Objective:With Persicaria capitata as test materials,we compared and analyzed the chloroplast(cp)genome characteristics as well as their phylogenetic relationships and evolutionary history with related species of Pers...Objective:With Persicaria capitata as test materials,we compared and analyzed the chloroplast(cp)genome characteristics as well as their phylogenetic relationships and evolutionary history with related species of Persicaria nepalensis,Persicaria japonica,Persicaria chinensis,Persicaria filiformis,Persicaria perfoliata,Persicaria pubescens,Persicaria hnydropiper.Methods:The Illumina HiSeq high-throughput sequencing platform was used for the first time for P.capitata cp genome sequencing.NOVOPlasty and CpGAVAS2 were used for assembly and annotation,and Codon W,DnaSP,and MISA were used to conduct a series of comparative genomic analyses between the plant and seven species of the same genus.A phylogenetic tree was constructed using the maximum likelihood(ML)and neighbor-joining(NJ)methods,and divergence time was estimated using BEAST.Results:The total length of P.capitata cp genome was 158,821 bp,with a guanine and cytosine(GC)content of 38.0%,exhibiting a typical circular tetrad structure.The genome contains 127 annotated genes,including 82 protein-coding and 45 tRNA-encoding genes.The cp genome harbors simple sequence repeat(SSR)loci primarily composed of A/T.The conserved species structure of this genus is reinforced by the expansion and contraction of the inverted repeat(IR)region.The non-coding regions of the cp genomes exhibited significant differences among the genera.Six different mutation hotspots(psbK-psbI,atpI-rps2,petN-psbD,atpB-rbcL,cemA-petA,ndhI-ndhA-ycf1)were screened from the non-coding regions of genes with high nucleotide variability(pI).These hotspots were expected to define the phylogenetic species of Persicaria.Furthermore,phylogenetic analysis of Polygonaceae plants showed that P.capitata was more closely related to P.chinensis than P.nepalensis.Analysis of divergence time indicated that Polygonaceae originated in the Late Cretaceous(~180 Ma)and began to differentiate during the Middle Miocene.Persicaria differentiated~66.44 million years ago,during the Miocene.Conclusions:Our findings will serve as a scientific basis for further research on species identification and evolution,population genetics,and phylogenetic analysis of P.capitata.Further,we provide valuable information for understanding the origin and evolution of Persicaria in Polygonaceae and estimating the differentiation time of Persicaria and its population.展开更多
The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution.However,the patterns of phylogenetic diversity(PD) and phylogenetic beta diversity...The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution.However,the patterns of phylogenetic diversity(PD) and phylogenetic beta diversity(PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America(EA-ENA disjuncts) and their associated factors remain unknown.Here we investigated the standardized effect size of PD(SES-PD),PBD,and potentially associated factors in 11natural mixed forest sites(five in EA and six in ENA) where abundant EA-ENA disjuncts occur.We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale(1.96vs-1.12),even though the number of disjunct species in ENA is much lower than in EA(128 vs 263).SESPD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites.The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites.Based on the unweighted unique fraction metric(UniFrac) distance and the phylogenetic community dissimilarity,PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites.Based on the standardized effect size of mean pairwise distances(SES-MPD),nine of eleven studied sites showed a neutral community structure(-1.96 ≤SES-MPD ≤1.96).Both Pearson’s r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time.Moreover,SES-PD of the EA-ENA disjuncts was positively correlated with temperaturerelated climatic factors,although negatively correlated with mean diversification rate and community structure.By applying approaches from phylogenetics and community ecology,our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.展开更多
Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir- tual majority of studies that use molecular sequences to estimate times of divergence among species h...Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir- tual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combination of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sorting. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny [Current Zoology 61 （5）： 874-885, 2015].展开更多
