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
Since 2007,the quality of Russula descriptions has improved and the use of molecular support for species delimitation and the number of published new species has increased.However,the description style is not consiste...Since 2007,the quality of Russula descriptions has improved and the use of molecular support for species delimitation and the number of published new species has increased.However,the description style is not consistent and has regional or author-specific patterns.Most recent publications still favour descriptions of spores compared to hymenium and pileipellis elements,and usually only the spore size is provided with statistical support.This study proposes standards for descriptions of the microscopic structure of Russula species(Russulaceae,Agaricomycetes).We present the description template,the template measurements table,the specific terminology and the essential chemical reagents.The proposed standards were tested by mycologists from 11 countries who met at the Russula Microscopy Workshop in Slovakia.Descriptions of 26 species from 9 countries and four continents were prepared,among them R.amarissima,R.castanopsidis,R.seperina and R.subtilis are re-described and 15 species are introduced as new:R.abietiphila,R.amerorecondita,R.aurantioflava,R.echidna,R.flavobrunnescens,R.fluvialis,R.fortunae,R.garyensis,R.gemmata,R.laevis,R.madrensis,R.olivaceohimalayensis,R.purpureogracilis,R.sancti-pauli and R.wielangtae.Seven descriptions for candidate new species are provided without a formal name assignment.Pairwise comparison of species described in this study with available similar descriptions of related species suggests that microscopic characters from all parts of the basidiomata can be equally important for species recognition and they deserve the same treatment including number of measurements and statistics.The majority of recent studies does not recognise differences between the pileus margin and centre,but more than one-third of the species described in this study show distinct differences between the pileus areas,emphasizing the importance to specify the origin of pileipellis observations.This study proved that there is frequently insufficient difference in the ITS barcode between closely related species and t展开更多
Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation.We used 2 mitochondrial(Cytb,CO1)and 3 nuclea...Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation.We used 2 mitochondrial(Cytb,CO1)and 3 nuclear(GHR,IRBP and RAG1)genes to clarify species phylogeography and geographical differentiation.Maximum likelihood(ML)and Bayesian phylogenetic inference(BI)trees consistently indicated that L.edwardsi is a species complex containing 3 main lineages with high Kimura-2-parameter(K2P)divergences(i.e.lineages LN,LS and LHN)found in the northern and southern China and Hainan Island,respectively.The 3 species delimitation methods,automated barcoding gap discovery,Bayesian poisson tree process analysis and Bayesian phylogenetics and phylogeography,consistently supported the existence of cryptic species.Divergence times among the main lineages were inferred to be during the Pleistocene,with LHN/LS split at 1.33 Ma and LN/(LHN+LS)at 2.61 Ma;the diversifications of L.edwardsi complex might be caused by the rapid uplifts of Tibetan Plateau,paleoclimate change and complex topography.The divergence between LHN and LS was probably related to the separation of Hainan Island from the mainland via the formation of the Qiongzhou Strait.Lineages LN and(LS+LHN)likely diverged due to the Wuyi-Nanling mountain range forming a dispersal barrier.Our results suggested that L.edwardsi complex contains at least 3 distinct species:LHN represents L.hainanensis,endemic to Hainan Island and previously considered as a subspecies L.e.hainanensis;LS represents a cryptic species distributed throughout the southern Chinese continent;and LN represents the nominotypical species L.edwardsi.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
