Inferring phylogenetic trees from molecular sequences is a cornerstone of evolutionary biology.Many standard phylogenetic methods(such as maximum-likelihood[ML])rely on explicit models of sequence evolution and thus o...Inferring phylogenetic trees from molecular sequences is a cornerstone of evolutionary biology.Many standard phylogenetic methods(such as maximum-likelihood[ML])rely on explicit models of sequence evolution and thus often suffer from model misspecification or inadequacy.The on-rising deep learning(DL)techniques offer a powerful alternative.Deep learning employs multi-layered artificial neural networks to progressively transform input data into more abstract and complex representations.DL methods can autonomously uncover meaningful patterns from data,thereby bypassing potential biases introduced by predefined features(Franklin,2005;Murphy,2012).Recent efforts have aimed to apply deep neural networks(DNNs)to phylogenetics,with a growing number of applications in tree reconstruction(Suvorov et al.,2020;Zou et al.,2020;Nesterenko et al.,2022;Smith and Hahn,2023;Wang et al.,2023),substitution model selection(Abadi et al.,2020;Burgstaller-Muehlbacher et al.,2023),and diversification rate inference(Voznica et al.,2022;Lajaaiti et al.,2023;Lambert et al.,2023).In phylogenetic tree reconstruction,PhyDL(Zou et al.,2020)and Tree_learning(Suvorov et al.,2020)are two notable DNN-based programs designed to infer unrooted quartet trees directly from alignments of four amino acid(AA)and DNA sequences,respectively.展开更多
Understanding the underlying mechanisms driving species assembly along elevational gradients is of great interest in ecology and biogeography.The Himalaya is one of the world’s hotspots of biodiversity,and the elevat...Understanding the underlying mechanisms driving species assembly along elevational gradients is of great interest in ecology and biogeography.The Himalaya is one of the world’s hotspots of biodiversity,and the elevational gradient of the central Himalaya in Nepal is one of the longest elevational gradients in the world.Mosses are important constituents of vegetation in the Himalaya,and knowledge of geographic patterns and ecological causes of phylogenetic structure of mosses along elevational gradients in the Himalaya is critical to understanding the assembly of plant diversity in general,and moss diversity in particular,in the Himalaya.Here,we investigate the relationships of phylogenetic structure metrics reflecting different evolutionary depths with elevation and climatic variables representing mean temperature and precipitation conditions,climate extremes,and climate seasonality for mosses distributed along an elevational gradient spanning about 5000 m in the central Himalaya,Nepal.For a given climatic variable,different metrics of phylogenetic structure show different spatial and climatic patterns,but all phylogenetic metrics standardized for species richness show that phylogenetic dispersion in moss assemblages tend to increase with increasing elevation and decreasing temperature.The standardized effect size of mean pairwise distance of moss assemblages shows a triphasic(zig-zag)pattern,which is generally consistent with the triphasic patterns previously found in angiosperms and ferns along the same elevational gradient.Our study shows that temperature-related variables and climate seasonality variables are more important drivers of phylogenetic dispersion in mosses in Nepal,compared with precipitation-related variables and climate extreme variables,respectively.展开更多
Topographic complexity supports the maintenance of a high diversity of microhabitats,which may act as important‘safe havens’-or microrefugia-for biodiversity.Microrefugia are sites with specific environmental condit...Topographic complexity supports the maintenance of a high diversity of microhabitats,which may act as important‘safe havens’-or microrefugia-for biodiversity.Microrefugia are sites with specific environmental conditions that facilitate the persistence of species during environmental changes and exhibit unique ecoevolutionary dynamics.However,our knowledge about how topographic complexity and related ecoevolutionary selective forces influence the functional and phylogenetic signatures of species assemblages in microrefugia is very limited.Although the conceptual framework on the systematic integration of plant functional traits into the study of refugia is well established,more empirical studies on functional trait composition and functional diversity in refugia are urgently needed for more effective conservation.Here we analyzed the distribution of various plant functional traits