Bangiales is the only order of the Bangiophyceae and has been suggested to be monophyletic. This order contains approximately 190 species and is distributed worldwide. Previous molecular studies have produced robust p...Bangiales is the only order of the Bangiophyceae and has been suggested to be monophyletic. This order contains approximately 190 species and is distributed worldwide. Previous molecular studies have produced robust phylogenies among the red algae, but the divergence times, historical biogeography and evolutionary rates of Bangiales have rarely been studied. Phylogenetic relationships within the Bangiales were examined using the concatenated gene sets from all available organellar genomes. This analysis has revealed the topology((( Bangia, Porphyra) Pyropia) Wildemania). Molecular dating indicates that Bangiales diversifi ed approximately 246.40 million years ago(95% highest posterior density(HPD)= 194.78–318.24 Ma, posterior probability(PP)=0.99) in the Late Permian and Early Triassic, and that the ancestral species most likely originated from eastern Gondwanaland(currently New Zealand and Australia) and subsequently began to spread and evolve worldwide. Based on pairwise comparisons, we found a slower rate of nucleotide substitutions and lower rates of diversifi cation in Bangiales relative to Florideophyceae. Compared with Viridiplantae(green algae and land plants), the evolutionary rates of Bangiales and other Rhodophyte groups were found to be dramatically faster, by more than 3-fold for plastid genome(ptDNA) and 15-fold for mitochondrial genome(mtDNA). In addition, an average 2.5-fold lower dN/dS was found for the algae than for the land plants, which indicates purifying selection of the algae.展开更多
The recognition of taxonomic ranks in the Linnean classification system is largely arbitrary.Some authors have proposed the use of divergence time as a universally standardized criterion.Agaricus(Agaricaceae,Agaricale...The recognition of taxonomic ranks in the Linnean classification system is largely arbitrary.Some authors have proposed the use of divergence time as a universally standardized criterion.Agaricus(Agaricaceae,Agaricales)is a mushroom genus that contains many species of high commercial value.Recent studies using ITS sequence data discovered 11 new phylogenetic lineages within the genus,however their taxonomic ranks were uncertain due to the lack of criteria to define them within traditional taxonomy.In this study,we analyzed ITS sequence data from 745 collections(nearly 600 being newly generated)including 86 from type specimens of previously recognized subgenera and sections.Many monophyletic groups were recognized,but most basal relationships were unresolved.One hundred and fourteen representatives of the identified ITS clades were selected in order to produce a multi-gene phylogeny based on combined LSU,tef-1α,and rpb2 sequence data.Divergence times within the multi-gene phylogeny were estimated using BEAST v1.8.Based on phylogenetic relationships and with respect to morphology,we propose a revised taxonomic system for Agaricus that considers divergence time as a standardized criterion for establishing taxonomic ranks.We propose to segregate Agaricus into five subgenera and 20 sections.Subgenus Pseudochitonia is substantially emended;circumscription of the subgenera Agaricus and Flavoagaricus is restricted to taxa of sections Agaricus and Arvenses,respectively;and two new subgenera(Minores and Spissicaules)are introduced.Within Pseudochitonia,sections Bivelares,Brunneopicti,Chitonioides,Nigrobrunnescentes,Sanguinolenti and Xanthodermatei are maintained,but the latter two are reduced because we raise subsection Bohusia to sectional rank and a clade within section Xanthodermatei is formally introduced as section Hondenses;and sections Rubricosi,Crassispori,Flocculenti,and Amoeni are introduced.Section Laeticolores is placed in the subgenus Minores and sections Rarolentes and Subrutilescentes are placed in the subgenus Spissicaules.Twenty-two new species belonging to various sections are described.This work exemplifies that ITS data,while useful at lower taxonomic levels(i.e.,detection of species and species groups),are of limited value for inferring deeper phylogenetic relationships.Finally,we suggest that the establishment of a standardized taxonomic system based on divergence times could result in a more objective,and biologically more meaningful,taxonomic ranking of fungi.展开更多
