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
The Hippoboscidae(Diptera:Calyptratae:Hippoboscoidea),or louse flies,are ectoparasites that suck blood of their avian or mammalian hosts with strong host specificity.Therefore,they are of great interest in evolutionar...The Hippoboscidae(Diptera:Calyptratae:Hippoboscoidea),or louse flies,are ectoparasites that suck blood of their avian or mammalian hosts with strong host specificity.Therefore,they are of great interest in evolutionary research.Here,we sequenced the mitochondrial genome of Ornithophila metallica(Schiner,1864)for the first time.It is 15,739 bp in length and possesses 37 mitochondrial genes,comprising 13 protein-coding genes(PCGs),22 tRNA and two rRNA genes,and a non-coding control region.The gene arrangement is consistent with that of most Dipteran mitochondrial genomes.The mitogenome is subsequently used for phylogeny reconstruction using all available mitogenomes of Hippoboscoidea.The Hippoboscidae is recovered as a monophyletic group,sister to the clade of(streblid+Nycteribiidae),which is the sister group to the monophyletic Glossinidae.Within the Hippoboscidae,the Ornithophila clusters together with Ornithomya,which is a sister group to(Melophagus+Lipoptena).This study broadens our knowledge of the Hippoboscidae and contributes to research in entomology,veterinary science,and ecology.展开更多
Penduline tits(genus Remiz)are small passerines distributed across Europe,Central and East Asia,and North Africa,renowned for their elaborate nests and unusually diverse mating systems.However,the taxonomy and evoluti...Penduline tits(genus Remiz)are small passerines distributed across Europe,Central and East Asia,and North Africa,renowned for their elaborate nests and unusually diverse mating systems.However,the taxonomy and evolutionary relationships within this genus have remained contentious due to overlapping breeding distributions and extensive hybridization.Using broad-range geographic sampling and whole-genome sequencing,here we report the phylogenetic relationships within this genus.Our results from maximum likelihood trees,species trees,population structure,and PCA analyses consistently identify four distinct,well-supported monophyletic clades.Based on these robust results,we support dividing Remiz into four species:the Eurasian Penduline Tit(R.pendulinus),Black-headed Penduline Tit(R.macronyx),White-crowned Penduline Tit(R.coronatus),and Chinese Penduline Tit(R.consobrinus).Among these species,R.consobrinus diverged earlier from other species,followed by R.coronatus,and then,R.pendulinus and R.macronyx.R.pendulinus and R.macronyx showed shallow genetic differentiation with recent divergence(~87,000 years ago)and ongoing gene flow.Our findings demonstrate the effectiveness of phylogenomic approaches in resolving taxonomic ambiguities and provide a robust evolutionary framework for tracing the diversification of life history traits,particularly nest structures and mating systems,across the genus.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
Understanding how diet and host phylogeny shape gut microbiota is fundamental to elucidating host-microbe interactions in extreme environments.The Qinghai-Tibet Plateau(QTP),characterized by harsh conditions,provides ...Understanding how diet and host phylogeny shape gut microbiota is fundamental to elucidating host-microbe interactions in extreme environments.The Qinghai-Tibet Plateau(QTP),characterized by harsh conditions,provides a natural laboratory for examining these relationships among sympatric species.Here,we investigated the dietary composition and gut microbiota of six passerine species inhabiting the QTP,comprising two endemic residents(White-rumped Snowfinch Onychostruthus taczanowskii and Ground Tit Pseudopodoces humilis),two nonendemic residents(Rock Sparrow Petronia petronia and Eurasian Tree Sparrow Passer montanus),and two nonendemic migratory species(Twite Linaria flavirostris and Black Redstart Phoenicurus ochruros),using highthroughput 18S and 16S rRNA sequencing.Our results revealed that dietary composition—dominated by Archaeplastida,Metazoa,Fungi,and the SAR supergroup—exhibited no significant interspecific variation,reflecting a high degree of trophic niche overlap.Although the overall diet was similar across species,the relative abundances of certain dietary components independently influenced specific microbial taxa.In particular,dietary Archaeplastida and Fungi showed phylogeny-independent positive correlations with 16 and 3 microbial genera,respectively,revealing fine-scale diet-microbiota associations.Evidence of phylosymbiosis was detected,as closely related species harbored more similar microbial communities driven by species-specific microbial biomarkers.Notably,our results suggested deterministic processes played a stronger role in endemic species,whereas stochastic community assembly dominated in non-endemic species,indicating distinct assembly mechanisms shaped by biogeographic history.Overall,this study reveals that while dietary similarity promotes convergent trophic niches among sympatric passerines,host phylogeny exerts a stronger influence on gut microbiota composition and assembly.These findings underline the synergistic roles of diet-microbiota interactions and phylosymbiosis dynamics as key adaptive strategies that enable birds to cope with the extreme environments of the QTP.展开更多
