An earlier version of V.PhyloMaker has been broadly used to generate phylogenetic trees of vascular plants for botanical,biogeographical and ecological studies.Here,we update and enlarge this package,which is now cal...An earlier version of V.PhyloMaker has been broadly used to generate phylogenetic trees of vascular plants for botanical,biogeographical and ecological studies.Here,we update and enlarge this package,which is now called‘V.PhyloMaker2’.With V.PhyloMaker2,one can generate a phylogenetic tree for vascular plants based on one of three different botanical nomenclature systems.V.PhyloMaker2 can generate phylogenies for very large species lists(the largest species list that we tested included 365,198 species).V.PhyloMaker2 generates phylogenies at a fast speed.We provide an example(including a sample species list and an R script to run it)in this paper to show how to use V.PhyloMaker2 to generate phylogenetic trees.展开更多
Phylogenies are essential to studies investigating the effect of evolutionary history on assembly of species in ecological communities and geographical and ecological patterns of phylogenetic structure of species asse...Phylogenies are essential to studies investigating the effect of evolutionary history on assembly of species in ecological communities and geographical and ecological patterns of phylogenetic structure of species assemblages.Because phylogenies well resolved at the species level are lacking for many major groups of organisms such as vascular plants,researchers often generate a species-level phylogenies using a phylogeny well resolved at the genus level as a backbone and attaching species to their respective genera in the phylogeny as polytomies or by using a megaphylogeny well resolved at the genus level as a backbone and adding additional species to the megaphylogeny as polytomies of their respective genera.However,whether the result of a study using species-level phylogenies generated in these ways is robust,compared to that based on phylogenies fully resolved at the species level,has not been assessed.Here,we use 1093 angiosperm tree assemblages(each in a 110110 km quadrat)in North America as a model system to address this question,by examining six commonly used metrics of phylogenetic structure(phylogenetic diversity and phylogenetic relatedness)and six climate variables commonly used in ecology.Our results showed that(1)the scores of phylogenetic metrics derived from species-level phylogenies resolved at the genus level with species being attached to their respective genera as polytomies are very strongly or perfectly correlated to those derived from a phylogeny fully resolved at the species level(the mean of correlation coefficients is 0.973),and(2)the relationships between the scores of phylogenetic metrics and climate variables are consistent between the two sets of analyses based on the two types of phylogeny.Our study suggests that using species-level phylogenies resolved at the genus level with species being attached to their genera as polytomies is appropriate in studies exploring patterns of phylogenetic structure of species in ecological communities across geographical and ecological gradients.展开更多
Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a...Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data.To dissect this classic cyto-nuclear conflict,we developed the‘PhyloForensics’framework,a novel diagnostic approach to systematically identify sources of phylogenetic instability.This framework revealed that signal heterogeneity(topological entropy variance)and information content(the proportion of informative sites)are the primary drivers of gene-tree conflict.Empirically validating this,we show that removing a small subset of“loudly conflicted”genes resolves deep-level incongruence,yielding a single,highly-supported topology previously obscured by noise.Finally,complementing this sequence-based resolution,we demonstrate that mitogenome architecture provides powerful phylogenetic signals,revealing predictable,mitogenome-wide evolutionary patterns,such as a significant negative correlation between branch length and both GC content and RNA editing sites.By integrating a validated conflict-resolution framework with architectural genomics,our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.展开更多
The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fr...The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fragment genes,such as COI.The intrafamily phylogenetic relationships are ambiguous,lacking support from reliable molecular data.In this study,the mitochondrial genomes of eight species of Chamidae were sequenced for the first time and then annotated.Their structures and compositional characteristics were analyzed.The mitochondrial gene order in this family differed significantly.Concurrently,the evolutionary position and phylogenetic relationship among Chamidae species were explored,and the Veneroida phylogenetic tree was recreated.Maximum Likelihood and Bayesian Inference analyses supported the monophyly of Chamidae.Additionally,the divergence time within Chamidae was estimated based on mitochondrial DNA sequences,with the most ancient divergence estimated to occur during the early Cretaceous period,128 MYA.This phylogeny is significant for understanding the diversity and taxonomic status of Chamidae.展开更多
