 possible cryptic species in this genus.Anisakis spp.contamination of fish products is unpleasant and a health concern considering human infection with larvae(anisakiasis)arises.展开更多
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
The Paramesotriton caudopunctatus species group is mainly distributed in the karst mountain ecosystems of Guizhou, China. Although some species have been included in previous phylogenetic studies, the evolutionary rel...The Paramesotriton caudopunctatus species group is mainly distributed in the karst mountain ecosystems of Guizhou, China. Although some species have been included in previous phylogenetic studies, the evolutionary relationships and divergence-time of members of this species group as a whole remain unexplored. In this study, we report the sequencing of one protein coding mitochondrial gene fragment(ND2) and one nuclear gene(POMC), and use a combination of phylogenetic analyses and coalescent simulations to explore the cryptic diversity and evolutionary history of the P. caudopunctatus species group. Phylogenetic relationships revealed that the P. caudopunctatus species group is composed of two major groups, i. e., East Clade and Western-South Clade. The divergence-time and ancestral area estimation suggested that the P. caudopunctatus species group likely originated in the Doupeng Mountains in Guizhou, China at 12.34 Ma(95% HPD: 8.30–14.73), and intraspecific divergence began at about 2.17 Ma(95% HPD: 1.39–2.97). This timing coincides with the orogenesis of the Miaoling Mountains during the Late Miocene to early Pleistocene. The delimitation of species in the P. caudopunctatus species group supports the existence of the currently identified species, and consensus was confirmed across methods for the existence of least to two cryptic species within what has been traditionally considered to be P. caudopunctatus species group. This study is of significance for understanding the species formation, dispersal, and diversity of the tailed amphibians in the karst mountains ecosystem of Guizhou and the role of the Miaoling Mountains as a geographical barrier to species dispersal.展开更多
基金Under the auspices of Shanghai Foundation Item for Philosophy and Social Sciences (No 2005BCK004)Research Center on Metropolitan Regions of China (No RCMRC 07006)
文摘In metropolitan regions, the change in the strength of "flows" between a core city and surrounding cities re-flects the range of the core city's influence, while the gravity between core city and other cities reflects the strength of potential relation between them. This article firstly attempts to delimit the boundary of metropolitan regions with the two dimensions measure combining "flows" and gravitation. The former is measured through the flow of people be-tween the core city and surrounding cities, and the latter is measured through both population and gross domestic products (GDP) of the core city and surrounding cities. The hierarchy of the cities within a metropolitan region is classified in order to emphasize the roles of the cities belonging to the metropolitan regions, different from the general way through population scale and administrative level, and is typical in China. This paper uses the Shanghai metropolitan region as a research case, determining boundary of this metropolitan region clearly and classifying hierarchy of the cities within the region. The final results are significantly different to previous work, even overthrowing the traditional system of urban hierarchy partly. It is helpful to highlight the function of cities in organizing the regional economy, the level structure of metropolitan regions, and each city's relative importance in a metropolitan region, which can be taken as scientific basis for planning integrated regions or urban systems.
基金funded by the National Natural Science Foundation of China(42171071,42211540718)Key Research Program of Frontier Sciences,CAS(ZDBS-LY-7001)+3 种基金Yunnan Fundamental Research Projects(202401AT070190,202201BC070001)Top-notch Young Talents Project of Yunnan Provincial“Ten Thousand Talents Program”(YNWR-QNBJ-2018-146,YNWR-QNBJ-2020-293)CAS“Light of West China”Programsupported by the China Scholarship Council(202304910135 and 202304910138)for a one-year study at the University of Toronto.
文摘Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades.Debregeasia(Urticaceae),an economically important genus,presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments.Here,we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia.We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia.Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter-and intra-specific levels.Three Debregeasia species were non-monophyletic and could not be discerned by any barcode;however,ultra-barcodes identified the remaining six(67%),outperforming standard barcodes(56%).Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia,although the placement between Debregeasia hekouensis and Debregeasia libera varied.There was extensive trait overlap in key morphologically diagnostic characters,with reticulation analysis showing potentially pervasive hybridization,likely influenced by speciation patterns and overlaps between species ranges.We inferred that Debregeasia crown diversification began at ca.12.82 Ma(95%HPD:11.54-14.63 Ma)in the mid-Miocene within Australia,followed by vicariance and later longdistance dispersal,mainly out of southern China.Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.
