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
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
The taxonomic status of Episoriculus umbrinus has been contentious.This study aims to clarify its taxonomic position through mitochondrial genome analysis.Specimens of E.umbrinus were obtained from Liupanshui City,Gui...The taxonomic status of Episoriculus umbrinus has been contentious.This study aims to clarify its taxonomic position through mitochondrial genome analysis.Specimens of E.umbrinus were obtained from Liupanshui City,Guizhou Province,China.Genomic DNA was extracted,and 15 primer pairs were designed to amplify and sequence the complete mitochondrial genome of E.umbrinus.The results revealed that the mitochondrial genome of E.umbrinus is a circular double-stranded structure with a length of 17,073 bp,comprising 13 protein-coding genes,1 control region,22 tRNA genes,2 rRNA genes,and 1 origin of L-strand replication.Compared with E.caudatus,differences were observed between the two species in terms of replication origins,gene overlap regions,base lengths,and termination codons.Genetic distance analysis of mitochondrial protein-coding genes showed that the genetic distance between E.umbrinus and E.caudatus ranged from 0.069 to 0.125.A phylogenetic tree constructed based on the concatenated sequences of the 13 protein-coding genes indicated that E.umbrinus clustered as a distinct branch with the other three species within the genus Episoriculus.This study confirmed at the molecular level that E.umbrinus is an independent species rather than a subspecies of E.caudatus.The mitochondrial genome sequence of E.umbrinus provides an important supplementary information for the genetic research of this species and offers new evidence for the phylogenetic study of the tribe Nectogalini.展开更多
Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris,but their cytological and evolutionary consequences remain poorly understood.Here,we investigated chromosome numbers an...Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris,but their cytological and evolutionary consequences remain poorly understood.Here,we investigated chromosome numbers and genome sizes in 64 accessions representing the morphological diversity across the genus.Chromosome numbers ranged from 12 to 33,with seven accessions newly identified,including L.chunxiaoensis(2n=33),two putative L.guangxiensis(2n=19),and fivenatural hybrids(2n=16,18,29,33).Genome sizes varied from 18.03 Gb(L.wulingensis)to 32.62 Gb(L.caldwellii).Although no significantcorrelationwas found between genome size and chromosome number across all accessions,a strong correlation within ploidy-level groups(i.e.,diploid or aneuploid)suggested roles for post-polyploid diploidization,aneuploidy,and dysploidy in speciation.Phylogenetic analyses based on chloroplast genomes and nuclear DNA sequences revealed significantdiscordance,indicating a complex reticulate evolution and historical hybridization,which may complicate morphological classification.Chromosome number aligned more closely with morphological groups,underscoring the necessity of integrating cytological,molecular,and morphological data for accurate taxonomy,particularly in largegenome taxa.Based on this evidence,we propose a putative speciation pathway involving multiple hybridization and polyploidization events,with allopolyploidy playing a predominant role.Furthermore,our results indicate that the species L.insularis and L.longifolia are geographic populations of L.sprengeri and L.aurea,respectively,and confirmedthe distribution of L.traubii and L.albiflora in China' Mainland.These findingsoffer new insights into the mechanisms underlying speciation,interspecificrelationships,and the evolutionary history of Lycoris.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
Urban wetlands are considered as"habitat islands"within the urban matrix that contribute to species conservation.Waterbirds are sensitive pollution indicators in terrestrial and aquatic ecosystems,and their ...Urban wetlands are considered as"habitat islands"within the urban matrix that contribute to species conservation.Waterbirds are sensitive pollution indicators in terrestrial and aquatic ecosystems,and their diversity in urban wetlands reflects the response of wildlife to urbanization.However,very few studies have investigated seasonal differences in the multidimensional diversity of waterbirds in urbanized landscapes.In this study,we analyzed various wetland parameters that could potentially affect the seasonal variations in multidimensional diversity of waterbirds in Nanjing,China.We surveyed waterbirds in 29 urban wetlands using the point count method during breeding and non-breeding seasons from November 2022 to June 2023.We then employed multiple linear regressions and information-theoretic approaches to investigate the impact of wetland characteristics on waterbird diversity.We found that water body area and buffer zone connectivity consistently emerged as positive factors affecting waterbird taxonomic and phylogenetic diversity across seasons.Conversely,the urbanization synthetic index was negatively correlated with waterbird diversity only during the breeding season.Regarding functional diversity,we found that the positive correlation between buffer zone connectivity and waterbird diversity was specific to the breeding season.Therefore,for effective conservation of waterbird diversity in our system,wetland planning should prioritize expanding wetland water body areas,enhancing wetland connectivity,minimizing human disturbance during the breeding season,and implementing ecological restoration measures in urbanized wetlands to mitigate adverse effects of urbanization.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
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
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
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.