The genus Lactarius Pers.(Russulales)is a cosmopolitan group of Basidiomycota that forms ectomycorrhizal relationships primarily with both deciduous and coniferous trees.Although the genus has been well-studied in Eur...The genus Lactarius Pers.(Russulales)is a cosmopolitan group of Basidiomycota that forms ectomycorrhizal relationships primarily with both deciduous and coniferous trees.Although the genus has been well-studied in Europe and North America,only fragmentary researches have been carried out on Asian species.In particular,the distribution of Lactarius species in South Korea is poorly understood due to insufficient morphological descriptions and a lack of DNA sequence data.In addition,the misuse of European and North American names has added to confusion regarding the taxonomy of Asian Lactarius species.In this study,the diversity of Lactarius in South Korea was evaluated by employing both morphological and phylogenetic approaches.A multi-locus phylogenetic analysis of 729 Lactarius specimens collected between 1960 and 2017 was performed using the internal transcribed spacer(ITS)region,partial nuclear ribosomal large subunit(nrLSU),partial second largest subunit of RNA polymerase II(rpb2),and minichromosome maintenance complex component 7(mcm7).49 Lactarius species were identified in three Lactarius subgenera:L.subg.Russularia(17 spp.),L.subg.Lactarius(22 spp.),and L.subg.Plinthogalus(10 spp.).Among them,28 Lactarius species were identified as new to science,while just 17 were previously described Lactarius species.Four of the taxa remain un-named due to paucity of materials.A key to Korean Lactarius species,molecular phylogenies,a summary of diversity,and detailed description are provided.展开更多
限制性酶切位点关联DNA测序技术(restriction-site-associated DNA sequencing,RAD-seq)是在二代测序技术基础上发展起来的一种简化基因组技术(reduced-representation genome sequencing,RRGS)。RAD-seq利用限性核酸内切酶使基因组片段...限制性酶切位点关联DNA测序技术(restriction-site-associated DNA sequencing,RAD-seq)是在二代测序技术基础上发展起来的一种简化基因组技术(reduced-representation genome sequencing,RRGS)。RAD-seq利用限性核酸内切酶使基因组片段化,经过修饰后连接含标记的接头构建文库并进行测序。因其具有操作简单、实验成本低、通量高等优点,在分子生态学、进化基因组学、保护遗传学等领域得到应用。目前发展起来的RAD-seq技术主要包括利用稀有酶和物理打断方式进行基因组片段化的mbRAD、利用稀有酶和常见酶组合酶切的方式进行基因组片段化的ddRAD、利用IIB型限制性内切酶得到短片段文库的2bRAD、利用同裂酶和Illumina试剂盒建库的ezRAD和完全利用Nextera试剂盒建库的nextRAD。本文对每种RAD-seq技术的特点及其在昆虫种群遗传学、群落生态学、物种界定、系统发育和遗传连锁图谱构建等研究领域的应用进行了综述。展开更多
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].
基金supported by the project on the survey and excavation of Korean indigenous species of the National Institute of Biological Resources(grant number NIBR201902113)。
文摘Since 2007,the quality of Russula descriptions has improved and the use of molecular support for species delimitation and the number of published new species has increased.However,the description style is not consistent and has regional or author-specific patterns.Most recent publications still favour descriptions of spores compared to hymenium and pileipellis elements,and usually only the spore size is provided with statistical support.This study proposes standards for descriptions of the microscopic structure of Russula species(Russulaceae,Agaricomycetes).We present the description template,the template measurements table,the specific terminology and the essential chemical reagents.The proposed standards were tested by mycologists from 11 countries who met at the Russula Microscopy Workshop in Slovakia.Descriptions of 26 species from 9 countries and four continents were prepared,among them R.amarissima,R.castanopsidis,R.seperina and R.subtilis are re-described and 15 species are introduced as new:R.abietiphila,R.amerorecondita,R.aurantioflava,R.echidna,R.flavobrunnescens,R.fluvialis,R.fortunae,R.garyensis,R.gemmata,R.laevis,R.madrensis,R.olivaceohimalayensis,R.purpureogracilis,R.sancti-pauli and R.wielangtae.Seven descriptions for candidate new species are provided without a formal name assignment.Pairwise comparison of species described in this study with available similar descriptions of related species suggests that microscopic characters from all parts of the basidiomata can be equally important for species recognition and they deserve the same treatment including number of measurements and statistics.The majority of recent studies does not recognise differences between the pileus margin and centre,but more than one-third of the species described in this study show distinct differences between the pileus areas,emphasizing the importance to specify the origin of pileipellis observations.This study proved that there is frequently insufficient difference in the ITS barcode between closely related species and t
基金the Major International(Regional)Joint Research Project of NSFC(Grant No.31110103910)the Japan Society for the Promotion of Science(JSPS)Core-to-Core Program B Asia-Africa Scientific Platforms,and the JSPS Grants-in-Aid for Scientific Research(26304009).