This study presents a comprehensive phylogenetic analysis on Batrachospermaceae based on key taxonomic identifiers(rbcL,psaA,psbA,and COI-5P)from some genera.To systematically explore the phylogenetic relationships an...This study presents a comprehensive phylogenetic analysis on Batrachospermaceae based on key taxonomic identifiers(rbcL,psaA,psbA,and COI-5P)from some genera.To systematically explore the phylogenetic relationships and taxonomy within Batrachospermaceae,we integrated molecular and morphological data,and explored the phylogeny,character evolution,and ancestral geographical origin and provided a theoretical support for the classification and geographic origination of Batrachospermaceae.Our findings reveal distinct relationships within the phylogenetic tree.Notably,10 genera(Sirodotia,Batrachospermum,Tuomeya,Volatus,Lympha,Nothocladus,Torularia,Sheathia,Nocturama,and Petrohua)are closely associated in the rbcL phylogenetic tree.Additionally,four genera(Kumanoa,Hoefkenia,Notohesperus,and Virescentia)exhibit high support ratios,indicating their close interrelations.Other genera,including Paludicola,Visia,Acarposporophycos,Macrosporophycos,Visioidea,Balliopsis,and Psilosiphon,exhibit clustering traits.Furthermore,the multigene sequences provide a robust support for Montagnia that forms a monophyletic group.Ancestral reconstruction of morphological characters identifies nine primitive character states,including whorl,fascicle length,cortical cells,secondary fascicles,the shape of carpogonical branch,spermatangia,carposporophyte,carpogonium and trichogyne,with Visia likely representing ancestral traits in Batrachospermaceae.Furthermore,geographical origin maps suggest a potential common ancestral of Batrachospermaceae origin in the American continent.Additional to conventional analyses,including evolutionary and ancestral reconstruction investigations into key morphological characters,we attempt to reconstruct the biogeography within the Batrachospermaceae,thus contributing to a nuanced understanding of its origin.展开更多
For the very first time,morpho-anatomical features of both fruiting bodies as well as below-ground structures have been confronted with a newly produced multigene phylogeny of root symbiotic basidiomycetes using one o...For the very first time,morpho-anatomical features of both fruiting bodies as well as below-ground structures have been confronted with a newly produced multigene phylogeny of root symbiotic basidiomycetes using one of the most speciose genera of ectomycorrhizal fungi(Russula,Russulales)as an example.In this first of two papers,the authors focus more specifically on below-ground structures.Our five-gene phylogeny divides the genus in five main clades,here interpreted as representing seven subgenera,all significantly supported.Although more conserved than features of fruiting bodies,the anatomy of ectomycorrhiza does not allow for an unambiguous characterization of the main clades resolved by phylogenetic analysis,but the anatomy of ectomycorrhiza performs better to naturally classify the species of this genus.Features of fruiting bodies remain much more adequate for the delimitation of terminal clades and are irreplaceable for morphological species identification.Tropical taxa mostly nest in ancient lineages,but are also present in some terminal clades of otherwise temperate species groups.The shift from plectenchymatic to pseudoparenchymatic ECM outer mantle structures happened most likely already in the paleotropics,and is here hypothesized to have facilitated a major diversification of the genus with new hosts in the northern hemisphere.Available data as well as our own observations on below ground structures of several Lactifluus species suggests that this genus shares with Russula the absence of lactifers in ECM mantles and rhizomorphs,contrary to species of Lactarius where lactifers are always present.First observations on rhizomorphs of species in Multifurca confirm the presence of vessel-like and ladder-like hyphae,also found in the other agarioid genera of this family,while distinct lactifers are only present in the lactarioid,but not in russuloid members of this genus.展开更多
The last decade has revealed an unexpected fungal diversity associated with natural rocks,often collected in environments influenced by harsh climatic conditions.Yet the phylogenetic affiliations and the taxonomy of m...The last decade has revealed an unexpected fungal diversity associated with natural rocks,often collected in environments influenced by harsh climatic conditions.Yet the phylogenetic affiliations and the taxonomy of many of these extreme fungi,mainly within Dothideomycetes,the largest class of Ascomycota,have only partially been described.In the present study we confirm that most rock inhabiting-fungi(RIF)are highly polyphyletic among Dothideomycetidae,mainly within the order Capnodiales,an order otherwise incorporating several families of major plant pathological importance.Novel taxa were identified within the two major and distinct clades of Teratosphaeriaceae,both comprising meristematic black fungi.Thirty one novel species and 13 new genera are proposed,based on ITS and partial nucLSU,RPB2 and BT2 sequences.展开更多
A controversial taxon,Hipparion plocodus,is reviewed in the present study.Hi.plocodus has been confirmed to be a valid species with definite diagnostic characteristics,represented by cranial specimens from Baode,Shanx...A controversial taxon,Hipparion plocodus,is reviewed in the present study.Hi.plocodus has been confirmed to be a valid species with definite diagnostic characteristics,represented by cranial specimens from Baode,Shanxi Province.The phylogenetic analysis performed in the present study,with a new matrix,shows that Hi.plocodus forms a monophyletic group with a European species,Hippotherium malpassii.Actually,no close relationship between so-called Hm.malpassii and the genus Hippotherium has been identified,and the record of stratigraphic range of this genus in late stage of Late Miocene is currently absent.Herein previously Hi.plocodus and Hm.malpassii have both attributed into“Hipparion”before the discovery of better material.Evolutionary stages and correlative absolute age showed that these two species should derive independently from some primitive clade.During the late stage of the Late Miocene,the development of the Asian summer monsoon enhanced the humidity of China,with forest and wood habitats expanding considerably under this setting.As the result,one Eurasian closed-habitat lineage thus extended its range into China,which had become very suited for it,give rise to“Hi.”plocodus.展开更多