The natricid snake genus Herpetoreas Günther,1860,is predominantly distributed throughout the southern Himalayan region.Over the past decade,intensive field investigations and taxonomic studies have led to the su...The natricid snake genus Herpetoreas Günther,1860,is predominantly distributed throughout the southern Himalayan region.Over the past decade,intensive field investigations and taxonomic studies have led to the successful discovery and description of four cryptic species within this group.Nevertheless,data suggest that species diversity remains significantly underestimated and that the systematic position of certain members still requires clarification.Five new specimens initially identified as Herpetoreas were collected during field work on the Qinghai-Xizang Plateau.Comprehensive molecular phylogenetic analyses and morphological comparisons confirmed that two specimens represented a cryptic species,while the remaining three were identified as the rare H.sieboldii Günther,1860.In addition to the significant genetic divergence,the new species exhibits diagnostic morphological characteristics that distinguish it from its congeners:(1)preoculars 2;(2)postoculars 2;(3)temporals 1+2 or 1+1+2;(4)dorsal scale rows 19-19-17,all keeled except the outer one,dorsal scale reduction from 19 to 17 rows at 109^(th)-111^(th)VS;(5)ventrals 215219;(6)cloacal plate divided;(7)subcaudals 89-90,paired;(8)reduction of tail dorsal scales from 8 to 6 rows at position 35-36 SC,and from 6 to 4 at 74 SC;(9)tail segments with 4 supracaudal scale rows constitutes 0.38%-0.42%of those with 6 rows;(10)a wide dark stripe extending from the posterior eye to the upper corner of the mouth;(11)dorsum brick-brown in life,speckled with short dark stripes;(12)body and tail venter immaculate,each shield decorated with dark spots on the lateral edges.The systematics of H.sieboldii and H.platyceps are also discussed based on molecular data.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
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
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
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funded by the National Natural Science Foundation of China(3220036532170450)the Fundamental Research Funds for the Central Universities(JCYJ202511).
文摘The Hippoboscidae(Diptera:Calyptratae:Hippoboscoidea),or louse flies,are ectoparasites that suck blood of their avian or mammalian hosts with strong host specificity.Therefore,they are of great interest in evolutionary research.Here,we sequenced the mitochondrial genome of Ornithophila metallica(Schiner,1864)for the first time.It is 15,739 bp in length and possesses 37 mitochondrial genes,comprising 13 protein-coding genes(PCGs),22 tRNA and two rRNA genes,and a non-coding control region.The gene arrangement is consistent with that of most Dipteran mitochondrial genomes.The mitogenome is subsequently used for phylogeny reconstruction using all available mitogenomes of Hippoboscoidea.The Hippoboscidae is recovered as a monophyletic group,sister to the clade of(streblid+Nycteribiidae),which is the sister group to the monophyletic Glossinidae.Within the Hippoboscidae,the Ornithophila clusters together with Ornithomya,which is a sister group to(Melophagus+Lipoptena).This study broadens our knowledge of the Hippoboscidae and contributes to research in entomology,veterinary science,and ecology.
基金supported by the National Natural Science Foundation of China(32161143024,32500368,31970405)the Third Xinjiang Scientific Expedition Program(2022xjkk0200)+2 种基金INSF-NSFC Joint Research Project(No.4002006)HUN-REN-Debrecen University Reproductive Strategies Research Group grant(Ref 1102207)supported by the Postdoctoral Fellowship Program of CPSF under Grant Number GZC20240121。
文摘Penduline tits(genus Remiz)are small passerines distributed across Europe,Central and East Asia,and North Africa,renowned for their elaborate nests and unusually diverse mating systems.However,the taxonomy and evolutionary relationships within this genus have remained contentious due to overlapping breeding distributions and extensive hybridization.Using broad-range geographic sampling and whole-genome sequencing,here we report the phylogenetic relationships within this genus.Our results from maximum likelihood trees,species trees,population structure,and PCA analyses consistently identify four distinct,well-supported monophyletic clades.Based on these robust results,we support dividing Remiz into four species:the Eurasian Penduline Tit(R.pendulinus),Black-headed Penduline Tit(R.macronyx),White-crowned Penduline Tit(R.coronatus),and Chinese Penduline Tit(R.consobrinus).Among these species,R.consobrinus diverged earlier from other species,followed by R.coronatus,and then,R.pendulinus and R.macronyx.R.pendulinus and R.macronyx showed shallow genetic differentiation with recent divergence(~87,000 years ago)and ongoing gene flow.Our findings demonstrate the effectiveness of phylogenomic approaches in resolving taxonomic ambiguities and provide a robust evolutionary framework for tracing the diversification of life history traits,particularly nest structures and mating systems,across the genus.