and phylogenetic patterns in microhabitats(south-and north-facing slopes,and bottoms)of 30 large topographic depressions(i.e.doline microrefugia)and microhabitats of the surrounding plateaus in two distant forested karst regions.We found that plant assemblages in the understory of dolines and their surroundings are characterized by unique functional values and combinations of traits.Doline bottoms had the highest functional diversity among doline microhabitats and supported plant assemblages with considerably different trait compositions from the plateaus.Bottoms also had the highest phylogenetic diversity.These results suggest that topographic complexity in forested dolines has a significant effect on the distribution of plant functional traits in the understory.High functional and phylogenetic diversity in doline bottoms can have important consequences for the long-term survival of plant populations,highlighting that these microhabitats may provide a higher resilience and support an adaptive community-level response to natural and anthropogenic stressors.Understanding mechanisms that drive the survival of species within microrefugia is required to determine the best conservation and management strategies.展开更多
Bocapavovirus,a member of the genus Bocaparvovirus within the subfamily Parvovirinae and the family Parvoviridae,is a small,non-enveloped,single-stranded DNA virus.This pathogen poses health risks to both humans and a...Bocapavovirus,a member of the genus Bocaparvovirus within the subfamily Parvovirinae and the family Parvoviridae,is a small,non-enveloped,single-stranded DNA virus.This pathogen poses health risks to both humans and animals.The Bocaparvovirus genome.展开更多
Dear Editor,Swinepox virus(SWPV)belongs to the family Poxviridae,subfamily Chordopoxvirinae,and genus Varicellovirus(Lefkowitz et al.,2018).It exhibits the typical brick-shaped morphology and envelope structure charac...Dear Editor,Swinepox virus(SWPV)belongs to the family Poxviridae,subfamily Chordopoxvirinae,and genus Varicellovirus(Lefkowitz et al.,2018).It exhibits the typical brick-shaped morphology and envelope structure characteristic of poxviruses.Its genome is a 146 kbp linear double-stranded DNA encoding approximately 150 genes(Moorkamp et al.,2008;Schwarz et al.,2024).SWPV is highly host-specific,infecting only domestic pigs and wild boars.Transmission occurs through direct contact with infectious scabs,congenital transmission,or mechanical transmission by arthropods such as pig lice and house flies.The disease is more likely to occur in pig farms with poor sanitation conditions(Borst et al.,1990;Jindal,2015;Kaiser et al.,2021;Kumar et al.,2023;Riyesh et al.,2016).展开更多
The acceleration of global urbanization has caused habitat loss,fragmentation,and decrease of habitat quality,often leading to a decline in biodiversity.However,most previous urbanization studies focused on taxonomic ...The acceleration of global urbanization has caused habitat loss,fragmentation,and decrease of habitat quality,often leading to a decline in biodiversity.However,most previous urbanization studies focused on taxonomic diversity,with relatively less research on functional and phylogenetic diversity.In this study,we examined the phylogenetic and functional diversity and underlying influencing factors of bird communities in 37 urban parks in Nanjing,China.We conducted a systematic survey of bird communities in Nanjing urban parks and selected six park characteristics that are generally considered to affect bird diversity.Model selection based on corrected Akaike Information Criterion(AICc)and model averaging showed that park area,habitat diversity and building index(a proxy for the degree of urbanization)were significant factors affecting avian phylogenetic and functional diversity in Nanjing urban parks.Specifically,habitat diversity and park area were positively correlated with bird diversity,while the building index was negatively correlated with bird diversity.Moreover,the phylogenetic and functional structures of urban bird communities exhibited a clustered pattern,indicating that environmental filtering might play a role in shaping community composition.In addition,building index had certain impact on the construction of bird phylogenetic communities in urban parks.Our results suggest that expanding park areas,increasing habitat diversity and reducing building indexes may be effective measures to increase the avian phylogenetic and functional diversity in our system.展开更多