Addressing the global challenge of uranium(U)-contaminated groundwater requires innovative bioremediation strategies.This study investigates Desulfovibrio desulfuricans,a neutrophilic and mesophilic sulfate-reducing b...Addressing the global challenge of uranium(U)-contaminated groundwater requires innovative bioremediation strategies.This study investigates Desulfovibrio desulfuricans,a neutrophilic and mesophilic sulfate-reducing bacteria(SRB)strain optimized for lowtemperature(15℃)and acidic(initial pH 4)conditions,to validate its bioaugmentation potential for uranium decontamination in groundwater.Our research aimed to assess its efficacy in treating U-contaminated groundwater and elucidate the optimal growth conditions for this strain in acidic and sulfate-enriched environments.We found that D.desulfuricans was phylogenetically distinct from the native microbial community in acidic Ucontaminated groundwater,while it maintained appreciable activity in sulfate reduction under contaminated groundwater conditions after accumulation.Acid-tolerant D.desulfuricans removed 75.87%of uranium and 30.64%of sulfate from acidic U-contaminated groundwater(pH 4.0)at 15℃ within 14 days.Furthermore,we explored the optimal sulfate concentration for bacterial growth,which was found to be 2000 mg/L,and an elevated Fe^(2+) concentration from 100 to 1000 mg/L increasingly stimulated sulfate-reducing activity.These findings provide a novel insight into the application of neutrophilic and mesophilic SRB in bioremediation of acidic and low-temperature groundwater after accumulation and underscore the feasibility of bioremediation by using exogenously pure SRB.展开更多
The collision of the Indian and Eurasian plates during the Eocene represents a major tectonic shift that significantly altered biotic dynamics and promoted species diversification across the Oriental region.To explain...The collision of the Indian and Eurasian plates during the Eocene represents a major tectonic shift that significantly altered biotic dynamics and promoted species diversification across the Oriental region.To explain the diversification of taxa from the Indian subcontinent into Southeast Asia,two principal hypotheses have been proposed:the“Biotic-ferry”and“Step-stone”models.The subfamily Perittopinae,a lineage of semi-aquatic bugs comprising a single genus and 20 extant species,provides an ideal system for testing these hypotheses due to its disjunct distribution spanning the Indian subcontinent and Southeast Asia.This study conducted a comprehensive taxonomic analysis of the entire subfamily,incorporating newly defined morphological characters and multilocus phylogenetic analyses to reconstruct evolutionary relationships and historical biogeography.Morphological and phylogenetic evidence confirmed the monophyly of Perittopinae and supported the establishment of three new genera-Indoperittopus gen.nov.,Pachyperittopus gen.nov.,and Falciperittopus gen.nov.-in addition to four new species and four new combinations.Biogeographic reconstructions indicated a southern Indian origin,with initial diversification potentially occurring during the mid-Paleocene,coinciding with the major phases of the India-Eurasia collision.Subsequent range expansion over marine barriers facilitated colonization of the northern Sunda Shelf,consistent with the“Step-stone”dispersal mechanism.Later northward expansion from the southern Sunda Shelf during the early Miocene triggered further diversification of the genus Perittopus within the Indo-China Peninsula.These findings advance understanding of Perittopinae systematics,phylogeny,and historical biogeography,identifying the northward drift of the Indian plate and its eventual collision with Eurasia as catalysts of diversification within this semi-aquatic lineage.展开更多
Two new species of Crassulaceae,Sedum baiwanense Yan S.Huang&Q.Fan and S.nankunshanense Yan S.Huang&Q.Fan,from Guangdong,China,are described and illustrated here.Phylogenetic analysis based on the internal tra...Two new species of Crassulaceae,Sedum baiwanense Yan S.Huang&Q.Fan and S.nankunshanense Yan S.Huang&Q.Fan,from Guangdong,China,are described and illustrated here.Phylogenetic analysis based on the internal transcribed spacer(ITS)region of nrDNA suggests that the two new species belong to Acre Clade,and are relative to S.subtile Miq.,S.tianmushanense Y.C.Ho&F.Chai,and S.jiulungshanense Y.C.Ho with high support values(node posterior probabilities=1).With high morphologically differences,we can easily distinguish species in this monophyletic group.展开更多
Coniophora is a widely distributed genus that includes species with resupinate basidiomata causing brown rot on fallen trees.In this study,two new species,Coniophora granulosa and Coniophora hainanensis,are described ...Coniophora is a widely distributed genus that includes species with resupinate basidiomata causing brown rot on fallen trees.In this study,two new species,Coniophora granulosa and Coniophora hainanensis,are described from Hainan Province based on molecular and morphological evidence.C.granulosa is characterized by having coriaceous basidiomata with granulose and light orange to grayish-orange hymenophore,relatively large and ellipsoid basidiospores measuring 12.5–14.2×8.2–9.5μm.C.hainanensis is characterized by having membranaceous basidiomata with smooth and grayish-orange to brownish orange hymenophore and fimbriate margin,and oblong-ellipsoid basidiospores measuring 9.8–12.2×5.2–6.5μm.Descriptions and illustrations are provided for the two new species.展开更多
In present study,morphological observation and phylogenetic relationship analyses by using multiple loci DNA sequences,including the internal transcribed spacer(ITS)regions,the large subunit nuclear ribosomal RNA gene...In present study,morphological observation and phylogenetic relationship analyses by using multiple loci DNA sequences,including the internal transcribed spacer(ITS)regions,the large subunit nuclear ribosomal RNA gene(nLSU),and the translation elongation factor 1-αgene(tef1),result in discovery of Sicyoideibasidia yunnanensis sp.nov.of Agaricales.The species is characterized by resupinate basidiomata with smooth,cream to yellowish hymenial surface,a monomitic hyphal system,generative hyphae bearing simple septa,and ellipsoid basidiospores.Phylogenetic analysis based on ITS+nLSU+tef1 data shows that the new species is closely related with S.bambusicola and S.punctata.展开更多
