The leaf muntjac （Muntiacus putaoensis） is an endemic deer species found in the east trans- Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little gene...The leaf muntjac （Muntiacus putaoensis） is an endemic deer species found in the east trans- Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little genetic data exists for this species, thus our knowledge of distribution rangs and population sizes likewise remain limited. We obtained mtDNA genes and the complete mitochondrial genome sequence of M. putaoensis using PCR, followed by direct sequencing. The complete mitogenome sequence was determined as a circular 16 349 bp mitochondrial genome, containing 13 protein-coding genes, two rRNA genes 22 tRNA genes, and one control region, the gene composition and order of which were similar to most other vertebrates so far reported. Most mitochondrial genes, except for ND6 and eight tRNAs, were encoded on the heavy strand. The overall base composition of the heavy strand was 33.1% A, 29.3% T, 24.2% C, and 13.4% G, with a strong AT bias of 62.4%. There were seven regions of gene overlap totaling 95 bp and 11 intergenic spacer regions totaling 74 bp. Phylogenetic analyses （ML and BI） among the Muntiacus genus based on the sequenced of mitogenome and ND4L-ND4 supported M. putaoensis as a member of Muntiacus, most closely related to M. vuquangensis. However, when analyses based on cyt b included two more muntjacs, M. truongsonensis was most closely related to M. putaoensis rather than M. vuquangensis, and together with M. rooseveltorum, likely forming a M. rooseveltorum complex of the species. This study will help in the exploration of the evolutionary history and taxonomic status of the leaf muntjac, as well as its protection as a genetic resource.展开更多
Dengue virus(DENV)is one of the most important arboviral pathogens in the tropics and subtropics,and nearly one-third of the world's population is at risk of infection.The transmission of DENV involves a sylvatic ...Dengue virus(DENV)is one of the most important arboviral pathogens in the tropics and subtropics,and nearly one-third of the world's population is at risk of infection.The transmission of DENV involves a sylvatic cycle between nonhuman primates(NHP)and Aedes genus mosquitoes,and an endemic cycle between human hosts and predominantly Aedes aegypti.DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes(DENV-1-4).Phylogenetic analyses of DENV have revealed its origin,epidemiology,and the drivers that determine its molecular evolution in nature.This review discusses how phyloge-netic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.展开更多
Understanding the level of genetic diversity in any population is an important requisite towards strategizing measures for conservation and improvement of stocks. This study focused on the assessment of phylogenetics ...Understanding the level of genetic diversity in any population is an important requisite towards strategizing measures for conservation and improvement of stocks. This study focused on the assessment of phylogenetics and molecular divergence of tilapia fish species obtained from two populations (Domita in South-South and Odeda in South-West, Nigeria) using the displacement loop (D-loop) and cytochrome b region of the mitochondrial deoxyribonucleic acid (mtDNA). A total of 28 samples (15 from South-South and 13 from South-West) were used for the genetic analysis. DNA was extracted from the tissue of all the samples using Quik-gDNATM miniPrep kit. The D-loop containing the hypervariable region was sequenced for all samples from the two populations, while cytochrome b (Cyt b) region of mtDNA was only sequenced for samples from South-South population. Chromatograms of the sequences were viewed and edited using Bioedit software. Multiple sequence alignment was carried out using molecular evolutionary genetic analysis (MEGA) software before subsequent genetic analyses. Phylogenetic analysis grouped the samples into two clusters based on population. Also, when the two mitochondrial regions were pooled together, they clustered into two major groups based on mitochondrial regions. Analysis of molecular variance (AMOVA) revealed 37.32% variation within population and 62.68% variation among population with a significant fixation index of 0.627 (p 0.05). The genetic distance inferred between D-loop regions of South-South and South-West populations was 0.243. Maternal lineage analysis revealed that the origin of tilapia fish from both populations could be traced to Oreochromis spirilus and Oreochromis leucostictus based on mitochondrial D-loop region. The findings of this study revealed molecular divergence among the tilapia populations and may serve as pivot information for the genetic improvement of this important species.展开更多