基金funded by the University of Colombo Research Grants,Sri Lanka(AP/3/2012/CG/15 and AP/3/2017/CG/27).
文摘The Ashy-headed Laughingthrush (Argya cinereifrons), a species endemic to Sri Lanka, has been historically considered a laughingthrush in the genus Garrulax. However, based on phylogenetic evidence, recent studies have suggested a new classification for the species under the genus Argya (true babblers). Despite the genetic signal showing affinity to true babblers Argya, as its common name suggests, the Ashy-headed Laughingthrush (AHLT) shows remarkable morphological similarities to other laughingthrushes of the Indo-Himalayan region. Here we attempted to address this incongruence in phenotypic and phylogenetic signals in this species by reconstructing the molecular phylogeny of babblers and comparing that with the key morphological, plumage, and vocal features of the two concerned groups. We hypothesized that the convergence of phenotype and vocalization of Garrulax in the wet evergreen forests of the Indian mainland and AHLT in the wet tropical rainforests of southern Sri Lanka has historically confused the taxonomists. The phylogenetic relationships were reconstructed using Bayesian inference using four mitochondrial and seven nuclear gene regions. The molecular phylogenetic tree placed the AHLT with India's Large Grey Babbler (A. malcolmi) as the sister taxon within the genus Argya. The hierarchical clustering based on body size, shape, plumage colour, and vocal properties resulted in the inconsistent placement of ALTH with babblers or laughingthrushes. Therefore, an incongruence in phenotype and genotype is observed. Our findings show that the convergent patterns of phenotypic evolution can confuse both historic and recent taxonomic delimitations in highly divergent groups such as Asian babblers.
基金Chinese Joint Seismological Science Foundation (100110).
文摘The seismic hazard of research area is evaluated by probabilistic analysis method for three different seismic statis-tical zone scenarios. The influence of uncertainty in seismic statistical zone delimiting on the evaluation result is discussed too. It can be seen that for those local sites along zone's border or within areas with vast change of upper bound magnitude among different scenarios the influence on seismic hazard result should not be neglected.
文摘This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny （A00）, species tree estimation when the assignment and species delimitation are fixed （A01）, species delimitation using a fixed guide tree （A10）, and joint species delimitation and species-tree estimation or unguided species delimitation （A11）. For the joint analysis （A11）, two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis [Current Zoology 61 （5）： 854-865, 2015].
文摘DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, partly driven by the new sequencing technologies, the focus has shifted to multi-locus sequence data and the identification of species within the frame-work of the multi-species coalescent （MSC）. In this paper, I discuss model-based Bayesian methods for species delimitation that have been developed in recent years using the MSC. Several approximate methods for species delimitation （and their limitations） are also discussed. Explicit species delimitation models have the advantage of clarifying more precisely what is being delimited and what assumptions we are making in doing so. Moreover, the methods can be very powerful when applied to large multi-locus datasets and thus take full advantage of data generated using today＇s technologies [Current Zoology 61 （5）： 846-853,2015].
文摘Geological anomaly is a geological body or geological body combination different from its surroundings in composition, structure, or genetic sequence. If there is a value (value interval ) that works as a valve representing the background field, exceeding or lower than the valve value,it is called a geological anomaly. Geological anomalies can be divided into high geological anomaly and low geological anomaly .The former shows the area that is more complex in composition, Structure or genetic sequence than its surroundings; while the latter just gives an opposite indication, i. e. much simpler. According to their distribution and delimitation markers, geological anomalies can be classified into (1)global geological anomaly; (2)regional geological anomaly; (3) local geological anomaly; (4) minor geological anomaly and (5)micro-geological anomaly .The methods for delimiting geological anomalies include (1)crustal elevation-subsidence coefficieat (G value ) determination; (2) geological complex coefficient (C value ) determination; (3) entropy (H value ) determination; (4) geological similarity coefficient (S value ) determination and (5 ) geological correlation coefficient (R value ) determination. As the result of the movements of Eurasian, Pacific and Indian Plates, the Chinese geological anomalies, including 11 regional ones and 32 main local ones, most Paleozoic in age, are distributed in strip on the margin or the outer and inner folded zones in the east and west arcs of the block symmetric arc tectonic system (BSATS), which controls the distribution of various minerals in China. Thus, geological anomaly theory is of great significance in searching for large, super-large and very large ore deposits.