基金supported by the Research Project of Mudanjiang Normal University(GP2022009,HX2023004)the Heilongjiang Provincial Natural Funds(LH2021C095).
文摘The taxonomic status of Episoriculus umbrinus has been contentious.This study aims to clarify its taxonomic position through mitochondrial genome analysis.Specimens of E.umbrinus were obtained from Liupanshui City,Guizhou Province,China.Genomic DNA was extracted,and 15 primer pairs were designed to amplify and sequence the complete mitochondrial genome of E.umbrinus.The results revealed that the mitochondrial genome of E.umbrinus is a circular double-stranded structure with a length of 17,073 bp,comprising 13 protein-coding genes,1 control region,22 tRNA genes,2 rRNA genes,and 1 origin of L-strand replication.Compared with E.caudatus,differences were observed between the two species in terms of replication origins,gene overlap regions,base lengths,and termination codons.Genetic distance analysis of mitochondrial protein-coding genes showed that the genetic distance between E.umbrinus and E.caudatus ranged from 0.069 to 0.125.A phylogenetic tree constructed based on the concatenated sequences of the 13 protein-coding genes indicated that E.umbrinus clustered as a distinct branch with the other three species within the genus Episoriculus.This study confirmed at the molecular level that E.umbrinus is an independent species rather than a subspecies of E.caudatus.The mitochondrial genome sequence of E.umbrinus provides an important supplementary information for the genetic research of this species and offers new evidence for the phylogenetic study of the tribe Nectogalini.
基金supported by the ScientificFund of Nanjing Botanical Garden Men.Sun Yat-Sen(JSPKLB202519)Jiangsu Provincial Crop Germplasm Resource Bank(Lycoris)(JS-ZW-K04)Forestry Science and Technology Popularization Demonstration Project of the Central Finance[Su(2024)TG06].
文摘Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris,but their cytological and evolutionary consequences remain poorly understood.Here,we investigated chromosome numbers and genome sizes in 64 accessions representing the morphological diversity across the genus.Chromosome numbers ranged from 12 to 33,with seven accessions newly identified,including L.chunxiaoensis(2n=33),two putative L.guangxiensis(2n=19),and fivenatural hybrids(2n=16,18,29,33).Genome sizes varied from 18.03 Gb(L.wulingensis)to 32.62 Gb(L.caldwellii).Although no significantcorrelationwas found between genome size and chromosome number across all accessions,a strong correlation within ploidy-level groups(i.e.,diploid or aneuploid)suggested roles for post-polyploid diploidization,aneuploidy,and dysploidy in speciation.Phylogenetic analyses based on chloroplast genomes and nuclear DNA sequences revealed significantdiscordance,indicating a complex reticulate evolution and historical hybridization,which may complicate morphological classification.Chromosome number aligned more closely with morphological groups,underscoring the necessity of integrating cytological,molecular,and morphological data for accurate taxonomy,particularly in largegenome taxa.Based on this evidence,we propose a putative speciation pathway involving multiple hybridization and polyploidization events,with allopolyploidy playing a predominant role.Furthermore,our results indicate that the species L.insularis and L.longifolia are geographic populations of L.sprengeri and L.aurea,respectively,and confirmedthe distribution of L.traubii and L.albiflora in China' Mainland.These findingsoffer new insights into the mechanisms underlying speciation,interspecificrelationships,and the evolutionary history of Lycoris.
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.
基金supported by the National Natural Science Foundation of China(32271743).
文摘Urban wetlands are considered as"habitat islands"within the urban matrix that contribute to species conservation.Waterbirds are sensitive pollution indicators in terrestrial and aquatic ecosystems,and their diversity in urban wetlands reflects the response of wildlife to urbanization.However,very few studies have investigated seasonal differences in the multidimensional diversity of waterbirds in urbanized landscapes.In this study,we analyzed various wetland parameters that could potentially affect the seasonal variations in multidimensional diversity of waterbirds in Nanjing,China.We surveyed waterbirds in 29 urban wetlands using the point count method during breeding and non-breeding seasons from November 2022 to June 2023.We then employed multiple linear regressions and information-theoretic approaches to investigate the impact of wetland characteristics on waterbird diversity.We found that water body area and buffer zone connectivity consistently emerged as positive factors affecting waterbird taxonomic and phylogenetic diversity across seasons.Conversely,the urbanization synthetic index was negatively correlated with waterbird diversity only during the breeding season.Regarding functional diversity,we found that the positive correlation between buffer zone connectivity and waterbird diversity was specific to the breeding season.Therefore,for effective conservation of waterbird diversity in our system,wetland planning should prioritize expanding wetland water body areas,enhancing wetland connectivity,minimizing human disturbance during the breeding season,and implementing ecological restoration measures in urbanized wetlands to mitigate adverse effects of urbanization.
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.
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.
