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
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
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
Phylogenetic and phylogeographic studies rely on the accurate quantification of biodiversity. In recent studies of taxonomically ambiguous groups, species boundaries are often determined based on multi-locus sequence ...Phylogenetic and phylogeographic studies rely on the accurate quantification of biodiversity. In recent studies of taxonomically ambiguous groups, species boundaries are often determined based on multi-locus sequence data. Bayesian Phylogenetics and Phylogeography （BPP） is a coalescent-based method frequently used to delimit species; however, empirical studies suggest that the requirement of a user-specified guide tree biases the range of possible outcomes. We evaluate fifteen multi-locus datasets using the most recent iteration of BPP, which eliminates the need for a user-specified guide tree and reconstructs the species tree in synchrony with species delimitation （= unguided species delimitation）. We found that the number of species recovered with guided versus unguided species delimitation was the same except for two cases, and that posterior probabilities were generally lower for the unguided analyses as a result of searching across species trees in addition to species delimitation models. The guide trees used in previous studies were often discordant with the species tree topologies estimated by BPP. We also compared species trees estimated using BPP and ＊BEAST and found that when the topologies are the same, BPP tends to give higher posterior probabilities [Current Zoology 61 （5）： 866-873, 2015].展开更多
Codium, one of the largest marine green algal genera, is difficult to delimit species boundary accurately based on morphological identification only. DNA barcoding is a powerful tool for discriminating species of seaw...Codium, one of the largest marine green algal genera, is difficult to delimit species boundary accurately based on morphological identification only. DNA barcoding is a powerful tool for discriminating species of seaweeds. The plastid elongation factor TU （tufA） is considered as maker to perform DNA barcoding of green algal species than rbcL gene due to universality and rapid evolution rate. We conducted DNA barcoding application to Codium specimens from the Jeju Island, Korea to overcome the limit of morphological identification and to confirm the species diversity. As a result of applying tufA marker, we newly generated fifty-five tufA barcodes to resolve eight species. TufA marker exhibited 6.1%–21.8% interspecific divergences, wider than the gap of rbcL exon 1, 3.5%–11.5%. Molecular analysis of rbcL exon 1 sequences of Codium revealed eight distinct species like tufA analysis separated in five phylogenetic groups. DNA barcoding of the genus Codium using tufA marker is more helpful to overcome the limit of morphological identification, and this is more potential to reveal cryptic species and to resolve the relationships among subspecies than rbcL analysis alone. The complement of tufA barcoding and rbcL analyses including morphology for the genus Codium in the northwestern Pacific will give much more reliable achievement for discovering species diversity and resolving the phylogenetic relationships.展开更多
The central value 23°26′17″ of the Tropic of Cancer is used for delimiting the standard position of the Tropic of Cancer as well as countries, regions and cities which the Tropic of Cancer traverses. It is conf...The central value 23°26′17″ of the Tropic of Cancer is used for delimiting the standard position of the Tropic of Cancer as well as countries, regions and cities which the Tropic of Cancer traverses. It is confirmed that the Tropic of Cancer runs through 19 countries and regions in the world, and it traverses Yunnan, Guangxi, Guangdong, Fujian （sea area） and Taiwan provinces in China. At the same time, regions which the Tropic of Cancer traverses are divided into three regions, namely the extensive Tropic of Cancer region, the Tropic of Cancer region and the core area of the Tropic of Cancer. The series of delimitation and division aims to explore ways of sustainable development under the restriction of resources and environment and build collaborative development areas of the Tropic of Cancer at all leaves, especially setting up the collaborative de- velopment zone of the Tropic of Cancer in China and international collaborative development circle of the Tropic of Cancer.展开更多
To solve some unreasonable problems in the acceptance process of the delimitation project of grain production functional zones,the acceptance results of grain production functional zones in Fangzi District,Weifang Cit...To solve some unreasonable problems in the acceptance process of the delimitation project of grain production functional zones,the acceptance results of grain production functional zones in Fangzi District,Weifang City were elaborated from the aspects of the third party organization,inspectors,expert group,acceptance criteria,acceptance method,acceptance contents,etc.,and the overall performance of the project was reviewed.The problems that need to be rectified during the implementation of the project were put forward,and the irrationality of the acceptance and the places that need to be improved were pointed out,which would provide a better guiding value for the delimitation of grain production functional zone and the acceptance and performance evaluation of similar projects.展开更多
The United Nations Convention on the Law of the Sea entitled the coastal States to naturally extend the continental shelf, which has caused more drastic disputes of maritime delimitation. This paper devotes to clarify...The United Nations Convention on the Law of the Sea entitled the coastal States to naturally extend the continental shelf, which has caused more drastic disputes of maritime delimitation. This paper devotes to clarifying the significant concept of natural prolongation through an effect method combing the legal principles and technical analysis. Firstly, the classic samples with respect of the development of geological features are traced. Based on these samples, the classification with a model is proposed in order to affirm the concept＇s significance under certain geomorphologic situations. Lastly, scientific analysis is used to present two potential prolongation situations and emphasize that all the technical analysis on maritime delimitation should be complied with international law and protect the common interest of all the mankind.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
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.