The molecular phylogenetics of the Lepidoptera （butterflies and moths） is well studied, but that of Trichoptera （caddisflies）, the sister clade of Lepidoptera, is less studied. The PCR primer libraries developed f...The molecular phylogenetics of the Lepidoptera （butterflies and moths） is well studied, but that of Trichoptera （caddisflies）, the sister clade of Lepidoptera, is less studied. The PCR primer libraries developed for lepidopteran phylogenetics might work in Trichoptera. DNA from 8 caddisfly species （Asynarchus nigriculus （Banks, 1908）, Grammotaulius lorettae Denning, 1941, Hesperophylax occidentalis （Banks, 1908）, Limnephilus externus Hagen, 1861, Limnephilus picturatus McLachlan, 1875, Limnephilus secludens Banks, 1914, Limnephilus sublunatus Provancher, 1877 and Agrypnia deflata （Milne, 1931）） was used to screen for amplification. 107 primer pairs for 45 nuclear and 3 mitochondrial genes were tested. Primers for 1 new gene （40S ribosomalprotein $2 （RPS2）） and 8 genes previously used in Trichopteran phylogenetics were recovered （16S rRNA, 18S rRNA, carbamoyl-phosphate synthetase （CAD）, cytoehrome oxidase I （CO1）, cytochrome oxidase 11 （COIl）, elongation factor-1 alpha （EF-1 alpha）, isoeitrate dehydrogenase （IDH）, and RNA polymerase-II （POL-I1））. New primer pairs extended the genomic region sampled for many genes. Evolution rates among loci varied by 2 orders of magnitude. Differences among evolution rates and modes of inheritance offer flexible tools for resolving phylogenetic questions and examining genome evolution in the Trichoptera. Screening libraries of PCR primers is a useful approach for identifying PCR primers in related taxa with limited molecular genetic resources.展开更多
The wood anatomy of corystosperms is fundamentally consistent with that of gymnosperms,yet their growth ring boundaries share anatomical features with extant angiosperms.This transitional morphology strongly supports ...The wood anatomy of corystosperms is fundamentally consistent with that of gymnosperms,yet their growth ring boundaries share anatomical features with extant angiosperms.This transitional morphology strongly supports the interpretation of corystosperms as an evolutionary intermediate between gymnosperms and angiosperms.The first application of X-Ray fluorescence(XRF)chemical analysis to fossil wood taxa of Fengweioxylon yielded the above conclusion.By using growth ring analysis and ecological reconstructions,we suggest that corystosperms were large evergreen trees with leaf retention periods of three to five years.They likely thrived in warm summer environments where prolonged foliage retention provided adaptive benefits.展开更多
The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies.However, there is no comprehen...The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies.However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China. We conducted a spatial phylogenetic analysis of the Chinese angiosperm flora at the generic level to identify centers of neo-and paleoendemism. Our results indicate that:(i) themajority of grid cells in China with significantly high phylogenetic endemism(PE) were located in the mountainous regions;(ii) four of the nine centers of endemism recognized, located in northern and western China, were recognized for the first time;(iii) arid and semiarid regions in Northwest China were commonly linked to significant PE, consistent with other spatial phylogenetic studies worldwide;and(iv) six highpriority conservation gaps were detected by overlaying the boundaries of China’s nature reserves on all significant PE cells. Overall, we conclude that the mountains of southern and northern China contain both paleo-endemics(ancient relictual lineages) and neo-endemics(recently diverged lineages). The areas we highlight as conservation priorities are important for broad-scale planning, especially in the context of evolutionary history preservation.展开更多
Despite worldwide distribution and rich diversity,the knowledge of mitochondrial genome(mtgenome)characteristics within the family Tenebrionidae(Coleoptera)is still very limited,and phylogenetics remain unresolved for...Despite worldwide distribution and rich diversity,the knowledge of mitochondrial genome(mtgenome)characteristics within the family Tenebrionidae(Coleoptera)is still very limited,and phylogenetics remain unresolved for the family.In this study,the mtgenomes for 12 species are newly sequenced and annotated.Three of the species represent the first report of complete mtgenomes from the subfamily Alleculinae.Comparative analysis of 36 tenebrionid mtgenomes finds that gene composition and order are the same as a theoretical ancestral insect mtgenome,and AT bias,length variation,and codon usage are consistent with other reported beetle mtgenomes.Some intergenic overlap and gap sequences may contain phylogenetically informative information,whereas neither the conserved nor repeat sequences in the control region do.The subfamilies Lagriinae,Pimeliinae,Stenochiinae,and Alleculinae are found to be monophyletic,and the subfamilies Diaperinae and Tenebrioninae polyphyletic in our study.Furthermore,Lagriinae is sister to the rest of the subfamilies.At the tribal level,the tribes Lagriini in the subfamily Lagrrinae;Strongyliini in Stenochiinae;Cteniopodini in Alleculinae;and Triboliini,Opatrini,and Amarygmini in Tenebrioninae are monophyletic;while Diaperini in Diaperinae,and Tenebrionini in Tenebrioninae are polyphyletic.展开更多
Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For ac...Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For accurately reconstructing the phylogeny and evolutionary history of plant groups,correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data.We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011.Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets,or did not address in detail possible reasons for incongruence between the two data sets.By reviewing various methods,we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data,which includes four steps:identifying significant incongruence,determining conflicting taxa,providing possible interpretations for incongruence,and reconstructing the phylogeny after treating incongruence.Particular attention is given to explanation of the cause of incongruence.We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.展开更多
The informal term‘dahongjun’or‘big red mushroom’is a group of red-coloured russulas widely collected and consumed in southern China,originally mistakenly recognized as the European Russula vinosa.Russula griseocar...The informal term‘dahongjun’or‘big red mushroom’is a group of red-coloured russulas widely collected and consumed in southern China,originally mistakenly recognized as the European Russula vinosa.Russula griseocarnosa was described from China in 2009,and since then,it has become the only available scientific name for‘dahongjun’.Nevertheless,several lineages exist within this complex,and whether these lineages represent real species is still an open question.Sampling in major producing areas of‘dahongjun’and phylogenetic species recognition using multi-locus data were conducted.Besides R.griseocarnosa nine additional species were identified under the commercial name‘dahongjun’,including R.dhakuriana,R.quercina,R.purpureozonata,R.yanheensis and a new species sister to R.griseocarnosa here described as R.occulta.The others were undescribed species close to R.laricina,R.lepida,and R.purpureozonata respectively.Six evolutionary lineages within R.griseocarnosa were defined by genealogical concordance phylogenetic species recognition based on five-locus DNA data.Conflicts among different genealogies suggested that R.griseocarnosa is best considered as a single phylogenetic species,comprising several infraspecific taxa.Lower coverage whole genome sequencing of R.griseocarnosa holotype discovered that its three individuals belong to three different clades.Lectotypification was made using one of the three individuals.A new variety R.griseocarnosa var.ailaoshanensis is described to name one of the terminal clades that is mainly distributed in Ailao Mountains.This variety differs morphologically from the type variety in its nearly white context,bigger spores and more inflated hyphae in the pileipellis.The morphological and molecular data provided in this study are helpful to identify wild edible mushrooms of Russula subgen.Russula.展开更多
The genus Boechera(Brassicaceae)serves as a model system for studying apomictic reproduction and ecological adaptations,with most species occurring in North America.The rare occurrence of Boechera species outside thei...The genus Boechera(Brassicaceae)serves as a model system for studying apomictic reproduction and ecological adaptations,with most species occurring in North America.The rare occurrence of Boechera species outside their typical range provides unique opportunities to investigate genome evolution in extralimital environments.One such species,B.calcarea,has been described from the Chandalaz Mountains in northeastern Asia(Russia).This study aimed to investigate the genome structure and evolutionary history of B.calcarea.However,our analyses reveal that the species does not belong to Boechera.Instead,an integrative approach combining cytogenetic,phylogenetic and repeatome analysis identified the species as a member of one of more ancestral clades in the tribe Arabideae.The diploid Parryodes calcarea(2n=16)exhibits Arabideae-specific chromosomal signatures,including multiple centromere repositionings.These findings clarify the misclassification of P.calcarea as Boechera,leaving Boechera falcata and Borodinia macrophylla as the only representatives of the Boechereae in the Old World.This study highlights the importance of an integrative approach in resolving taxonomic ambiguities and provides new insights into the diversification of the largest cruciferous tribe,the Arabideae.展开更多