There have been several investigations into the genus Heterobasidion,however,differentiation of species in these studies have depended on the gene regions analyzed.Reliable defining of species,establishing species div...There have been several investigations into the genus Heterobasidion,however,differentiation of species in these studies have depended on the gene regions analyzed.Reliable defining of species,establishing species divergence times and establishing species biogeographical distributions have been challenging.Here,we used a multilocus phylogenetic approach and maximum parsimony,maximum likehood,and Bayesian analyses to infer the phylogenetic relationships of Heterobasidion species.In addition,we focused on a fungus fossil-based approach and used the largest subunit of RNA polymerase II-the second subunit of RNA polymerase II(RPB1-RPB2)dataset to perform maximum likelihoodbased estimation and Bayesian binary analyses,to assess the divergence and biogeographical distributions of Heterobasidion species.The Heterobasidion annousum/H.insulare species complex clusters in three groups in the phylogenetic analyses.Molecular dating suggests that ancestral Heterobasidion species originated in Eurasia during the Early Miocene,followed by dispersal and speciation to other continents during the Middle Miocene and Early Pliocene.Our data are compatible with the previous viewpoint that H.irregulare and H.occidentale colonized North America via different routes,which has been interpreted as Beringian and Thulean North Atlantic vicariance.In addition,we propose that the occurrence of H.araucariae in the southern Hemisphere was probably due to recent human-mediated introductions.Plate tectonics and long-distance dispersal are the most likely factors that influenced Heterobasidion speciation and biogeography.展开更多
Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformat...Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.展开更多
Chalcidoidea is one of the most biologically diverse groups among Hymenoptera.Members are characterized by extraordinary parasitic lifestyles and extensive host ranges,among which several species attack plants or serv...Chalcidoidea is one of the most biologically diverse groups among Hymenoptera.Members are characterized by extraordinary parasitic lifestyles and extensive host ranges,among which several species attack plants or serve as pollinators.However,higher-level chalcidoid relationships remain controversial.Here,we performed mitochondrial phylogenomic analyses for major clades(18out of 25 families)of Chalcidoidea based on 139 mitochondrial genomes.The compositional heterogeneity and conflicting backbone relationships in Chalcidoidea were assessed using various datasets and tree inferences.Our phylogenetic results supported the monophyly of 16families and polyphyly of Aphelinidae and Pteromalidae.Our preferred topology recovered the relationship(Mymaridae+(Signiphoridae+Leucospidae)+(Chalcididae+((Perilampidae+Eucharitidae)+remaining Chalcidoidea))).The monophyly of Agaonidae and Sycophaginae was rejected,while the gall-associated((Megastigmidae+Ormyridae)+(Ormocerinae+Eurytomidae))relationship was supported in most results.A six-gene inversion may be a synapomorphy for most families,whereas other derived gene orders may introduce confusion in phylogenetic signals at deeper nodes.Dating estimates suggested that Chalcidoidea arose near the Jurassic/Cretaceous boundary and that two dynamic shifts in diversification occurred during the evolution of Chalcidoidea.We hypothesized that the potential codiversification between chalcidoids and their hosts may be crucial for accelerating the diversification of Chalcidoidea.Ancestral state reconstruction analyses supported the hypothesis that gallinducers were mainly derived from parasitoids of gallinducers,while other gall-inducers were derived from phytophagous groups.Taken together,these findings advance our understanding of mitochondrial genome evolution in the major interfamilial phylogeny of Chalcidoidea.展开更多
We describe a new species of Discostella from Guiyang based on light and scanning electron microscopic observations,as well as molecular analysis.This species is morphologically distinguished from other species by a r...We describe a new species of Discostella from Guiyang based on light and scanning electron microscopic observations,as well as molecular analysis.This species is morphologically distinguished from other species by a relatively smooth and slightly recessed central area with marginal striae of unequal lengths forked near the margin.Marginal fultoportulae and a single rimoportula are situated between every two costae or on the costae.Both morphological characters and the concatenated data of rbc L and SSU rDNA indicate that Discostella guiyangensis is a unique and new species.According to divergence time estimation analysis,Discostella guiyangensis is the oldest species among the Discostella species sequenced currently.In addition,we complement molecular data of Discostella asterocostata and Discostella stelligera.展开更多