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.
基金supported by the National Key Research and Development Program of China(2024YFC2310303)the National Natural Science Foundation of China(NSFC,No.32471572)awarded to D.L.+1 种基金NSFC(No.32171490)awarded to Y.W.Hebei Natural Science Foundation(HNSF,C2021204059)awarded to Y.S。
文摘Understanding how diet and host phylogeny shape gut microbiota is fundamental to elucidating host-microbe interactions in extreme environments.The Qinghai-Tibet Plateau(QTP),characterized by harsh conditions,provides a natural laboratory for examining these relationships among sympatric species.Here,we investigated the dietary composition and gut microbiota of six passerine species inhabiting the QTP,comprising two endemic residents(White-rumped Snowfinch Onychostruthus taczanowskii and Ground Tit Pseudopodoces humilis),two nonendemic residents(Rock Sparrow Petronia petronia and Eurasian Tree Sparrow Passer montanus),and two nonendemic migratory species(Twite Linaria flavirostris and Black Redstart Phoenicurus ochruros),using highthroughput 18S and 16S rRNA sequencing.Our results revealed that dietary composition—dominated by Archaeplastida,Metazoa,Fungi,and the SAR supergroup—exhibited no significant interspecific variation,reflecting a high degree of trophic niche overlap.Although the overall diet was similar across species,the relative abundances of certain dietary components independently influenced specific microbial taxa.In particular,dietary Archaeplastida and Fungi showed phylogeny-independent positive correlations with 16 and 3 microbial genera,respectively,revealing fine-scale diet-microbiota associations.Evidence of phylosymbiosis was detected,as closely related species harbored more similar microbial communities driven by species-specific microbial biomarkers.Notably,our results suggested deterministic processes played a stronger role in endemic species,whereas stochastic community assembly dominated in non-endemic species,indicating distinct assembly mechanisms shaped by biogeographic history.Overall,this study reveals that while dietary similarity promotes convergent trophic niches among sympatric passerines,host phylogeny exerts a stronger influence on gut microbiota composition and assembly.These findings underline the synergistic roles of diet-microbiota interactions and phylosymbiosis dynamics as key adaptive strategies that enable birds to cope with the extreme environments of the QTP.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(2024QZKK0200)the National Natural Science Foundation of China(NSFC 32370486).
文摘The natricid snake genus Herpetoreas Günther,1860,is predominantly distributed throughout the southern Himalayan region.Over the past decade,intensive field investigations and taxonomic studies have led to the successful discovery and description of four cryptic species within this group.Nevertheless,data suggest that species diversity remains significantly underestimated and that the systematic position of certain members still requires clarification.Five new specimens initially identified as Herpetoreas were collected during field work on the Qinghai-Xizang Plateau.Comprehensive molecular phylogenetic analyses and morphological comparisons confirmed that two specimens represented a cryptic species,while the remaining three were identified as the rare H.sieboldii Günther,1860.In addition to the significant genetic divergence,the new species exhibits diagnostic morphological characteristics that distinguish it from its congeners:(1)preoculars 2;(2)postoculars 2;(3)temporals 1+2 or 1+1+2;(4)dorsal scale rows 19-19-17,all keeled except the outer one,dorsal scale reduction from 19 to 17 rows at 109^(th)-111^(th)VS;(5)ventrals 215219;(6)cloacal plate divided;(7)subcaudals 89-90,paired;(8)reduction of tail dorsal scales from 8 to 6 rows at position 35-36 SC,and from 6 to 4 at 74 SC;(9)tail segments with 4 supracaudal scale rows constitutes 0.38%-0.42%of those with 6 rows;(10)a wide dark stripe extending from the posterior eye to the upper corner of the mouth;(11)dorsum brick-brown in life,speckled with short dark stripes;(12)body and tail venter immaculate,each shield decorated with dark spots on the lateral edges.The systematics of H.sieboldii and H.platyceps are also discussed based on molecular data.
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 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.
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.