Lignin is a significant secondary metabolite produced through the phenylpropanoid pathway.As a vital component of the plant cell wall,lignin affects various fruit characteristics,including size,seed quantity,and firmn...Lignin is a significant secondary metabolite produced through the phenylpropanoid pathway.As a vital component of the plant cell wall,lignin affects various fruit characteristics,including size,seed quantity,and firmness.In this study,we conducted comprehensive identification and phylogenetic analysis of 265 Caffeic acid O-methyltransferase(COMT)genes across ten different plant species,including Vaccinium corymbosum and four other Vaccinium species.The results reveal that VcCOMT38 is a promising structural gene for the biosynthesis of lignin in blueberry.An in vitro enzymatic assay of VcCOMT38 demonstrated that it is a special enzyme in the lignin biosynthesis pathway and prefers to use caffeic acid as a substrate over 5-hydroxyferulic acid.Transient overexpression and silencing of VcCOMT38 in Vaccinium corymbosum‘Northland’fruits demonstrated that VcCOMT38 participates in lignin biosynthesis and contributes to both an increased number of immature seeds and enhanced fruit firmness.The heterologous overexpression of VcCOMT38 in Nicotiana benthamiana revealed that this gene could increase the lignin content and the syringyl/guaiacyl(S/G)ratio,which determines the maximum monomer yield during lignin depolymerization.These results highlight VcCOMT38 as a crucial gene in lignin biosynthesis and its potential for improving lignin production in industry through genetically modified woody plants.展开更多
Conservationists have long debated whether fragmented habitats are best conserved by protecting a single large patch(SL)or several small patches(SS),i.e.,the SLOSS debate.Although this SLOSS debate has provided import...Conservationists have long debated whether fragmented habitats are best conserved by protecting a single large patch(SL)or several small patches(SS),i.e.,the SLOSS debate.Although this SLOSS debate has provided important insights into biodiversity conservation,research has predominantly focused on only one dimension of diversity(i.e.,taxonomic),failing to consider how phylogenetic and functional diversity might inform conservation strategies.In this study,we determined whether grasslands in the agro-pastoral ecotone of the Tabu River Basin,Inner Mongolia should be conserved by protecting a single large patch or several small patches.For this purpose,we quantified the relationships between three dimensions of biodiversity(taxonomic,phylogenetic,and functional diversity)and grassland patch area.We found species richness and the standardized effect size of phylogenetic diversity increased with patch area,whereas the standardized effect size of functional diversity decreased.Taxonomic measures of diversity indicated that the best strategy for conserving Tabu River Basin grasslands is to protect several small habitat patches;in contrast,phylogenetic and functional measures of diversity indicated that conserving a single large habitat patch was best.Our study emphasizes the necessity of considering multiple dimensions of diversity when designing conservation strategies for fragmented landscapes to achieve comprehensive biodiversity conservation.展开更多
基金supported by a grant from the Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(Y4ZK111B01)
文摘The leaf muntjac （Muntiacus putaoensis） is an endemic deer species found in the east trans- Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little genetic data exists for this species, thus our knowledge of distribution rangs and population sizes likewise remain limited. We obtained mtDNA genes and the complete mitochondrial genome sequence of M. putaoensis using PCR, followed by direct sequencing. The complete mitogenome sequence was determined as a circular 16 349 bp mitochondrial genome, containing 13 protein-coding genes, two rRNA genes 22 tRNA genes, and one control region, the gene composition and order of which were similar to most other vertebrates so far reported. Most mitochondrial genes, except for ND6 and eight tRNAs, were encoded on the heavy strand. The overall base composition of the heavy strand was 33.1% A, 29.3% T, 24.2% C, and 13.4% G, with a strong AT bias of 62.4%. There were seven regions of gene overlap totaling 95 bp and 11 intergenic spacer regions totaling 74 bp. Phylogenetic analyses （ML and BI） among the Muntiacus genus based on the sequenced of mitogenome and ND4L-ND4 supported M. putaoensis as a member of Muntiacus, most closely related to M. vuquangensis. However, when analyses based on cyt b included two more muntjacs, M. truongsonensis was most closely related to M. putaoensis rather than M. vuquangensis, and together with M. rooseveltorum, likely forming a M. rooseveltorum complex of the species. This study will help in the exploration of the evolutionary history and taxonomic status of the leaf muntjac, as well as its protection as a genetic resource.