Pachytriton,and Paramesotriton,are primarily distributed across East Asia,displaying a broad range of environmental adaptations,including generalists inhabiting both lotic and lentic habitats and lotic specializations...Pachytriton,and Paramesotriton,are primarily distributed across East Asia,displaying a broad range of environmental adaptations,including generalists inhabiting both lotic and lentic habitats and lotic specializations.Despite recent studies on their biogeographic history,how these species adapted to geographical changes remains unclear.In this study,divergence times and reconstructed ancestral traits were estimated based on phylogenetic analysis of mitochondrial and nuclear DNA sequences,totaling 4048 bp.Results indicated that the divergence between lotic-specialized and generalist species occurred during the middle to late Miocene(95% confidence interval(CI):16-13 million years ago(Ma)),correlating with the long-lasting arid period(14-12 Ma)and uplift of the Wuyi-Nanling mountains(15-11 Ma).Ancestral trait reconstruction revealed notable morphological changes associated with the emergence of lotic-specialized lineages.Specifically,male body size increased from 130 mm to 140 mm,and epibranchial traits shifted from thin to thick structures.Additionally,variation in tongue movability and skin texture were observed among lotic species.Each morphological shift is hypothesized to have an ecological basis,facilitating adaptation to specific environmental conditions.Overall,this study represents the first comprehensive attempt to elucidate the evolution of ancestral traits among divergent species of modern Asian newts,providing a deeper understanding of their adaptive responses to historical geographical and climatic changes.展开更多
A molecular phytogeny is presented for the subfamily Dorippinae (including 9 individuals, representing 5 species and 4 genera), based on the sequence data from 16S rRNA gene. Two-cluster test between lineages in these...A molecular phytogeny is presented for the subfamily Dorippinae (including 9 individuals, representing 5 species and 4 genera), based on the sequence data from 16S rRNA gene. Two-cluster test between lineages in these phylogenetic trees has been performed. On the basis of rate constancy, the rate of nucleotide substitutions of 16S rDNA sequence data is estimated as 0.27% per million years. The analysis strongly supports the recognition of the Dorippinae as a monophyletic subfamily. Phylogenetic tree indicates that the subfamily Dorippinae is divided into two main clades, and genus Dorippe appears basal in the subfamily, diverging from other species 36.6 Ma ago. It is also clear that the Heikea is closely related to the genus Neodorippe. The divergence time between them is 15.8 Ma.展开更多
基金supported by the National Natural Science Foundation of China(82060913).
文摘Objective:With Persicaria capitata as test materials,we compared and analyzed the chloroplast(cp)genome characteristics as well as their phylogenetic relationships and evolutionary history with related species of Persicaria nepalensis,Persicaria japonica,Persicaria chinensis,Persicaria filiformis,Persicaria perfoliata,Persicaria pubescens,Persicaria hnydropiper.Methods:The Illumina HiSeq high-throughput sequencing platform was used for the first time for P.capitata cp genome sequencing.NOVOPlasty and CpGAVAS2 were used for assembly and annotation,and Codon W,DnaSP,and MISA were used to conduct a series of comparative genomic analyses between the plant and seven species of the same genus.A phylogenetic tree was constructed using the maximum likelihood(ML)and neighbor-joining(NJ)methods,and divergence time was estimated using BEAST.Results:The total length of P.capitata cp genome was 158,821 bp,with a guanine and cytosine(GC)content of 38.0%,exhibiting a typical circular tetrad structure.The genome contains 127 annotated genes,including 82 protein-coding and 45 tRNA-encoding genes.The cp genome harbors simple sequence repeat(SSR)loci primarily composed of A/T.The conserved species structure of this genus is reinforced by the expansion and contraction of the inverted repeat(IR)region.The non-coding regions of the cp genomes exhibited significant differences among the genera.Six different mutation hotspots(psbK-psbI,atpI-rps2,petN-psbD,atpB-rbcL,cemA-petA,ndhI-ndhA-ycf1)were screened from the non-coding regions of genes with high nucleotide variability(pI).These hotspots were expected to define the phylogenetic species of Persicaria.Furthermore,phylogenetic analysis of Polygonaceae plants showed that P.capitata was more closely related to P.chinensis than P.nepalensis.Analysis of divergence time indicated that Polygonaceae originated in the Late Cretaceous(~180 Ma)and began to differentiate during the Middle Miocene.Persicaria differentiated~66.44 million years ago,during the Miocene.Conclusions:Our findings will serve as a scientific basis for further research on species identification and evolution,population genetics,and phylogenetic analysis of P.capitata.Further,we provide valuable information for understanding the origin and evolution of Persicaria in Polygonaceae and estimating the differentiation time of Persicaria and its population.