The authors regret that an error occurred during the preparation of their article:One of the official databases,which was used for functional trait collections,contained an incorrect term–'chametophytes'–for...The authors regret that an error occurred during the preparation of their article:One of the official databases,which was used for functional trait collections,contained an incorrect term–'chametophytes'–for the life form category'chamaephytes'.Unfortunately,this incorrect term was used throughout the article following the nomenclature of this official database:in one instance in the main text,in Fig.3 and its caption,in Fig.5,and in two instances in the supplementary material.展开更多
Rorippa indica is a wild oilseed crop of Brassicaceae with good environmental adaptability and strong stress resistance.This plant has become an important wild relative species for rapeseed(Brassica napus L.)and is us...Rorippa indica is a wild oilseed crop of Brassicaceae with good environmental adaptability and strong stress resistance.This plant has become an important wild relative species for rapeseed(Brassica napus L.)and is used to improve its agronomic traits,with important development and utilization value.However,the research of R.indica genetics is still lacking.And no mitochondrial genome(mitogenome)in the genus Rorippa has been expounded.To analyze the structural characteristics of the R.indica mitogenome,second-generation and third-generation sequencing techniques were made to assemble its mitogenome.The results showed that its mitogenome is composed of a single master circle DNA molecule,with 59 genes(33 protein-coding,23 tRNA,and 3 ribosomal RNA genes)annotated.The length of the circular genome is 219,775 bp,with aGCcontent of 45.24%.Themitochondrial genome contains 55 SSRs,17 tandem repeats,and 252 scattered repeat sequences,with scattered repeat sequences accounting for 77.78%.The top two codons with the highest expression levels are TTT and AUU.Moreover,377 RNA editing sites were forecasted in the R.indica mitogenome.And 22 collinear gene fragments were discriminated in the R.indica chloroplast andmitogenomes,with a total 13,153 bp length,accounting for 4.08%of the mitogenome sequence.The longest gene migration fragment is 2186 bp,and the shortest fragment is 42 bp.Furthermore,12 genes undergo complete migration between the two genomes,and 10 genes undergo partial migration.Systematic evolutionary analysis shows that R.indica and Brassica napus are grouped,indicating a close genetic relationship between the two.Herein,the R.indica mitogenome was sequenced and annotated,and it was compared with other Brassicaceae mitogenomes.A genomic data foundation was supplied for elucidating the R.indica origin and evolution.展开更多
Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry(phylogeny)from those of ecological or trait-based predictors on species traits.Phylogenetic Gene...Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry(phylogeny)from those of ecological or trait-based predictors on species traits.Phylogenetic Generalized Linear Models(PGLMs)address this issue by integrating phylogenetic relationships into statistical models.However,accurately partitioning explained variance among correlated predictors remains challenging.The phylolm.hp R package tackles this problem by extending the concept of“average shared variance”to PGLMs,enabling nuanced quantificationof the relative importance of phylogeny and other predictors.The package calculates individual likelihood-based R^(2) contributions of phylogeny and each predictor,accounting for both unique and shared explained variance.This approach overcomes limitations of traditional partial R^(2) methods,which often fail to sum the total R^(2) due to multicollinearity.We demonstrate the functionality of phylolm.hp through two case studies:one involving continuous trait data(maximum tree height in Californian species)and another focusing on binary trait data(species invasiveness in North American forests).The phylolm.hp package offers researchers a powerful tool to disentangle the contributions of phylogenetic and ecological predictors in comparative analyses.展开更多