基金National Key Research and Development Plan of China,Grant/Award Number:2018YFA0507202,2020YFC1200100 and 2021YFC2300200National Natural Science Foundation of China,Grant/Award Number:31825001,32188101,81730063,81961160737 and 82102389+5 种基金Provincial Innovation Team for the Prevention and Control of Highly Pathogenic Pathogens,Institute of Medical Biology,Chinese Academy of Medical Sciences,Grant/Award Number:202105AE160020Shenzhen San-Ming Project for Prevention and Research on Vector-borne Diseases,Grant/Award Number:SZSM201611064Shenzhen Science and Technology Project,Grant/Award Number:JSGG20191129144225464Tsinghua University Spring Breeze Fund,Grant/Award Number:2020Z99CFG017Young Elite Scientists Sponsorship Program,Grant/Award Number:2021QNRC001Yunnan Cheng Gong Expert Work-Station,Grant/Award Number:202005AF150034。
文摘Dengue virus(DENV)is one of the most important arboviral pathogens in the tropics and subtropics,and nearly one-third of the world's population is at risk of infection.The transmission of DENV involves a sylvatic cycle between nonhuman primates(NHP)and Aedes genus mosquitoes,and an endemic cycle between human hosts and predominantly Aedes aegypti.DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes(DENV-1-4).Phylogenetic analyses of DENV have revealed its origin,epidemiology,and the drivers that determine its molecular evolution in nature.This review discusses how phyloge-netic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.
文摘Understanding the level of genetic diversity in any population is an important requisite towards strategizing measures for conservation and improvement of stocks. This study focused on the assessment of phylogenetics and molecular divergence of tilapia fish species obtained from two populations (Domita in South-South and Odeda in South-West, Nigeria) using the displacement loop (D-loop) and cytochrome b region of the mitochondrial deoxyribonucleic acid (mtDNA). A total of 28 samples (15 from South-South and 13 from South-West) were used for the genetic analysis. DNA was extracted from the tissue of all the samples using Quik-gDNATM miniPrep kit. The D-loop containing the hypervariable region was sequenced for all samples from the two populations, while cytochrome b (Cyt b) region of mtDNA was only sequenced for samples from South-South population. Chromatograms of the sequences were viewed and edited using Bioedit software. Multiple sequence alignment was carried out using molecular evolutionary genetic analysis (MEGA) software before subsequent genetic analyses. Phylogenetic analysis grouped the samples into two clusters based on population. Also, when the two mitochondrial regions were pooled together, they clustered into two major groups based on mitochondrial regions. Analysis of molecular variance (AMOVA) revealed 37.32% variation within population and 62.68% variation among population with a significant fixation index of 0.627 (p 0.05). The genetic distance inferred between D-loop regions of South-South and South-West populations was 0.243. Maternal lineage analysis revealed that the origin of tilapia fish from both populations could be traced to Oreochromis spirilus and Oreochromis leucostictus based on mitochondrial D-loop region. The findings of this study revealed molecular divergence among the tilapia populations and may serve as pivot information for the genetic improvement of this important species.