文摘Objective:To examine and study the morphology,epidemiology,and molecular phylogeny of Anisakis larvae in blue mackerel[Scomber australasicus(Cuvier,1832)]and Indian mackerel[Rastrelliger kanagurta(Cuvier,1816)]using light microscope,scanning electron microscope,molecular phylogeny,and species delimitation methods for confirmation and investigation of Anisakis species and their evolutionary relationship.Methods:A total of 90 fish(45 per species)were purchased from a department store in Chiang Mai,Thailand.Anisakis samples were investigated for morphological characteristics using light and scanning electron microscopes.Molecular phylogeny and species delimitation methods based on the cox2 gene were performed.Results:The prevalence,mean intensity(Mean±SEM),and mean abundance of Anisakis larvae(Mean±SEM)in blue mackerel were 77.78%,6.74±1.320,and 5.24±1.107,respectively,and in Indian mackerel,these values were 13.33%,2.50±0.764,and 0.33±0.159,respectively.Scanning electron microscopy showed the detail of morphological characteristics and provided the different shapes of mucron and excretory pores in Anisakis larvae congruent with the phylogenetic tree.The species tree was congruent with the phylogenetic tree.Conclusions:The prevalence,mean intensity,and mean abundance of Anisakis larvae were higher in blue mackerel.To the best of our knowledge,this is the first time that Anisakis pegreffii was found in blue mackerel in Thailand.The phylogenetic tree also supported the morphological data of Anisakis larvae.However,species delimitation based on cox2 revealed 1-3 possible cryptic species in this genus.Anisakis spp.contamination of fish products is unpleasant and a health concern considering human infection with larvae(anisakiasis)arises.
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 programs of the Strategic Priority Research Program B of the Chinese Academy of Sciences (CAS) (No. XDB31000000)the National Natural Science Foundation of China (Grant No. 31460091)+2 种基金the Na tional Animal Collection Resource Center, China (Grant No. 2005DKA21402)the Application of Amphibian Natural Antioxidant Peptides as Cosmetic Raw Material Antioxidants (QKZYD [2020]4002)the National Top Discipline Construction Project of Guizhou Province,Geography in Guizhou Normal University (No. 85 2017 Qianjiao Keyan Fa)。
文摘The Paramesotriton caudopunctatus species group is mainly distributed in the karst mountain ecosystems of Guizhou, China. Although some species have been included in previous phylogenetic studies, the evolutionary relationships and divergence-time of members of this species group as a whole remain unexplored. In this study, we report the sequencing of one protein coding mitochondrial gene fragment(ND2) and one nuclear gene(POMC), and use a combination of phylogenetic analyses and coalescent simulations to explore the cryptic diversity and evolutionary history of the P. caudopunctatus species group. Phylogenetic relationships revealed that the P. caudopunctatus species group is composed of two major groups, i. e., East Clade and Western-South Clade. The divergence-time and ancestral area estimation suggested that the P. caudopunctatus species group likely originated in the Doupeng Mountains in Guizhou, China at 12.34 Ma(95% HPD: 8.30–14.73), and intraspecific divergence began at about 2.17 Ma(95% HPD: 1.39–2.97). This timing coincides with the orogenesis of the Miaoling Mountains during the Late Miocene to early Pleistocene. The delimitation of species in the P. caudopunctatus species group supports the existence of the currently identified species, and consensus was confirmed across methods for the existence of least to two cryptic species within what has been traditionally considered to be P. caudopunctatus species group. This study is of significance for understanding the species formation, dispersal, and diversity of the tailed amphibians in the karst mountains ecosystem of Guizhou and the role of the Miaoling Mountains as a geographical barrier to species dispersal.