Eucalyptus urophylla×E.grandis is a major hybrid species of timber plantations.However,our under-standing of Eucalyptus mitochondrial genome,especially within the Myrtaceae family,is limited.In this study,we empl...Eucalyptus urophylla×E.grandis is a major hybrid species of timber plantations.However,our under-standing of Eucalyptus mitochondrial genome,especially within the Myrtaceae family,is limited.In this study,we employed hybrid sequencing combining the Illumina and Oxford Nanopore sequencing to assemble and annotate the mitogenome(mtDNA)of E.urophylla×E.grandis.Our results reveal a structure characterized by one circular mol-ecule,with a cumulative length of 483,907 base pairs(bp)and a GC content of 44.96%.The circular molecule collec-tively harbored 59 annotated genes.Among these,38 were unique protein-coding genes(PCGs),accompanied by 18 transfer RNA(tRNA)genes and 3 ribosomal RNA(rRNA)genes.Our study also examined repetitive sequences,RNA editing sites,and intracellular sequence transfers within the mtDNA.Furthermore,we conducted a phylogenetic analy-sis between E.urophylla×E.grandis and 30 closely related species based on genetic affinities.The outcomes furnish a high-quality organelle genome for E.urophylla×E.grandis,thereby explaining basic insights into organelle genome evo-lution and phylogenetic relationships.展开更多
The H4 subtype of avian influenza virus(AIV)is prevalent worldwide,but only receives little attention due to its low pathogenicity in poultry.Consequently,it remains largely unclear whether H4 AIVs pose a potential th...The H4 subtype of avian influenza virus(AIV)is prevalent worldwide,but only receives little attention due to its low pathogenicity in poultry.Consequently,it remains largely unclear whether H4 AIVs pose a potential threat to the poultry industry and public health.During the period from 2011 to 2022,we conducted an active surveillance programm.A total of 154,762 swab samples were collected across various provinces,and 427 H4 viruses were detected,resulting in a positivity rate of 0.28%.All H4 viruses were isolated from poultry,primarily from ducks in live poultry markets.We further investigated the genetic evolutionary characteristics and pathogenicity of 20 H4Nx viruses isolated in our program.Phylogenetic analysis revealed that the 20 H4Nx viruses belonged to the Eurasian lineage and exhibited significant genetic diversity,with 19 distinct genotypes identified.Molecular characterization indicated that these viruses were low-pathogenicity AIVs with limited binding affinity to human receptors,yet they contained mutations associated with enhanced viral replication and pathogenicity in mammals.Pathogenicity tests conducted in ducks demonstrated that H4 viruses were weakly pathogenic,exhibiting limited replication and transmission capabilities.However,some viruses were able to replicate effectively in mice and induce weight loss.For instance,DK/AH/AG61/11(H4N6)can replicate efficiently in MDCK cells,indicating a potential threat to mammals.These findings underscore the importance of ongoing surveillance of H4 AIVs to better understand their evolution and transmission dynamics and to prevent potential public health risks.展开更多
Mitogenomes have been widely used in phylogenetic and taxonomic research,due to their maternal inheritance,accelerated evolutionary rates,compact circular structure,and the absence of introns.Although their utility is...Mitogenomes have been widely used in phylogenetic and taxonomic research,due to their maternal inheritance,accelerated evolutionary rates,compact circular structure,and the absence of introns.Although their utility is well-established,efficient mitogenome sequencing still poses a challenge for evolutionary studies.Here,we presented a novel hybridization capture protocol that enables high-fidelity sequencing of the complete mitogenome(16535 bp)of Odorrana nasuta.This genome exhibits typical anuran characteristics,including an A+T nucleotide bias(56.37%)and conserved gene composition.Notably,we identified a lineage-specific trnH transposition event that reorganizes the typical gene order into a unique trnH-trnL1-trnT-trnP-trnF cluster,which may be a potential synapomorphic trait for the genus Odorrana.Phylogenetic reconstruction using 13 protein-coding genes from 59 anuran species strongly supported the monophyly of Ranidae and its constituent genera(Odorrana,Rana,Lithobates,Amolops,Pelophylax,Glandirana),yet reveals the incongruence in the placement of Hylarana.The conflicting topologies observed for Hylarana and Glandirana across different studies highlight critical methodological limitations,including taxonomic sampling biases and data type dependency,which collectively compromise phylogenetic resolution.By integrating mitogenomic structure signatures with sequence-based phylogenies,this work advances our understanding of the systematics within Odorrana and highlights the need of multi-locus genomic datasets for resolving deep phylogenetic conflicts within Ranidae.展开更多
基金supported by the National Key R&D Program of China(2022YFD1401600)the National Science Foundation for Distinguished Young Scholars of Zhejang Province,China(LR23C140001)supported by the Key Area Research and Development Program of Guangdong Province,China(2018B020205003 and 2020B0202090001).