基金provided by a University of Manitoba Graduate Fellowshipthe University of Manitoba Research Grants Program+3 种基金the Field Work Support Program of the Faculty of Science at the University of Manitobaa Rocky Mountain Biological Laboratory Research Fellowshipan NSERC Discovery Grant RGPIN386337-2011a Canada Foundation for Innovation Award
文摘The molecular phylogenetics of the Lepidoptera （butterflies and moths） is well studied, but that of Trichoptera （caddisflies）, the sister clade of Lepidoptera, is less studied. The PCR primer libraries developed for lepidopteran phylogenetics might work in Trichoptera. DNA from 8 caddisfly species （Asynarchus nigriculus （Banks, 1908）, Grammotaulius lorettae Denning, 1941, Hesperophylax occidentalis （Banks, 1908）, Limnephilus externus Hagen, 1861, Limnephilus picturatus McLachlan, 1875, Limnephilus secludens Banks, 1914, Limnephilus sublunatus Provancher, 1877 and Agrypnia deflata （Milne, 1931）） was used to screen for amplification. 107 primer pairs for 45 nuclear and 3 mitochondrial genes were tested. Primers for 1 new gene （40S ribosomalprotein $2 （RPS2）） and 8 genes previously used in Trichopteran phylogenetics were recovered （16S rRNA, 18S rRNA, carbamoyl-phosphate synthetase （CAD）, cytoehrome oxidase I （CO1）, cytochrome oxidase 11 （COIl）, elongation factor-1 alpha （EF-1 alpha）, isoeitrate dehydrogenase （IDH）, and RNA polymerase-II （POL-I1））. New primer pairs extended the genomic region sampled for many genes. Evolution rates among loci varied by 2 orders of magnitude. Differences among evolution rates and modes of inheritance offer flexible tools for resolving phylogenetic questions and examining genome evolution in the Trichoptera. Screening libraries of PCR primers is a useful approach for identifying PCR primers in related taxa with limited molecular genetic resources.
基金supported by the National Natural Science Foundation of China(U2544204,42172034,42330208,42288201)the China Geological Survey Project(Grant Nos.DD20243469,DD20221829).
文摘The wood anatomy of corystosperms is fundamentally consistent with that of gymnosperms,yet their growth ring boundaries share anatomical features with extant angiosperms.This transitional morphology strongly supports the interpretation of corystosperms as an evolutionary intermediate between gymnosperms and angiosperms.The first application of X-Ray fluorescence(XRF)chemical analysis to fossil wood taxa of Fengweioxylon yielded the above conclusion.By using growth ring analysis and ecological reconstructions,we suggest that corystosperms were large evergreen trees with leaf retention periods of three to five years.They likely thrived in warm summer environments where prolonged foliage retention provided adaptive benefits.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000 and XDA19050103)the International Partnership Program of the Chinese Academy of Sciences(151853KYSB20190027)+4 种基金the National Natural Science Foundation of China(NNSF31800178,31870506,and 32122009)the Sino-Africa Joint Research Center,the Chinese Academy of Sciences CAS International Research and Education Development Program(SAJC202101)the Jiangsu Natural Science Foundation(BK20181398)the Hundred Talents Program of CAS(Y8C3041100)supported in part by the Young Elite Scientists Sponsorship Program by China Association for Science and Technology(2018QNRC001)。
文摘The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies.However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China. We conducted a spatial phylogenetic analysis of the Chinese angiosperm flora at the generic level to identify centers of neo-and paleoendemism. Our results indicate that:(i) themajority of grid cells in China with significantly high phylogenetic endemism(PE) were located in the mountainous regions;(ii) four of the nine centers of endemism recognized, located in northern and western China, were recognized for the first time;(iii) arid and semiarid regions in Northwest China were commonly linked to significant PE, consistent with other spatial phylogenetic studies worldwide;and(iv) six highpriority conservation gaps were detected by overlaying the boundaries of China’s nature reserves on all significant PE cells. Overall, we conclude that the mountains of southern and northern China contain both paleo-endemics(ancient relictual lineages) and neo-endemics(recently diverged lineages). The areas we highlight as conservation priorities are important for broad-scale planning, especially in the context of evolutionary history preservation.
基金This research was supported by the following.The National Natural Science Foundation of China(31872262,31672363)National Key Program of Science and Technology Foundation Work of China(2015FY210300).Conccived and designed the research:BC,CW.Per-formed the specimens cllecting and experiments:BC,YZ,TT,TIL.Analyzed the data and wrote the paper:CW,BC.