基金supported by the National Natural Science Foundation of China (Grant No.31461123001 to C.X.F.)the US National Science Foundation Dimensions of Biodiversity US-China Program (DEB-1442280 to P.S.S.and D.E.S.)+1 种基金the HZAU Talent Start-up Fund (Grant no.11042210014 to M.S.)the China Scholarship Council (Grant no.201806320056 to H.Y.L.)。
文摘The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution.However,the patterns of phylogenetic diversity(PD) and phylogenetic beta diversity(PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America(EA-ENA disjuncts) and their associated factors remain unknown.Here we investigated the standardized effect size of PD(SES-PD),PBD,and potentially associated factors in 11natural mixed forest sites(five in EA and six in ENA) where abundant EA-ENA disjuncts occur.We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale(1.96vs-1.12),even though the number of disjunct species in ENA is much lower than in EA(128 vs 263).SESPD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites.The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites.Based on the unweighted unique fraction metric(UniFrac) distance and the phylogenetic community dissimilarity,PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites.Based on the standardized effect size of mean pairwise distances(SES-MPD),nine of eleven studied sites showed a neutral community structure(-1.96 ≤SES-MPD ≤1.96).Both Pearson’s r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time.Moreover,SES-PD of the EA-ENA disjuncts was positively correlated with temperaturerelated climatic factors,although negatively correlated with mean diversification rate and community structure.By applying approaches from phylogenetics and community ecology,our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.
文摘Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir- tual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combination of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sorting. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny [Current Zoology 61 （5）： 874-885, 2015].
基金Supported by the National Natural Science Foundation of China(No.31372517)the Scientific and Technological Innovation Project supported by the Qingdao National Laboratory for Marine Science and Technology(No.2015ASKJ02)the National Infrastructure of Fishery Germplasm Resources(No.2016DKA30470)
文摘Bangiales is the only order of the Bangiophyceae and has been suggested to be monophyletic. This order contains approximately 190 species and is distributed worldwide. Previous molecular studies have produced robust phylogenies among the red algae, but the divergence times, historical biogeography and evolutionary rates of Bangiales have rarely been studied. Phylogenetic relationships within the Bangiales were examined using the concatenated gene sets from all available organellar genomes. This analysis has revealed the topology((( Bangia, Porphyra) Pyropia) Wildemania). Molecular dating indicates that Bangiales diversifi ed approximately 246.40 million years ago(95% highest posterior density(HPD)= 194.78–318.24 Ma, posterior probability(PP)=0.99) in the Late Permian and Early Triassic, and that the ancestral species most likely originated from eastern Gondwanaland(currently New Zealand and Australia) and subsequently began to spread and evolve worldwide. Based on pairwise comparisons, we found a slower rate of nucleotide substitutions and lower rates of diversifi cation in Bangiales relative to Florideophyceae. Compared with Viridiplantae(green algae and land plants), the evolutionary rates of Bangiales and other Rhodophyte groups were found to be dramatically faster, by more than 3-fold for plastid genome(ptDNA) and 15-fold for mitochondrial genome(mtDNA). In addition, an average 2.5-fold lower dN/dS was found for the algae than for the land plants, which indicates purifying selection of the algae.
基金supported by grants from the National Natural Science Foundation of China to RLZ(Project IDs 31000013,31360014 and 31470152)the Thailand Research Fund to KDH(grant BRG 5580009)the Natural Sciences and Engineering Research Council of Canada and the ROM Governors to JMM.Dr.Richard Kerrigan made valuable comments and suggestions to improve this paper.
文摘The recognition of taxonomic ranks in the Linnean classification system is largely arbitrary.Some authors have proposed the use of divergence time as a universally standardized criterion.Agaricus(Agaricaceae,Agaricales)is a mushroom genus that contains many species of high commercial value.Recent studies using ITS sequence data discovered 11 new phylogenetic lineages within the genus,however their taxonomic ranks were uncertain due to the lack of criteria to define them within traditional taxonomy.In this study,we analyzed ITS sequence data from 745 collections(nearly 600 being newly generated)including 86 from type specimens of previously recognized subgenera and sections.Many monophyletic groups were recognized,but most basal relationships were unresolved.One hundred and fourteen representatives of the identified ITS clades were selected in order to produce a multi-gene phylogeny based on combined LSU,tef-1α,and rpb2 sequence data.Divergence times within the multi-gene phylogeny were estimated using BEAST v1.8.Based on phylogenetic relationships and with respect to morphology,we propose a revised taxonomic system for Agaricus that considers divergence time as a standardized criterion for establishing taxonomic ranks.We propose to segregate Agaricus into five subgenera and 20 sections.Subgenus Pseudochitonia is substantially emended;circumscription of the subgenera Agaricus and Flavoagaricus is restricted to taxa of sections Agaricus and Arvenses,respectively;and two new subgenera(Minores and Spissicaules)are introduced.Within Pseudochitonia,sections Bivelares,Brunneopicti,Chitonioides,Nigrobrunnescentes,Sanguinolenti and Xanthodermatei are maintained,but the latter two are reduced because we raise subsection Bohusia to sectional rank and a clade within section Xanthodermatei is formally introduced as section Hondenses;and sections Rubricosi,Crassispori,Flocculenti,and Amoeni are introduced.Section Laeticolores is placed in the subgenus Minores and sections Rarolentes and Subrutilescentes are placed in the subgenus Spissicaules.Twenty-two new species belonging to various sections are described.This work exemplifies that ITS data,while useful at lower taxonomic levels(i.e.,detection of species and species groups),are of limited value for inferring deeper phylogenetic relationships.Finally,we suggest that the establishment of a standardized taxonomic system based on divergence times could result in a more objective,and biologically more meaningful,taxonomic ranking of fungi.
基金We thank Dr.Natalia Arhipova(Latvia)for providing a photo of H.araucariae.We express our gratitude to Drs.Bang Feng and Xi-Hui Du(HKAS,China)for helping us in informative analyses and improving this manuscript.The research was supported by the Fundamental Research Funds for the Central Universities(Project Nos.JC2013-1 and BLYJ201403)。
文摘There have been several investigations into the genus Heterobasidion,however,differentiation of species in these studies have depended on the gene regions analyzed.Reliable defining of species,establishing species divergence times and establishing species biogeographical distributions have been challenging.Here,we used a multilocus phylogenetic approach and maximum parsimony,maximum likehood,and Bayesian analyses to infer the phylogenetic relationships of Heterobasidion species.In addition,we focused on a fungus fossil-based approach and used the largest subunit of RNA polymerase II-the second subunit of RNA polymerase II(RPB1-RPB2)dataset to perform maximum likelihoodbased estimation and Bayesian binary analyses,to assess the divergence and biogeographical distributions of Heterobasidion species.The Heterobasidion annousum/H.insulare species complex clusters in three groups in the phylogenetic analyses.Molecular dating suggests that ancestral Heterobasidion species originated in Eurasia during the Early Miocene,followed by dispersal and speciation to other continents during the Middle Miocene and Early Pliocene.Our data are compatible with the previous viewpoint that H.irregulare and H.occidentale colonized North America via different routes,which has been interpreted as Beringian and Thulean North Atlantic vicariance.In addition,we propose that the occurrence of H.araucariae in the southern Hemisphere was probably due to recent human-mediated introductions.Plate tectonics and long-distance dispersal are the most likely factors that influenced Heterobasidion speciation and biogeography.
基金supported by the National Natural Science Foundation of China Project(Grant No.32260097)the National Guidance Foundation for Local Science and Technology Development of China(Grant No.[2023]009)the Natural Science Foundation for Distinguished Young Scholars of Hebei(Grant No.C2022209010)。
文摘Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.
基金supported by the Key International Joint Research Program of the National Natural Science Foundation of China(31920103005)General Program of the National Natural Science Foundation of China(32070467)+3 种基金Provincial Key R&D Program of Zhejiang,China(2021C02045)Key Project of Laboratory of Lingnan Modern Agriculture(NT2021003)Fundamental Research Funds for the Central UniversitiesSpecial Research Fund for Distinguished Scholars of Zhejiang Province,China(2018R51004)。
文摘Chalcidoidea is one of the most biologically diverse groups among Hymenoptera.Members are characterized by extraordinary parasitic lifestyles and extensive host ranges,among which several species attack plants or serve as pollinators.However,higher-level chalcidoid relationships remain controversial.Here,we performed mitochondrial phylogenomic analyses for major clades(18out of 25 families)of Chalcidoidea based on 139 mitochondrial genomes.The compositional heterogeneity and conflicting backbone relationships in Chalcidoidea were assessed using various datasets and tree inferences.Our phylogenetic results supported the monophyly of 16families and polyphyly of Aphelinidae and Pteromalidae.Our preferred topology recovered the relationship(Mymaridae+(Signiphoridae+Leucospidae)+(Chalcididae+((Perilampidae+Eucharitidae)+remaining Chalcidoidea))).The monophyly of Agaonidae and Sycophaginae was rejected,while the gall-associated((Megastigmidae+Ormyridae)+(Ormocerinae+Eurytomidae))relationship was supported in most results.A six-gene inversion may be a synapomorphy for most families,whereas other derived gene orders may introduce confusion in phylogenetic signals at deeper nodes.Dating estimates suggested that Chalcidoidea arose near the Jurassic/Cretaceous boundary and that two dynamic shifts in diversification occurred during the evolution of Chalcidoidea.We hypothesized that the potential codiversification between chalcidoids and their hosts may be crucial for accelerating the diversification of Chalcidoidea.Ancestral state reconstruction analyses supported the hypothesis that gallinducers were mainly derived from parasitoids of gallinducers,while other gall-inducers were derived from phytophagous groups.Taken together,these findings advance our understanding of mitochondrial genome evolution in the major interfamilial phylogeny of Chalcidoidea.
基金Supported by the National Natural Science Foundation of China(No.31970217)the Scientific and Technological Innovation Programs of Higher Education Institution in Shanxi(No.2019L0070)。
文摘We describe a new species of Discostella from Guiyang based on light and scanning electron microscopic observations,as well as molecular analysis.This species is morphologically distinguished from other species by a relatively smooth and slightly recessed central area with marginal striae of unequal lengths forked near the margin.Marginal fultoportulae and a single rimoportula are situated between every two costae or on the costae.Both morphological characters and the concatenated data of rbc L and SSU rDNA indicate that Discostella guiyangensis is a unique and new species.According to divergence time estimation analysis,Discostella guiyangensis is the oldest species among the Discostella species sequenced currently.In addition,we complement molecular data of Discostella asterocostata and Discostella stelligera.
基金supported by the Japan Science and Technology Agency:Support for Pioneering Research Initiated by the Next Generation presented by the Division of Graduate Studies,Kyoto University(A94231600003)and the Nagao Project。
文摘Pachytriton,and Paramesotriton,are primarily distributed across East Asia,displaying a broad range of environmental adaptations,including generalists inhabiting both lotic and lentic habitats and lotic specializations.Despite recent studies on their biogeographic history,how these species adapted to geographical changes remains unclear.In this study,divergence times and reconstructed ancestral traits were estimated based on phylogenetic analysis of mitochondrial and nuclear DNA sequences,totaling 4048 bp.Results indicated that the divergence between lotic-specialized and generalist species occurred during the middle to late Miocene(95% confidence interval(CI):16-13 million years ago(Ma)),correlating with the long-lasting arid period(14-12 Ma)and uplift of the Wuyi-Nanling mountains(15-11 Ma).Ancestral trait reconstruction revealed notable morphological changes associated with the emergence of lotic-specialized lineages.Specifically,male body size increased from 130 mm to 140 mm,and epibranchial traits shifted from thin to thick structures.Additionally,variation in tongue movability and skin texture were observed among lotic species.Each morphological shift is hypothesized to have an ecological basis,facilitating adaptation to specific environmental conditions.Overall,this study represents the first comprehensive attempt to elucidate the evolution of ancestral traits among divergent species of modern Asian newts,providing a deeper understanding of their adaptive responses to historical geographical and climatic changes.
文摘A molecular phytogeny is presented for the subfamily Dorippinae (including 9 individuals, representing 5 species and 4 genera), based on the sequence data from 16S rRNA gene. Two-cluster test between lineages in these phylogenetic trees has been performed. On the basis of rate constancy, the rate of nucleotide substitutions of 16S rDNA sequence data is estimated as 0.27% per million years. The analysis strongly supports the recognition of the Dorippinae as a monophyletic subfamily. Phylogenetic tree indicates that the subfamily Dorippinae is divided into two main clades, and genus Dorippe appears basal in the subfamily, diverging from other species 36.6 Ma ago. It is also clear that the Heikea is closely related to the genus Neodorippe. The divergence time between them is 15.8 Ma.