文摘Inferring phylogenetic trees from molecular sequences is a cornerstone of evolutionary biology.Many standard phylogenetic methods(such as maximum-likelihood[ML])rely on explicit models of sequence evolution and thus often suffer from model misspecification or inadequacy.The on-rising deep learning(DL)techniques offer a powerful alternative.Deep learning employs multi-layered artificial neural networks to progressively transform input data into more abstract and complex representations.DL methods can autonomously uncover meaningful patterns from data,thereby bypassing potential biases introduced by predefined features(Franklin,2005;Murphy,2012).Recent efforts have aimed to apply deep neural networks(DNNs)to phylogenetics,with a growing number of applications in tree reconstruction(Suvorov et al.,2020;Zou et al.,2020;Nesterenko et al.,2022;Smith and Hahn,2023;Wang et al.,2023),substitution model selection(Abadi et al.,2020;Burgstaller-Muehlbacher et al.,2023),and diversification rate inference(Voznica et al.,2022;Lajaaiti et al.,2023;Lambert et al.,2023).In phylogenetic tree reconstruction,PhyDL(Zou et al.,2020)and Tree_learning(Suvorov et al.,2020)are two notable DNN-based programs designed to infer unrooted quartet trees directly from alignments of four amino acid(AA)and DNA sequences,respectively.
文摘Understanding the underlying mechanisms driving species assembly along elevational gradients is of great interest in ecology and biogeography.The Himalaya is one of the world’s hotspots of biodiversity,and the elevational gradient of the central Himalaya in Nepal is one of the longest elevational gradients in the world.Mosses are important constituents of vegetation in the Himalaya,and knowledge of geographic patterns and ecological causes of phylogenetic structure of mosses along elevational gradients in the Himalaya is critical to understanding the assembly of plant diversity in general,and moss diversity in particular,in the Himalaya.Here,we investigate the relationships of phylogenetic structure metrics reflecting different evolutionary depths with elevation and climatic variables representing mean temperature and precipitation conditions,climate extremes,and climate seasonality for mosses distributed along an elevational gradient spanning about 5000 m in the central Himalaya,Nepal.For a given climatic variable,different metrics of phylogenetic structure show different spatial and climatic patterns,but all phylogenetic metrics standardized for species richness show that phylogenetic dispersion in moss assemblages tend to increase with increasing elevation and decreasing temperature.The standardized effect size of mean pairwise distance of moss assemblages shows a triphasic(zig-zag)pattern,which is generally consistent with the triphasic patterns previously found in angiosperms and ferns along the same elevational gradient.Our study shows that temperature-related variables and climate seasonality variables are more important drivers of phylogenetic dispersion in mosses in Nepal,compared with precipitation-related variables and climate extreme variables,respectively.
基金funded by the National Research,Development and Innovation Office(NKFIH FK 142428 grant)The contribution of Z.B.was supported by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences and by the New National Excellence Program of the Ministry for Culture and Innovation from the source of the National Research,Development and Innovation Fund(ÚNKP-23-5-SZTE-697)+2 种基金K.F.was supported by the New National Excellence Program of the Ministry for Culture and Innovation from the source of the National Research,Development and Innovation Fund(ÚNKP-23-3-SZTE-441)C.T.was supported by the NKFIH K 146137 grantA.E-V.was supported by the long-term research development project of the Czech Academy of Sciences(RVO 67985939).