文摘Despite worldwide distribution and rich diversity,the knowledge of mitochondrial genome(mtgenome)characteristics within the family Tenebrionidae(Coleoptera)is still very limited,and phylogenetics remain unresolved for the family.In this study,the mtgenomes for 12 species are newly sequenced and annotated.Three of the species represent the first report of complete mtgenomes from the subfamily Alleculinae.Comparative analysis of 36 tenebrionid mtgenomes finds that gene composition and order are the same as a theoretical ancestral insect mtgenome,and AT bias,length variation,and codon usage are consistent with other reported beetle mtgenomes.Some intergenic overlap and gap sequences may contain phylogenetically informative information,whereas neither the conserved nor repeat sequences in the control region do.The subfamilies Lagriinae,Pimeliinae,Stenochiinae,and Alleculinae are found to be monophyletic,and the subfamilies Diaperinae and Tenebrioninae polyphyletic in our study.Furthermore,Lagriinae is sister to the rest of the subfamilies.At the tribal level,the tribes Lagriini in the subfamily Lagrrinae;Strongyliini in Stenochiinae;Cteniopodini in Alleculinae;and Triboliini,Opatrini,and Amarygmini in Tenebrioninae are monophyletic;while Diaperini in Diaperinae,and Tenebrionini in Tenebrioninae are polyphyletic.
基金supported by the National Natural Science Foundation of China (31270269,30800059,30990241)the Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-Z-2)
文摘Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For accurately reconstructing the phylogeny and evolutionary history of plant groups,correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data.We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011.Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets,or did not address in detail possible reasons for incongruence between the two data sets.By reviewing various methods,we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data,which includes four steps:identifying significant incongruence,determining conflicting taxa,providing possible interpretations for incongruence,and reconstructing the phylogeny after treating incongruence.Particular attention is given to explanation of the cause of incongruence.We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.
基金supported by the National Natural Science Foundation of China(32170022)the 2023 Biodiversity Monitoring-special Investigation of Wild Fungi Issued by Chuxiong Management Bureau of Yunnan Ailao Mountains National Nature Reserve,the Biodiversity Survey and Assessment Project(2019HJ2096001006)the“Investigation of Macrofungi of Maguan County”Issued by Ministry of Ecology and Environment of the People’s Republic of China.
文摘The informal term‘dahongjun’or‘big red mushroom’is a group of red-coloured russulas widely collected and consumed in southern China,originally mistakenly recognized as the European Russula vinosa.Russula griseocarnosa was described from China in 2009,and since then,it has become the only available scientific name for‘dahongjun’.Nevertheless,several lineages exist within this complex,and whether these lineages represent real species is still an open question.Sampling in major producing areas of‘dahongjun’and phylogenetic species recognition using multi-locus data were conducted.Besides R.griseocarnosa nine additional species were identified under the commercial name‘dahongjun’,including R.dhakuriana,R.quercina,R.purpureozonata,R.yanheensis and a new species sister to R.griseocarnosa here described as R.occulta.The others were undescribed species close to R.laricina,R.lepida,and R.purpureozonata respectively.Six evolutionary lineages within R.griseocarnosa were defined by genealogical concordance phylogenetic species recognition based on five-locus DNA data.Conflicts among different genealogies suggested that R.griseocarnosa is best considered as a single phylogenetic species,comprising several infraspecific taxa.Lower coverage whole genome sequencing of R.griseocarnosa holotype discovered that its three individuals belong to three different clades.Lectotypification was made using one of the three individuals.A new variety R.griseocarnosa var.ailaoshanensis is described to name one of the terminal clades that is mainly distributed in Ailao Mountains.This variety differs morphologically from the type variety in its nearly white context,bigger spores and more inflated hyphae in the pileipellis.The morphological and molecular data provided in this study are helpful to identify wild edible mushrooms of Russula subgen.Russula.
基金supported by the Czech Science Foundation(projects 24-11371S to TM and 23-06840S to MAL)Masaryk University Grant Agency(project MUNI/R/1268/2022 to TM)Additional support(PT)was provided as part of a long-term research project of the Czech Academy of Sciences,Institute of Botany(RVO 67985939).