The exploration and understanding of myxosporean,one of the crucial stressors causing fish disease,have always been highly regarded.The present study aims to fully understand a novel myxobolid species,Thelohanellus xi...The exploration and understanding of myxosporean,one of the crucial stressors causing fish disease,have always been highly regarded.The present study aims to fully understand a novel myxobolid species,Thelohanellus xiushanensis n.sp.infecting the gill filaments of Carassius auratus from Chongqing,China,as well as the associated pathological impacts.A multifaceted analysis at various levels and perspectives was carried out by the approach integrating morphology,molecular systematics,histopathology,combined host and habitat,as well as SSU rDNA data.The results indicated that its mature myxospores displayed a tapering anterior and a blunt-rounded posterior,with a dropshape in front view and melon-seed shape in sutural view in morphology.The outer surface was covered with a transparent membrane sheath in valve view.The dimensions of myxospores were average(19.2±1.1)(17.1-21.0)×(10.0±0.7)(8.7-12.1)×(9.7±0.5)(9.1-10.8)μm.An elliptical polar capsule,containing four to five turns of single polar filament,measures(8.0±0.6)(6.9-9.1)×(6.6±0.3)(6.1-7.1)μm.Its SSU rDNA sequence demonstrated the closest similarity(99.95%)with an actinosporean Neoactinomyxum sp.NEO-7.Histopathological results indicated that numerous myxoplasmodia of T.xiushanensis n.sp.were located in the tips of the gill filaments,resulting in deformation and rupture of partial gill filaments.Furthermore,severely infected gill lamellae exhibited hyperplasia and fusion,accompanied by infiltration of numerous eosinophils.In addition,regenerated gill filaments were observed at the bases of partially ruptured gill filaments,indicating that the host’s gill tissue has the innate capacity to shed diseased tissues and regenerate new ones.This study has proved the present species and Neoactinomyxum sp.NEO-7 belong to the same myxosporean species but corresponding to different developmental stage,designated as a new species.This novel species is a potential pathogen for the host,which should not be ignored.This study not only enriches myxobolid biodiversity and demonstrates a potentially pathogenic agent,but also provides a valid diagnosis for the gill myxoboliosis caused by the present pathogen in aquaculture.展开更多
Over the past two decades,our understanding of Lauraceae,a large family of woody plants,has undergone significant advances in phylogeny,taxonomy,and biogeography.Molecular systematic studies have elucidated the basic ...Over the past two decades,our understanding of Lauraceae,a large family of woody plants,has undergone significant advances in phylogeny,taxonomy,and biogeography.Molecular systematic studies have elucidated the basic relationships within the family with plastid phylogenomic analyses providing robust support for deep-level relationships between Lauraceae lineages,leading to the recognition of nine tribes:Hypodaphnideae,Cryptocaryeae,Cassytheae,Neocinnamomeae,Caryodaphnopsideae,Mezilaureae,Perseeae,Laureae,and Cinnamomeae,with Mezilaureae validated here.Nuclear genomes and comparative genomics studies have also clarified aspects of the family’s evolutionary history and metabolic diversity.Taxonomic studies have focused mainly on the most diverse regions,e.g.,tropical Asia,tropical America,and Africa(Madagascar),with six new genera described and five reinstated since the last major overview of the family.The extensive fossil record suggests that Lauraceae diversified globally during the Late Cretaceous and Early Cenozoic.Biogeographic studies indicate that different lineages of the family are sorted into Gondwanan and Laurasian lineages,with patterns resulting from the disruption of boreotropical flora and multiple long-distance dispersal events.Phylogeographic studies,predominantly from East Asia,have shown patterns of in situ survival and demographic stability or expansion during the Quaternary.Nevertheless,many systematic relationships within the family remain unresolved and further research is needed into the complex biogeographic history and ecological roles of Lauraceae.A multifaceted approach integrating genomic studies,field work,morphological and ecological investigations is therefore needed to understand the evolution and diversity of this ecologically and economically significant plant family.展开更多
A new species of Bothriolepis(Placodermi,Antiarcha),B.zhujiangyuanensis sp.nov.,is described from the Eifelian(Middle Devonian)Shangshuanghe Formation at the Pearl River Source Scenic Area,Qujing,Yunnan Province,south...A new species of Bothriolepis(Placodermi,Antiarcha),B.zhujiangyuanensis sp.nov.,is described from the Eifelian(Middle Devonian)Shangshuanghe Formation at the Pearl River Source Scenic Area,Qujing,Yunnan Province,southwestern China and is characterized by a broad postpineal plate bearing a straight anterior margin,a premedian plate wider than long,and a weakly developed dorsal median ridge of the trunk shield.As the eighth Bothriolepis taxon in China,B.zhujiangyuanensis sp.nov.provides a wealth of morphological data to clarify the intrageneric interrelationships.Maximum parsimony analysis,using a revised data set of the genus with 76 ingroup taxa and 72 characters,yields a well-resolved consensus tree for Bothriolepis.The phylogenetic result shows a sister-group relationship between B.zhujiangyuanensis and B.babichevi from Kazakhstan,corroborating the biogeographic proximity between the South China and Kazakhstania blocks during the Middle Devonian.展开更多
基金supported by the Natural Science and Technology Foundation of Guizhou Province[[2020]1Z013](to Y.J.)the Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province[U1812401](to Y.J.).
文摘An earlier version of V.PhyloMaker has been broadly used to generate phylogenetic trees of vascular plants for botanical,biogeographical and ecological studies.Here,we update and enlarge this package,which is now called‘V.PhyloMaker2’.With V.PhyloMaker2,one can generate a phylogenetic tree for vascular plants based on one of three different botanical nomenclature systems.V.PhyloMaker2 can generate phylogenies for very large species lists(the largest species list that we tested included 365,198 species).V.PhyloMaker2 generates phylogenies at a fast speed.We provide an example(including a sample species list and an R script to run it)in this paper to show how to use V.PhyloMaker2 to generate phylogenetic trees.