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].
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We thank the authors of species delimitation studies listed in Table 1 for permission to use their datasets in our study. We also thank J. Grummer for providing feedback on an earlier draft of the manuscript. This work was facilitated though the use of advanced computational, storage, and networking infrastructure provided by the Hyak supercomputer system at the University of Washington. I.W.C.S. was supported by a graduate scholarship from the Consejo Nacional de Ciencia y Tecnologia （CONACYT）, and N.M.B was supported by the National Science Foundation Graduate Research Fellowship （NSF-GRFP）.
文摘Phylogenetic and phylogeographic studies rely on the accurate quantification of biodiversity. In recent studies of taxonomically ambiguous groups, species boundaries are often determined based on multi-locus sequence data. Bayesian Phylogenetics and Phylogeography （BPP） is a coalescent-based method frequently used to delimit species; however, empirical studies suggest that the requirement of a user-specified guide tree biases the range of possible outcomes. We evaluate fifteen multi-locus datasets using the most recent iteration of BPP, which eliminates the need for a user-specified guide tree and reconstructs the species tree in synchrony with species delimitation （= unguided species delimitation）. We found that the number of species recovered with guided versus unguided species delimitation was the same except for two cases, and that posterior probabilities were generally lower for the unguided analyses as a result of searching across species trees in addition to species delimitation models. The guide trees used in previous studies were often discordant with the species tree topologies estimated by BPP. We also compared species trees estimated using BPP and ＊BEAST and found that when the topologies are the same, BPP tends to give higher posterior probabilities [Current Zoology 61 （5）： 866-873, 2015].
基金A grant from the National Institute of Biological Resources(NIBR)funded by the Ministry of Environment(MOE) of the Republic of Korea under contract No.2013-02-013
文摘Codium, one of the largest marine green algal genera, is difficult to delimit species boundary accurately based on morphological identification only. DNA barcoding is a powerful tool for discriminating species of seaweeds. The plastid elongation factor TU （tufA） is considered as maker to perform DNA barcoding of green algal species than rbcL gene due to universality and rapid evolution rate. We conducted DNA barcoding application to Codium specimens from the Jeju Island, Korea to overcome the limit of morphological identification and to confirm the species diversity. As a result of applying tufA marker, we newly generated fifty-five tufA barcodes to resolve eight species. TufA marker exhibited 6.1%–21.8% interspecific divergences, wider than the gap of rbcL exon 1, 3.5%–11.5%. Molecular analysis of rbcL exon 1 sequences of Codium revealed eight distinct species like tufA analysis separated in five phylogenetic groups. DNA barcoding of the genus Codium using tufA marker is more helpful to overcome the limit of morphological identification, and this is more potential to reveal cryptic species and to resolve the relationships among subspecies than rbcL analysis alone. The complement of tufA barcoding and rbcL analyses including morphology for the genus Codium in the northwestern Pacific will give much more reliable achievement for discovering species diversity and resolving the phylogenetic relationships.
文摘The central value 23°26′17″ of the Tropic of Cancer is used for delimiting the standard position of the Tropic of Cancer as well as countries, regions and cities which the Tropic of Cancer traverses. It is confirmed that the Tropic of Cancer runs through 19 countries and regions in the world, and it traverses Yunnan, Guangxi, Guangdong, Fujian （sea area） and Taiwan provinces in China. At the same time, regions which the Tropic of Cancer traverses are divided into three regions, namely the extensive Tropic of Cancer region, the Tropic of Cancer region and the core area of the Tropic of Cancer. The series of delimitation and division aims to explore ways of sustainable development under the restriction of resources and environment and build collaborative development areas of the Tropic of Cancer at all leaves, especially setting up the collaborative de- velopment zone of the Tropic of Cancer in China and international collaborative development circle of the Tropic of Cancer.
文摘To solve some unreasonable problems in the acceptance process of the delimitation project of grain production functional zones,the acceptance results of grain production functional zones in Fangzi District,Weifang City were elaborated from the aspects of the third party organization,inspectors,expert group,acceptance criteria,acceptance method,acceptance contents,etc.,and the overall performance of the project was reviewed.The problems that need to be rectified during the implementation of the project were put forward,and the irrationality of the acceptance and the places that need to be improved were pointed out,which would provide a better guiding value for the delimitation of grain production functional zone and the acceptance and performance evaluation of similar projects.
基金The National Social Science Foundation of China under contract No.16CFX069China Postdoctoral Science Foundations under contract Nos 2015M581913 and 2016T90531the Fundamental Research Funds for the Central Universities
文摘The United Nations Convention on the Law of the Sea entitled the coastal States to naturally extend the continental shelf, which has caused more drastic disputes of maritime delimitation. This paper devotes to clarifying the significant concept of natural prolongation through an effect method combing the legal principles and technical analysis. Firstly, the classic samples with respect of the development of geological features are traced. Based on these samples, the classification with a model is proposed in order to affirm the concept＇s significance under certain geomorphologic situations. Lastly, scientific analysis is used to present two potential prolongation situations and emphasize that all the technical analysis on maritime delimitation should be complied with international law and protect the common interest of all the mankind.
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.