文摘The genus Boechera(Brassicaceae)serves as a model system for studying apomictic reproduction and ecological adaptations,with most species occurring in North America.The rare occurrence of Boechera species outside their typical range provides unique opportunities to investigate genome evolution in extralimital environments.One such species,B.calcarea,has been described from the Chandalaz Mountains in northeastern Asia(Russia).This study aimed to investigate the genome structure and evolutionary history of B.calcarea.However,our analyses reveal that the species does not belong to Boechera.Instead,an integrative approach combining cytogenetic,phylogenetic and repeatome analysis identified the species as a member of one of more ancestral clades in the tribe Arabideae.The diploid Parryodes calcarea(2n=16)exhibits Arabideae-specific chromosomal signatures,including multiple centromere repositionings.These findings clarify the misclassification of P.calcarea as Boechera,leaving Boechera falcata and Borodinia macrophylla as the only representatives of the Boechereae in the Old World.This study highlights the importance of an integrative approach in resolving taxonomic ambiguities and provides new insights into the diversification of the largest cruciferous tribe,the Arabideae.
文摘Lignin is a significant secondary metabolite produced through the phenylpropanoid pathway.As a vital component of the plant cell wall,lignin affects various fruit characteristics,including size,seed quantity,and firmness.In this study,we conducted comprehensive identification and phylogenetic analysis of 265 Caffeic acid O-methyltransferase(COMT)genes across ten different plant species,including Vaccinium corymbosum and four other Vaccinium species.The results reveal that VcCOMT38 is a promising structural gene for the biosynthesis of lignin in blueberry.An in vitro enzymatic assay of VcCOMT38 demonstrated that it is a special enzyme in the lignin biosynthesis pathway and prefers to use caffeic acid as a substrate over 5-hydroxyferulic acid.Transient overexpression and silencing of VcCOMT38 in Vaccinium corymbosum‘Northland’fruits demonstrated that VcCOMT38 participates in lignin biosynthesis and contributes to both an increased number of immature seeds and enhanced fruit firmness.The heterologous overexpression of VcCOMT38 in Nicotiana benthamiana revealed that this gene could increase the lignin content and the syringyl/guaiacyl(S/G)ratio,which determines the maximum monomer yield during lignin depolymerization.These results highlight VcCOMT38 as a crucial gene in lignin biosynthesis and its potential for improving lignin production in industry through genetically modified woody plants.
基金supported by the Natural Science Foundation of Inner Mongolia Key Project(2023ZD24)the Erdos City Major Science and Technology Special Project(ZD20232305)+3 种基金the Inner Mongolia Autonomous Region Science and Technology Plan Project(2025KYPT0012)the Inner Mongolia Autonomous Region Science and Technology Plan Project(2022ZD007)the Inner Mongolia Autonomous Region Education Department Project(NMGIRT2409)the Inner Mongolia First-Class Disciplines Scientific Research Special Project(YLXKZX-ND-047).
文摘Conservationists have long debated whether fragmented habitats are best conserved by protecting a single large patch(SL)or several small patches(SS),i.e.,the SLOSS debate.Although this SLOSS debate has provided important insights into biodiversity conservation,research has predominantly focused on only one dimension of diversity(i.e.,taxonomic),failing to consider how phylogenetic and functional diversity might inform conservation strategies.In this study,we determined whether grasslands in the agro-pastoral ecotone of the Tabu River Basin,Inner Mongolia should be conserved by protecting a single large patch or several small patches.For this purpose,we quantified the relationships between three dimensions of biodiversity(taxonomic,phylogenetic,and functional diversity)and grassland patch area.We found species richness and the standardized effect size of phylogenetic diversity increased with patch area,whereas the standardized effect size of functional diversity decreased.Taxonomic measures of diversity indicated that the best strategy for conserving Tabu River Basin grasslands is to protect several small habitat patches;in contrast,phylogenetic and functional measures of diversity indicated that conserving a single large habitat patch was best.Our study emphasizes the necessity of considering multiple dimensions of diversity when designing conservation strategies for fragmented landscapes to achieve comprehensive biodiversity conservation.