文摘Topographic complexity supports the maintenance of a high diversity of microhabitats,which may act as important‘safe havens’-or microrefugia-for biodiversity.Microrefugia are sites with specific environmental conditions that facilitate the persistence of species during environmental changes and exhibit unique ecoevolutionary dynamics.However,our knowledge about how topographic complexity and related ecoevolutionary selective forces influence the functional and phylogenetic signatures of species assemblages in microrefugia is very limited.Although the conceptual framework on the systematic integration of plant functional traits into the study of refugia is well established,more empirical studies on functional trait composition and functional diversity in refugia are urgently needed for more effective conservation.Here we analyzed the distribution of various plant functional traits and phylogenetic patterns in microhabitats(south-and north-facing slopes,and bottoms)of 30 large topographic depressions(i.e.doline microrefugia)and microhabitats of the surrounding plateaus in two distant forested karst regions.We found that plant assemblages in the understory of dolines and their surroundings are characterized by unique functional values and combinations of traits.Doline bottoms had the highest functional diversity among doline microhabitats and supported plant assemblages with considerably different trait compositions from the plateaus.Bottoms also had the highest phylogenetic diversity.These results suggest that topographic complexity in forested dolines has a significant effect on the distribution of plant functional traits in the understory.High functional and phylogenetic diversity in doline bottoms can have important consequences for the long-term survival of plant populations,highlighting that these microhabitats may provide a higher resilience and support an adaptive community-level response to natural and anthropogenic stressors.Understanding mechanisms that drive the survival of species within microrefugia is required to determine the best conservation and management strategies.
基金supported by the Natural Science Foundation of Sichuan Province,China(2024NSFSC1272)the Innovation Team Development Funds for Sichuan Mutton Goat&Sheep,China(SCCXTD-2024-14)Scientific and Technological Innovation Team for Qinghai-Tibetan Plateau Research in Southwest Minzu University,China(2024CXTD08)。
文摘Bocapavovirus,a member of the genus Bocaparvovirus within the subfamily Parvovirinae and the family Parvoviridae,is a small,non-enveloped,single-stranded DNA virus.This pathogen poses health risks to both humans and animals.The Bocaparvovirus genome.
基金supported by National Key R&D Program of China(2021YFD1800300 and 2022YFD1800800)National Natural Science Foundation of China(32072841).
文摘Dear Editor,Swinepox virus(SWPV)belongs to the family Poxviridae,subfamily Chordopoxvirinae,and genus Varicellovirus(Lefkowitz et al.,2018).It exhibits the typical brick-shaped morphology and envelope structure characteristic of poxviruses.Its genome is a 146 kbp linear double-stranded DNA encoding approximately 150 genes(Moorkamp et al.,2008;Schwarz et al.,2024).SWPV is highly host-specific,infecting only domestic pigs and wild boars.Transmission occurs through direct contact with infectious scabs,congenital transmission,or mechanical transmission by arthropods such as pig lice and house flies.The disease is more likely to occur in pig farms with poor sanitation conditions(Borst et al.,1990;Jindal,2015;Kaiser et al.,2021;Kumar et al.,2023;Riyesh et al.,2016).
基金supported by the National Natural Science Foundation of China(No.32271734)。
文摘The acceleration of global urbanization has caused habitat loss,fragmentation,and decrease of habitat quality,often leading to a decline in biodiversity.However,most previous urbanization studies focused on taxonomic diversity,with relatively less research on functional and phylogenetic diversity.In this study,we examined the phylogenetic and functional diversity and underlying influencing factors of bird communities in 37 urban parks in Nanjing,China.We conducted a systematic survey of bird communities in Nanjing urban parks and selected six park characteristics that are generally considered to affect bird diversity.Model selection based on corrected Akaike Information Criterion(AICc)and model averaging showed that park area,habitat diversity and building index(a proxy for the degree of urbanization)were significant factors affecting avian phylogenetic and functional diversity in Nanjing urban parks.Specifically,habitat diversity and park area were positively correlated with bird diversity,while the building index was negatively correlated with bird diversity.Moreover,the phylogenetic and functional structures of urban bird communities exhibited a clustered pattern,indicating that environmental filtering might play a role in shaping community composition.In addition,building index had certain impact on the construction of bird phylogenetic communities in urban parks.Our results suggest that expanding park areas,increasing habitat diversity and reducing building indexes may be effective measures to increase the avian phylogenetic and functional diversity in our system.
文摘The authors regret that an error occurred during the preparation of their article:One of the official databases,which was used for functional trait collections,contained an incorrect term–'chametophytes'–for the life form category'chamaephytes'.Unfortunately,this incorrect term was used throughout the article following the nomenclature of this official database:in one instance in the main text,in Fig.3 and its caption,in Fig.5,and in two instances in the supplementary material.
基金supported by the Jiangxi Province Higher Education Teaching Research Project(JXJG-22-23-3,NSJG-21-25)Jiangxi Province Key Laboratory of Oil Crops Biology(YLKFKT202203).
文摘Rorippa indica is a wild oilseed crop of Brassicaceae with good environmental adaptability and strong stress resistance.This plant has become an important wild relative species for rapeseed(Brassica napus L.)and is used to improve its agronomic traits,with important development and utilization value.However,the research of R.indica genetics is still lacking.And no mitochondrial genome(mitogenome)in the genus Rorippa has been expounded.To analyze the structural characteristics of the R.indica mitogenome,second-generation and third-generation sequencing techniques were made to assemble its mitogenome.The results showed that its mitogenome is composed of a single master circle DNA molecule,with 59 genes(33 protein-coding,23 tRNA,and 3 ribosomal RNA genes)annotated.The length of the circular genome is 219,775 bp,with aGCcontent of 45.24%.Themitochondrial genome contains 55 SSRs,17 tandem repeats,and 252 scattered repeat sequences,with scattered repeat sequences accounting for 77.78%.The top two codons with the highest expression levels are TTT and AUU.Moreover,377 RNA editing sites were forecasted in the R.indica mitogenome.And 22 collinear gene fragments were discriminated in the R.indica chloroplast andmitogenomes,with a total 13,153 bp length,accounting for 4.08%of the mitogenome sequence.The longest gene migration fragment is 2186 bp,and the shortest fragment is 42 bp.Furthermore,12 genes undergo complete migration between the two genomes,and 10 genes undergo partial migration.Systematic evolutionary analysis shows that R.indica and Brassica napus are grouped,indicating a close genetic relationship between the two.Herein,the R.indica mitogenome was sequenced and annotated,and it was compared with other Brassicaceae mitogenomes.A genomic data foundation was supplied for elucidating the R.indica origin and evolution.
基金supported by the National Natural Science Foundation of China(32271551,32571954)National Key Research and Development Program of China(2023YFF0805800)the Metasequoia funding of Nanjing Forestry University.
文摘Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry(phylogeny)from those of ecological or trait-based predictors on species traits.Phylogenetic Generalized Linear Models(PGLMs)address this issue by integrating phylogenetic relationships into statistical models.However,accurately partitioning explained variance among correlated predictors remains challenging.The phylolm.hp R package tackles this problem by extending the concept of“average shared variance”to PGLMs,enabling nuanced quantificationof the relative importance of phylogeny and other predictors.The package calculates individual likelihood-based R^(2) contributions of phylogeny and each predictor,accounting for both unique and shared explained variance.This approach overcomes limitations of traditional partial R^(2) methods,which often fail to sum the total R^(2) due to multicollinearity.We demonstrate the functionality of phylolm.hp through two case studies:one involving continuous trait data(maximum tree height in Californian species)and another focusing on binary trait data(species invasiveness in North American forests).The phylolm.hp package offers researchers a powerful tool to disentangle the contributions of phylogenetic and ecological predictors in comparative analyses.
基金supported by the Fundamental Research Funds for the Central Universities(2021ZY62)the National Natural ScienceFoundation of China(31901337)the 5·5 Engineering Research&Innovation Team Project of Beijing Forestry University(BLRC2023C06).
文摘Eucalyptus urophylla×E.grandis is a major hybrid species of timber plantations.However,our under-standing of Eucalyptus mitochondrial genome,especially within the Myrtaceae family,is limited.In this study,we employed hybrid sequencing combining the Illumina and Oxford Nanopore sequencing to assemble and annotate the mitogenome(mtDNA)of E.urophylla×E.grandis.Our results reveal a structure characterized by one circular mol-ecule,with a cumulative length of 483,907 base pairs(bp)and a GC content of 44.96%.The circular molecule collec-tively harbored 59 annotated genes.Among these,38 were unique protein-coding genes(PCGs),accompanied by 18 transfer RNA(tRNA)genes and 3 ribosomal RNA(rRNA)genes.Our study also examined repetitive sequences,RNA editing sites,and intracellular sequence transfers within the mtDNA.Furthermore,we conducted a phylogenetic analy-sis between E.urophylla×E.grandis and 30 closely related species based on genetic affinities.The outcomes furnish a high-quality organelle genome for E.urophylla×E.grandis,thereby explaining basic insights into organelle genome evo-lution and phylogenetic relationships.
基金funded by the National Key Research and Development Program of China(Grant No.2021YFD1800201).
文摘The H4 subtype of avian influenza virus(AIV)is prevalent worldwide,but only receives little attention due to its low pathogenicity in poultry.Consequently,it remains largely unclear whether H4 AIVs pose a potential threat to the poultry industry and public health.During the period from 2011 to 2022,we conducted an active surveillance programm.A total of 154,762 swab samples were collected across various provinces,and 427 H4 viruses were detected,resulting in a positivity rate of 0.28%.All H4 viruses were isolated from poultry,primarily from ducks in live poultry markets.We further investigated the genetic evolutionary characteristics and pathogenicity of 20 H4Nx viruses isolated in our program.Phylogenetic analysis revealed that the 20 H4Nx viruses belonged to the Eurasian lineage and exhibited significant genetic diversity,with 19 distinct genotypes identified.Molecular characterization indicated that these viruses were low-pathogenicity AIVs with limited binding affinity to human receptors,yet they contained mutations associated with enhanced viral replication and pathogenicity in mammals.Pathogenicity tests conducted in ducks demonstrated that H4 viruses were weakly pathogenic,exhibiting limited replication and transmission capabilities.However,some viruses were able to replicate effectively in mice and induce weight loss.For instance,DK/AH/AG61/11(H4N6)can replicate efficiently in MDCK cells,indicating a potential threat to mammals.These findings underscore the importance of ongoing surveillance of H4 AIVs to better understand their evolution and transmission dynamics and to prevent potential public health risks.
基金the National Natural Science Foundation of China(NSFC)to Zhuo CHEN(Grant Nos.32270440 and 31601848)and Xiaohong CHEN(Grant No.U21A20192).
文摘Mitogenomes have been widely used in phylogenetic and taxonomic research,due to their maternal inheritance,accelerated evolutionary rates,compact circular structure,and the absence of introns.Although their utility is well-established,efficient mitogenome sequencing still poses a challenge for evolutionary studies.Here,we presented a novel hybridization capture protocol that enables high-fidelity sequencing of the complete mitogenome(16535 bp)of Odorrana nasuta.This genome exhibits typical anuran characteristics,including an A+T nucleotide bias(56.37%)and conserved gene composition.Notably,we identified a lineage-specific trnH transposition event that reorganizes the typical gene order into a unique trnH-trnL1-trnT-trnP-trnF cluster,which may be a potential synapomorphic trait for the genus Odorrana.Phylogenetic reconstruction using 13 protein-coding genes from 59 anuran species strongly supported the monophyly of Ranidae and its constituent genera(Odorrana,Rana,Lithobates,Amolops,Pelophylax,Glandirana),yet reveals the incongruence in the placement of Hylarana.The conflicting topologies observed for Hylarana and Glandirana across different studies highlight critical methodological limitations,including taxonomic sampling biases and data type dependency,which collectively compromise phylogenetic resolution.By integrating mitogenomic structure signatures with sequence-based phylogenies,this work advances our understanding of the systematics within Odorrana and highlights the need of multi-locus genomic datasets for resolving deep phylogenetic conflicts within Ranidae.