文摘Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation.We used 2 mitochondrial(Cytb,CO1)and 3 nuclear(GHR,IRBP and RAG1)genes to clarify species phylogeography and geographical differentiation.Maximum likelihood(ML)and Bayesian phylogenetic inference(BI)trees consistently indicated that L.edwardsi is a species complex containing 3 main lineages with high Kimura-2-parameter(K2P)divergences(i.e.lineages LN,LS and LHN)found in the northern and southern China and Hainan Island,respectively.The 3 species delimitation methods,automated barcoding gap discovery,Bayesian poisson tree process analysis and Bayesian phylogenetics and phylogeography,consistently supported the existence of cryptic species.Divergence times among the main lineages were inferred to be during the Pleistocene,with LHN/LS split at 1.33 Ma and LN/(LHN+LS)at 2.61 Ma;the diversifications of L.edwardsi complex might be caused by the rapid uplifts of Tibetan Plateau,paleoclimate change and complex topography.The divergence between LHN and LS was probably related to the separation of Hainan Island from the mainland via the formation of the Qiongzhou Strait.Lineages LN and(LS+LHN)likely diverged due to the Wuyi-Nanling mountain range forming a dispersal barrier.Our results suggested that L.edwardsi complex contains at least 3 distinct species:LHN represents L.hainanensis,endemic to Hainan Island and previously considered as a subspecies L.e.hainanensis;LS represents a cryptic species distributed throughout the southern Chinese continent;and LN represents the nominotypical species L.edwardsi.
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 the project on the survey and excavation of Korean indigenous species of the National Institute of Biological Resources(NIBR 201701104 and NIBR 201801105)under the Ministry of Environment of the Republic of Korea.
文摘The genus Lactarius Pers.(Russulales)is a cosmopolitan group of Basidiomycota that forms ectomycorrhizal relationships primarily with both deciduous and coniferous trees.Although the genus has been well-studied in Europe and North America,only fragmentary researches have been carried out on Asian species.In particular,the distribution of Lactarius species in South Korea is poorly understood due to insufficient morphological descriptions and a lack of DNA sequence data.In addition,the misuse of European and North American names has added to confusion regarding the taxonomy of Asian Lactarius species.In this study,the diversity of Lactarius in South Korea was evaluated by employing both morphological and phylogenetic approaches.A multi-locus phylogenetic analysis of 729 Lactarius specimens collected between 1960 and 2017 was performed using the internal transcribed spacer(ITS)region,partial nuclear ribosomal large subunit(nrLSU),partial second largest subunit of RNA polymerase II(rpb2),and minichromosome maintenance complex component 7(mcm7).49 Lactarius species were identified in three Lactarius subgenera:L.subg.Russularia(17 spp.),L.subg.Lactarius(22 spp.),and L.subg.Plinthogalus(10 spp.).Among them,28 Lactarius species were identified as new to science,while just 17 were previously described Lactarius species.Four of the taxa remain un-named due to paucity of materials.A key to Korean Lactarius species,molecular phylogenies,a summary of diversity,and detailed description are provided.
基金Young Scientist Fund(2010BLX01)the Fundamental Research Funds(YX2011-23)in BJFU Research Fund for the Doctoral Program of Higher Education of China(2011DD14120014)an open funding(K1004)from Beijing Normal University to FKD
文摘限制性酶切位点关联DNA测序技术(restriction-site-associated DNA sequencing,RAD-seq)是在二代测序技术基础上发展起来的一种简化基因组技术(reduced-representation genome sequencing,RRGS)。RAD-seq利用限性核酸内切酶使基因组片段化,经过修饰后连接含标记的接头构建文库并进行测序。因其具有操作简单、实验成本低、通量高等优点,在分子生态学、进化基因组学、保护遗传学等领域得到应用。目前发展起来的RAD-seq技术主要包括利用稀有酶和物理打断方式进行基因组片段化的mbRAD、利用稀有酶和常见酶组合酶切的方式进行基因组片段化的ddRAD、利用IIB型限制性内切酶得到短片段文库的2bRAD、利用同裂酶和Illumina试剂盒建库的ezRAD和完全利用Nextera试剂盒建库的nextRAD。本文对每种RAD-seq技术的特点及其在昆虫种群遗传学、群落生态学、物种界定、系统发育和遗传连锁图谱构建等研究领域的应用进行了综述。
基金Supported by the National Natural Science Foundation of China(30970020,31093440 and 31970031)the Innovation Program of the Chinese Academy of Sciences(KSCX2-YW-Z-0926)the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment,China(2019HJ2096001006,20110404)。