文摘Phylogenies are essential to studies investigating the effect of evolutionary history on assembly of species in ecological communities and geographical and ecological patterns of phylogenetic structure of species assemblages.Because phylogenies well resolved at the species level are lacking for many major groups of organisms such as vascular plants,researchers often generate a species-level phylogenies using a phylogeny well resolved at the genus level as a backbone and attaching species to their respective genera in the phylogeny as polytomies or by using a megaphylogeny well resolved at the genus level as a backbone and adding additional species to the megaphylogeny as polytomies of their respective genera.However,whether the result of a study using species-level phylogenies generated in these ways is robust,compared to that based on phylogenies fully resolved at the species level,has not been assessed.Here,we use 1093 angiosperm tree assemblages(each in a 110110 km quadrat)in North America as a model system to address this question,by examining six commonly used metrics of phylogenetic structure(phylogenetic diversity and phylogenetic relatedness)and six climate variables commonly used in ecology.Our results showed that(1)the scores of phylogenetic metrics derived from species-level phylogenies resolved at the genus level with species being attached to their respective genera as polytomies are very strongly or perfectly correlated to those derived from a phylogeny fully resolved at the species level(the mean of correlation coefficients is 0.973),and(2)the relationships between the scores of phylogenetic metrics and climate variables are consistent between the two sets of analyses based on the two types of phylogeny.Our study suggests that using species-level phylogenies resolved at the genus level with species being attached to their genera as polytomies is appropriate in studies exploring patterns of phylogenetic structure of species in ecological communities across geographical and ecological gradients.
基金funded by the Shenzhen Science and Technology Program(Grant No.JCYJ20241202130723030)the National Natural Science Foundation of China(Grant No.32170238)+2 种基金the Guangdong Pearl River Talent Program(Grant No.2021QN02N792)the Shenzhen Fundamental Research Program(Grant No.JCYJ20220818103212025)the Chinese Academy of Agricultural Sciences Elite Youth Program(110243160001007)to Z.W.
文摘Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data.To dissect this classic cyto-nuclear conflict,we developed the‘PhyloForensics’framework,a novel diagnostic approach to systematically identify sources of phylogenetic instability.This framework revealed that signal heterogeneity(topological entropy variance)and information content(the proportion of informative sites)are the primary drivers of gene-tree conflict.Empirically validating this,we show that removing a small subset of“loudly conflicted”genes resolves deep-level incongruence,yielding a single,highly-supported topology previously obscured by noise.Finally,complementing this sequence-based resolution,we demonstrate that mitogenome architecture provides powerful phylogenetic signals,revealing predictable,mitogenome-wide evolutionary patterns,such as a significant negative correlation between branch length and both GC content and RNA editing sites.By integrating a validated conflict-resolution framework with architectural genomics,our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.
基金supported by grants from the Agriculture Seed Improvement Projects of Shandong Province(Nos.2022LZGCQY010,2021ZLGX03,and 2021TSGC 1240)the China Agriculture Research System Project(No.CARS-49)。
文摘The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fragment genes,such as COI.The intrafamily phylogenetic relationships are ambiguous,lacking support from reliable molecular data.In this study,the mitochondrial genomes of eight species of Chamidae were sequenced for the first time and then annotated.Their structures and compositional characteristics were analyzed.The mitochondrial gene order in this family differed significantly.Concurrently,the evolutionary position and phylogenetic relationship among Chamidae species were explored,and the Veneroida phylogenetic tree was recreated.Maximum Likelihood and Bayesian Inference analyses supported the monophyly of Chamidae.Additionally,the divergence time within Chamidae was estimated based on mitochondrial DNA sequences,with the most ancient divergence estimated to occur during the early Cretaceous period,128 MYA.This phylogeny is significant for understanding the diversity and taxonomic status of Chamidae.
基金Supported by the National Natural Science Foundation of China(No.32170204)。
文摘This study presents a comprehensive phylogenetic analysis on Batrachospermaceae based on key taxonomic identifiers(rbcL,psaA,psbA,and COI-5P)from some genera.To systematically explore the phylogenetic relationships and taxonomy within Batrachospermaceae,we integrated molecular and morphological data,and explored the phylogeny,character evolution,and ancestral geographical origin and provided a theoretical support for the classification and geographic origination of Batrachospermaceae.Our findings reveal distinct relationships within the phylogenetic tree.Notably,10 genera(Sirodotia,Batrachospermum,Tuomeya,Volatus,Lympha,Nothocladus,Torularia,Sheathia,Nocturama,and Petrohua)are closely associated in the rbcL phylogenetic tree.Additionally,four genera(Kumanoa,Hoefkenia,Notohesperus,and Virescentia)exhibit high support ratios,indicating their close interrelations.Other genera,including Paludicola,Visia,Acarposporophycos,Macrosporophycos,Visioidea,Balliopsis,and Psilosiphon,exhibit clustering traits.Furthermore,the multigene sequences provide a robust support for Montagnia that forms a monophyletic group.Ancestral reconstruction of morphological characters identifies nine primitive character states,including whorl,fascicle length,cortical cells,secondary fascicles,the shape of carpogonical branch,spermatangia,carposporophyte,carpogonium and trichogyne,with Visia likely representing ancestral traits in Batrachospermaceae.Furthermore,geographical origin maps suggest a potential common ancestral of Batrachospermaceae origin in the American continent.Additional to conventional analyses,including evolutionary and ancestral reconstruction investigations into key morphological characters,we attempt to reconstruct the biogeography within the Batrachospermaceae,thus contributing to a nuanced understanding of its origin.
文摘For the very first time,morpho-anatomical features of both fruiting bodies as well as below-ground structures have been confronted with a newly produced multigene phylogeny of root symbiotic basidiomycetes using one of the most speciose genera of ectomycorrhizal fungi(Russula,Russulales)as an example.In this first of two papers,the authors focus more specifically on below-ground structures.Our five-gene phylogeny divides the genus in five main clades,here interpreted as representing seven subgenera,all significantly supported.Although more conserved than features of fruiting bodies,the anatomy of ectomycorrhiza does not allow for an unambiguous characterization of the main clades resolved by phylogenetic analysis,but the anatomy of ectomycorrhiza performs better to naturally classify the species of this genus.Features of fruiting bodies remain much more adequate for the delimitation of terminal clades and are irreplaceable for morphological species identification.Tropical taxa mostly nest in ancient lineages,but are also present in some terminal clades of otherwise temperate species groups.The shift from plectenchymatic to pseudoparenchymatic ECM outer mantle structures happened most likely already in the paleotropics,and is here hypothesized to have facilitated a major diversification of the genus with new hosts in the northern hemisphere.Available data as well as our own observations on below ground structures of several Lactifluus species suggests that this genus shares with Russula the absence of lactifers in ECM mantles and rhizomorphs,contrary to species of Lactarius where lactifers are always present.First observations on rhizomorphs of species in Multifurca confirm the presence of vessel-like and ladder-like hyphae,also found in the other agarioid genera of this family,while distinct lactifers are only present in the lactarioid,but not in russuloid members of this genus.
基金The authors would like to thank PNRA(Italian National Program for Antarctic Research)for supporting sample collecting in the Antarctic,and the Italian National Antarctic Museum“Felice Ippolito”for supporting CCFEE(Culture Collection of Fungi From Extreme Environments)MIUR-PRIN 2008 is gratefully acknowledged for financial support concerning RIF studies in Italian Alps and ApenninesLaboratory work at the CBS was financed by the Royal Dutch Academy of Arts and Science(KNAW)and the Fonds voor Economische Stuctuurversterking(FES)with the grant‘Barcoding the CBS collections’.
文摘The last decade has revealed an unexpected fungal diversity associated with natural rocks,often collected in environments influenced by harsh climatic conditions.Yet the phylogenetic affiliations and the taxonomy of many of these extreme fungi,mainly within Dothideomycetes,the largest class of Ascomycota,have only partially been described.In the present study we confirm that most rock inhabiting-fungi(RIF)are highly polyphyletic among Dothideomycetidae,mainly within the order Capnodiales,an order otherwise incorporating several families of major plant pathological importance.Novel taxa were identified within the two major and distinct clades of Teratosphaeriaceae,both comprising meristematic black fungi.Thirty one novel species and 13 new genera are proposed,based on ITS and partial nucLSU,RPB2 and BT2 sequences.
文摘A controversial taxon,Hipparion plocodus,is reviewed in the present study.Hi.plocodus has been confirmed to be a valid species with definite diagnostic characteristics,represented by cranial specimens from Baode,Shanxi Province.The phylogenetic analysis performed in the present study,with a new matrix,shows that Hi.plocodus forms a monophyletic group with a European species,Hippotherium malpassii.Actually,no close relationship between so-called Hm.malpassii and the genus Hippotherium has been identified,and the record of stratigraphic range of this genus in late stage of Late Miocene is currently absent.Herein previously Hi.plocodus and Hm.malpassii have both attributed into“Hipparion”before the discovery of better material.Evolutionary stages and correlative absolute age showed that these two species should derive independently from some primitive clade.During the late stage of the Late Miocene,the development of the Asian summer monsoon enhanced the humidity of China,with forest and wood habitats expanding considerably under this setting.As the result,one Eurasian closed-habitat lineage thus extended its range into China,which had become very suited for it,give rise to“Hi.”plocodus.
基金supported by the Centralized R&D Project of China National Nuclear Corporation(CNNC[2021]No.144)the Key Research and Development Program of Hunan Province(Nos.2022SK2076 and 2020WK2022)+2 种基金the Natural Science Foundation of Changsha(No.kq2202089)the Postdoctoral Fellowship Program of CPSF(No.BX20230437)the Natural Science Foundation of Hunan Province(No.2023JJ30658).
文摘Addressing the global challenge of uranium(U)-contaminated groundwater requires innovative bioremediation strategies.This study investigates Desulfovibrio desulfuricans,a neutrophilic and mesophilic sulfate-reducing bacteria(SRB)strain optimized for lowtemperature(15℃)and acidic(initial pH 4)conditions,to validate its bioaugmentation potential for uranium decontamination in groundwater.Our research aimed to assess its efficacy in treating U-contaminated groundwater and elucidate the optimal growth conditions for this strain in acidic and sulfate-enriched environments.We found that D.desulfuricans was phylogenetically distinct from the native microbial community in acidic Ucontaminated groundwater,while it maintained appreciable activity in sulfate reduction under contaminated groundwater conditions after accumulation.Acid-tolerant D.desulfuricans removed 75.87%of uranium and 30.64%of sulfate from acidic U-contaminated groundwater(pH 4.0)at 15℃ within 14 days.Furthermore,we explored the optimal sulfate concentration for bacterial growth,which was found to be 2000 mg/L,and an elevated Fe^(2+) concentration from 100 to 1000 mg/L increasingly stimulated sulfate-reducing activity.These findings provide a novel insight into the application of neutrophilic and mesophilic SRB in bioremediation of acidic and low-temperature groundwater after accumulation and underscore the feasibility of bioremediation by using exogenously pure SRB.
基金supported by the Natural Science Foundation of Tianjin,China(24JCYBJC01910)National Natural Science Foundation of China(32322012,32470467)。
文摘The collision of the Indian and Eurasian plates during the Eocene represents a major tectonic shift that significantly altered biotic dynamics and promoted species diversification across the Oriental region.To explain the diversification of taxa from the Indian subcontinent into Southeast Asia,two principal hypotheses have been proposed:the“Biotic-ferry”and“Step-stone”models.The subfamily Perittopinae,a lineage of semi-aquatic bugs comprising a single genus and 20 extant species,provides an ideal system for testing these hypotheses due to its disjunct distribution spanning the Indian subcontinent and Southeast Asia.This study conducted a comprehensive taxonomic analysis of the entire subfamily,incorporating newly defined morphological characters and multilocus phylogenetic analyses to reconstruct evolutionary relationships and historical biogeography.Morphological and phylogenetic evidence confirmed the monophyly of Perittopinae and supported the establishment of three new genera-Indoperittopus gen.nov.,Pachyperittopus gen.nov.,and Falciperittopus gen.nov.-in addition to four new species and four new combinations.Biogeographic reconstructions indicated a southern Indian origin,with initial diversification potentially occurring during the mid-Paleocene,coinciding with the major phases of the India-Eurasia collision.Subsequent range expansion over marine barriers facilitated colonization of the northern Sunda Shelf,consistent with the“Step-stone”dispersal mechanism.Later northward expansion from the southern Sunda Shelf during the early Miocene triggered further diversification of the genus Perittopus within the Indo-China Peninsula.These findings advance understanding of Perittopinae systematics,phylogeny,and historical biogeography,identifying the northward drift of the Indian plate and its eventual collision with Eurasia as catalysts of diversification within this semi-aquatic lineage.
基金Supported by Forest Ecosystem Monitoring Project of Baiwan Provincial Nature Reserve,Qingxin,Guangdong(QCCG2025-003)Guangdong Provincial EQI Monitoring Project(GPCGD241115FG155F)Preliminary Survey and Monitoring and Conservation of Rare and Endangered Plant Species in Qingyuan Karst Mountain Botanical Garden(HT-99982024-0030)。
文摘Two new species of Crassulaceae,Sedum baiwanense Yan S.Huang&Q.Fan and S.nankunshanense Yan S.Huang&Q.Fan,from Guangdong,China,are described and illustrated here.Phylogenetic analysis based on the internal transcribed spacer(ITS)region of nrDNA suggests that the two new species belong to Acre Clade,and are relative to S.subtile Miq.,S.tianmushanense Y.C.Ho&F.Chai,and S.jiulungshanense Y.C.Ho with high support values(node posterior probabilities=1).With high morphologically differences,we can easily distinguish species in this monophyletic group.
基金supported by the National Natural Science Foundation of China(32270014)the Fundamental Research Funds for the Central Universities(QNTD202307).
文摘Coniophora is a widely distributed genus that includes species with resupinate basidiomata causing brown rot on fallen trees.In this study,two new species,Coniophora granulosa and Coniophora hainanensis,are described from Hainan Province based on molecular and morphological evidence.C.granulosa is characterized by having coriaceous basidiomata with granulose and light orange to grayish-orange hymenophore,relatively large and ellipsoid basidiospores measuring 12.5–14.2×8.2–9.5μm.C.hainanensis is characterized by having membranaceous basidiomata with smooth and grayish-orange to brownish orange hymenophore and fimbriate margin,and oblong-ellipsoid basidiospores measuring 9.8–12.2×5.2–6.5μm.Descriptions and illustrations are provided for the two new species.
文摘In present study,morphological observation and phylogenetic relationship analyses by using multiple loci DNA sequences,including the internal transcribed spacer(ITS)regions,the large subunit nuclear ribosomal RNA gene(nLSU),and the translation elongation factor 1-αgene(tef1),result in discovery of Sicyoideibasidia yunnanensis sp.nov.of Agaricales.The species is characterized by resupinate basidiomata with smooth,cream to yellowish hymenial surface,a monomitic hyphal system,generative hyphae bearing simple septa,and ellipsoid basidiospores.Phylogenetic analysis based on ITS+nLSU+tef1 data shows that the new species is closely related with S.bambusicola and S.punctata.
基金National Natural Science Foundation of China(31970409)Projects of Chongqing Science and Technology Commission(cstc2021jcyj-msxmX0731)。
文摘The exploration and understanding of myxosporean,one of the crucial stressors causing fish disease,have always been highly regarded.The present study aims to fully understand a novel myxobolid species,Thelohanellus xiushanensis n.sp.infecting the gill filaments of Carassius auratus from Chongqing,China,as well as the associated pathological impacts.A multifaceted analysis at various levels and perspectives was carried out by the approach integrating morphology,molecular systematics,histopathology,combined host and habitat,as well as SSU rDNA data.The results indicated that its mature myxospores displayed a tapering anterior and a blunt-rounded posterior,with a dropshape in front view and melon-seed shape in sutural view in morphology.The outer surface was covered with a transparent membrane sheath in valve view.The dimensions of myxospores were average(19.2±1.1)(17.1-21.0)×(10.0±0.7)(8.7-12.1)×(9.7±0.5)(9.1-10.8)μm.An elliptical polar capsule,containing four to five turns of single polar filament,measures(8.0±0.6)(6.9-9.1)×(6.6±0.3)(6.1-7.1)μm.Its SSU rDNA sequence demonstrated the closest similarity(99.95%)with an actinosporean Neoactinomyxum sp.NEO-7.Histopathological results indicated that numerous myxoplasmodia of T.xiushanensis n.sp.were located in the tips of the gill filaments,resulting in deformation and rupture of partial gill filaments.Furthermore,severely infected gill lamellae exhibited hyperplasia and fusion,accompanied by infiltration of numerous eosinophils.In addition,regenerated gill filaments were observed at the bases of partially ruptured gill filaments,indicating that the host’s gill tissue has the innate capacity to shed diseased tissues and regenerate new ones.This study has proved the present species and Neoactinomyxum sp.NEO-7 belong to the same myxosporean species but corresponding to different developmental stage,designated as a new species.This novel species is a potential pathogen for the host,which should not be ignored.This study not only enriches myxobolid biodiversity and demonstrates a potentially pathogenic agent,but also provides a valid diagnosis for the gill myxoboliosis caused by the present pathogen in aquaculture.
基金supported by the National Natural Science Foundation of China(31970222,31770569,31500454,31500165,32260060,32270217,32260056,31970223,32400180)the Science and Technology Basic Resources Investigation Program of China(2017FY100100,2017FY100102)+7 种基金Biodiversity Conservation Program of Chinese Academy of Sciences(ZSSD-013)National Key Research and Development Program of China(2022YFC2601200,2023YFF0805800)Yunnan Fundamental Research Projects(202201AS070055,202301AU070224)the 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy of Sciences(XTBG-1450101)Australian Research Council grant(DP130104314)RSNZ Marsden grant(11-UOO-043)Xingdian Talent Support Program(XDRC-QNRC-2022-0323)Shandong Provincial Natural Science Foundation(ZR2022QC214).
文摘Over the past two decades,our understanding of Lauraceae,a large family of woody plants,has undergone significant advances in phylogeny,taxonomy,and biogeography.Molecular systematic studies have elucidated the basic relationships within the family with plastid phylogenomic analyses providing robust support for deep-level relationships between Lauraceae lineages,leading to the recognition of nine tribes:Hypodaphnideae,Cryptocaryeae,Cassytheae,Neocinnamomeae,Caryodaphnopsideae,Mezilaureae,Perseeae,Laureae,and Cinnamomeae,with Mezilaureae validated here.Nuclear genomes and comparative genomics studies have also clarified aspects of the family’s evolutionary history and metabolic diversity.Taxonomic studies have focused mainly on the most diverse regions,e.g.,tropical Asia,tropical America,and Africa(Madagascar),with six new genera described and five reinstated since the last major overview of the family.The extensive fossil record suggests that Lauraceae diversified globally during the Late Cretaceous and Early Cenozoic.Biogeographic studies indicate that different lineages of the family are sorted into Gondwanan and Laurasian lineages,with patterns resulting from the disruption of boreotropical flora and multiple long-distance dispersal events.Phylogeographic studies,predominantly from East Asia,have shown patterns of in situ survival and demographic stability or expansion during the Quaternary.Nevertheless,many systematic relationships within the family remain unresolved and further research is needed into the complex biogeographic history and ecological roles of Lauraceae.A multifaceted approach integrating genomic studies,field work,morphological and ecological investigations is therefore needed to understand the evolution and diversity of this ecologically and economically significant plant family.
基金supported by the National Natural Science Foundation of China(4213020942002015)+3 种基金Youth Innovation Promotion Association CAS(2021070)General Project of Yunnan Provincial Science and Technology Department(202101BA070001-076)Project of Young and Middle-aged Academic and Technical Talents(202405AC350098)Meemann Chang Academician Workstation in Yunnan Province(202205AF150002)。
文摘A new species of Bothriolepis(Placodermi,Antiarcha),B.zhujiangyuanensis sp.nov.,is described from the Eifelian(Middle Devonian)Shangshuanghe Formation at the Pearl River Source Scenic Area,Qujing,Yunnan Province,southwestern China and is characterized by a broad postpineal plate bearing a straight anterior margin,a premedian plate wider than long,and a weakly developed dorsal median ridge of the trunk shield.As the eighth Bothriolepis taxon in China,B.zhujiangyuanensis sp.nov.provides a wealth of morphological data to clarify the intrageneric interrelationships.Maximum parsimony analysis,using a revised data set of the genus with 76 ingroup taxa and 72 characters,yields a well-resolved consensus tree for Bothriolepis.The phylogenetic result shows a sister-group relationship between B.zhujiangyuanensis and B.babichevi from Kazakhstan,corroborating the biogeographic proximity between the South China and Kazakhstania blocks during the Middle Devonian.
