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central asia revealed as a key area in evolution of Eremurus (Asphodelaceae)

Plant Diversity 2024年第3期46卷 333-343页

作者： Dilmurod Makhmudjanov Sergei Volis Ziyoviddin Yusupov Inom Juramurodov Komiljon Tojibaev Tao Deng Hang Sun CAS Key laboratory for Plant Diversity and Biogeography of East asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina Yunnan International Joint Laboratory for Biodiversity of Central Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina Institute of Botany Academy Sciences of UzbekistanTashkent 100125Uzbekistan University of Chinese Academy of Sciences Beijing 100864China

Eremurus was described at the beginning of the 19th century.However,due to limited sampling and the small number of gene markers to date,its phylogeny and evolution are largely unknown.In this study,we analyzed plastomes from 27 species belonging to 2 subgenera and 3 sections of Eremurus,which are found in central asia(its center of diversity)and China.We also analyzed nuclear DNA ITS of 33 species,encompassing all subgenera and sections of the genus in central asia,southwest asia and China.Our findings revealed that the genus was monophyletic,although both subgenera Eremurus and Henningia were found to be paraphyletic.Both plastome and nrDNA-based phylogenetic trees had three clades that did not reflect the current taxonomy of the genus.Our biogeographical and time-calibrated trees suggest that Eremurus originated in the ancient Tethyan area in the second half of the Eocene.Diversification of Eremurus occurred from the early Oligocene to the late Miocene.Paratethys Sea retreat and several orogenetic events,such as the progressive uplift of the Qinghai-Tibet Plateau and surrounding mountain belts(Altai,Pamir,Tian Shan),caused serious topographic and climate(aridification)changes in central asia that may have triggered a split of clades and speciation.In this transformed central asia,speciation proceeded rapidly driven mainly by vicariance caused by numerous mountain chains and specialization to a variety of climatic,topographic and soil conditions that exist in this region.

关键词： Asphodelaceae Asphodeloideae Plastome central asia Qinghai-Tibet Plateau

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Leaf fossils of Sabalites(Arecaceae)from the Oligocene of northern Vietnam and their paleoclimatic implications

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Plant Diversity 2022年第4期44卷 406-416页

作者： Ai Song Jia Liu Shui-Qing Liang Truong Van Do Hung Ba Nguyen Wei-Yu-Dong Deng Lin-Bo Jia Cedric Del Rio Gaurav Srivastava Zhuo Feng Zhe-Kun Zhou Jian Huang Tao Su Institute of Palaeontology Yunnan Key Laboratory for PalaeobiologyMEC International Joint Laboratory for Palaeobiology and PalaeoenvironmentYunnan Key Laboratory of Earth System ScienceYunnan UniversityKunming650500China CAS Key laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMengla666303China Vietnam National Museum of Nature Vietnam Academy of Science and Technology18 Hoang Quoc VietHanoiViet Nam Graduate Academy of Science and Technology Vietnam Academy of Science and Technology18 Hoang Quoc VietHanoiViet Nam CAS Key laboratory of Plant Diversity and Biogeography of East asia Kunming Institute of BotanyChinese Academy of SciencesKunming650204China Birbal Sahni Institute of Palaeosciences Lucknow226007India

Recent paleobotanical investigations in Vietnam provide a good opportunity to improve our understanding of the biodiversity and paleoclimatic conditions in the geological past of Southeast asia.Palms(Arecaceae)are a diverse family of typical thermophilous plants with a relatively low tolerance for freezing.In this study,we describe well-preserved fossil palm leaves from the Oligocene Dong Ho Formation of Hoanh Bo Basin,northern Vietnam.Characters of the fossil leaves,such as a fan-shaped costapalmate lamina,an unarmed petiole,a costa slightly enlarged at the base that then tapers distally into the blade,and well-preserved amphistomatic leaves with cuticles,suggest that they represent a new fossil species,which we herein designate Sabalites colaniae A.Song,T.Su,T.V.Do et Z.K.Zhou sp.nov.Together with other paleontological and palaeoclimatic evidence,we conclude that a warm climate prevailed in northern Vietnam and nearby areas during the Oligocene.

关键词： Fossil Leaf Oligocene Paleoclimate Palm Vietnam

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Genomic convergence underlying high-altitude adaptation in alpine plants

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Journal of Integrative Plant Biology 2023年第7期65卷 1620-1635页

作者： Xu Zhang Tianhui Kuang Wenlin Dong Zhihao Qian Huajie Zhang Jacob BLandis Tao Feng Lijuan Li Yanxia Sun Jinling Huang Tao Deng Hengchang Wang Hang Sun CAS Key laboratory of Plant Germplasm Enhancement and Specialty Agriculture The Chinese Academy of SciencesWuhan Botanical GardenWuhan 430074China Center of Conservation Biology Core Botanical GardensThe Chinese Academy of SciencesWuhan 430074China Yunnan International Joint Laboratory for Biodiversity of Central Asia Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyThe Chinese Academy of SciencesKunming 650201China University of Chinese Academy of Sciences Beijing 100049China School of Integrative Plant Science Section of Plant Biology and the L.H.Bailey HortoriumCornell UniversityIthacaNew York 14850USA BTI Computational Biology Center Boyce Thompson InstituteIthacaNew York 14853USA State Key laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China Department of Biology East Carolina UniversityGreenvilleNorth Carolina 27858USA

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection.However, genomic evidence for convergent adaptation to extreme environments remains scarce.Here, we assembled reference genomes of two alpine plants, Saussurea obvallata(Asteraceae)and Rheum alexandrae(Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes,we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of diseaseresistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present.We identified signatures of positive selection on a set of genes involved in reproduction and respiration(e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification,DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive “greenhouse” morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level,aiding in a deep understanding of genetic adaptation to complex environments.

关键词： adaptation alpine plants evolutionary rates genomic convergence “greenhouse”morphology high altitude

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The effects of climate and land use change on the potential distribution and nesting habitat of the Lesser Adjutant in Nepal

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Avian Research 2023年第3期14卷 326-335页

作者： Hem Bahadur Katuwal Hari Prasad Sharma Prashant Rokka Krishna Prasad Bhusal Bishnu Prasad Bhattarai Sabina Koirala Sandeep Chhetri Luitel Shailendra Yadav Ganesh Sah Hem Sagar Baral Laxman Prasad Poudyal Lin Wang Rui-Chang Quan Center for Integrative Conservation Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan666303China Southeast asia biodiversity Research Institute Chinese Academy of SciencesYezinNay Pyi Taw05282Myanmar yunnan international joint laboratory of Southeast asia biodiversity Conservation MenglaYunnan666303China Nepal Zoological Society Kathmandu44600Nepal central Department of Zoology Institute of Science and TechnologyTribhuvan UniversityKathmandu44600Nepal Faculty of Forestry Agriculture and Forestry UniversityHetaudaMakwanpur44107Nepal IUCN SSC Bird Red List Authority Rue Mauverney1196GlandSwitzerland Mithila Wildlife Trust JanakpurdhamDhanusa45600Nepal Zoological Society of London-Nepal Office Kathmandu44600Nepal Institute of Land Water and SocietySchool of Environmental SciencesCharles Sturt UniversityAlbury-WodongaAustralia Shivapuri-Nagarjun National Park Department of National Parks and Wildlife ConservationKathmanduNepal

Climate change and land use change pose a threat to the world’s biodiversity and have significant impacts on the geographic distribution and composition of many bird species,but little is known about how they affect threatened large-sized waterbird species that rely on agricultural landscapes.To address this gap,we investigated how climate and land use changes influence the distribution and nesting habitats of the globally vulnerable Lesser Adjutant(Leptoptilos javanicus) in Nepal.Between 2012 and 2023,we collected distribution data from 24 districts and nesting site information from 18 districts.In a nation-wide breeding survey conducted in 2020,we documented a total of 581 fledglings from 346 nests in 109 colonies.The ensemble model predicted a current potential distribution of 15%(21,637 km2) and a potential nesting habitat of 13%(19,651 km2) for the species in Nepal.The highest predicted current suitable distribution and nesting habitat was in Madhesh Province,while none was predicted in Karnali Province.The majority of this predicted distributional and nesting habitat falls on agricultural landscapes(>70%).Our model showed a likely range expansion of up to 15%(21,573 km2) for the distribution and up to 12%(17,482 km2) for the nesting habitat under SSP5-8.5 scenarios for the 2070s.The range expansion is expected to occur mainly within the current distribution and breeding range(Tarai and some regions of Siwalk),particularly in Lumbini and Sudurpashchim provinces,and extend to the northern portions(Siwalik and Mid-hill regions) in other provinces.However,the current Protected Areas and Important Bird and biodiversity Areas are inadequate for providing optimal habitats for the species.Although the model suggests range expansion,the use of such novel habitats is primarily contingent on the availability and protection of large-sized trees(particularly Bombax ceiba,observed in 65% of colonies) in agricultural regions where nesting occurs.Therefore,our research suggests that agricultural landscapes should be priori

关键词： Agricultural landscapes Bombax ceiba Ensemble modeling Farmland bird IBA Nest site

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Phylogenomics of Allium section Cepa(Amaryllidaceae)provides new insights on domestication of onion

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Plant Diversity 2021年第2期43卷 102-110页

作者： Ziyoviddin Yusupov Tao Deng Sergei Volis Furkat Khassanov Dilmurod Makhmudjanov Komiljon Tojibaev Hang Sun CAS Key laboratory for Plant Diversity and Biogeography of East asia Kunming Institute of BotanyChinese Academy of SciencesKunming650201China international joint Lab for Molecular Phylogeny and Biogeography Institute of BotanyAcademy Sciences of UzbekistanTashkent100125Uzbekistan University of Chinese Academy of Sciences BeijingChina

Allium sect.Cepa(Amaryllidaceae)comprises economically important plants,yet resolving the phylogenetic relationships within the section has been difficult as nuclear and chloroplast-based phylogenetic trees have been incongruent.Until now,phylogenetic studies of the section have been based on a few genes.In this study,we sequenced the complete chloroplast genome(plastomes)of four central asian species of sect.Cepa:Allium oschaninii,A.praemixtum,A.pskemense and A.galanthum.Their chloroplast(cp)genomes included 114 unique genes of which 80 coded proteins.Seven protein-coding genes were highly variable and therefore promising for future phylogenetic and phylogeographic studies.Our plastome-based phylogenetic tree of Allium sect.Cepa revealed two separate clades:one comprising the central asian species A.oschaninii,A.praemixtum,and A.pskemense,and another comprising A.galanthum,A.altaicum,and two cultivated species,A.cepa and A.fistulosum.These findings contradict previously reported phylogenies that relied on ITS and morphology.Possible explanations for this discrepancy are related to interspecific hybridization of species ancestral to A.galanthum and A.cepa followed by chloroplast capture;however,this is impossible to prove without additional data.Our results suggest that the central asian Allium species did not play a role in the domestication of the common onion.Among the chloroplast genes,rpoC2 was identified as a gene of choice in further phylogeographical studies of the genus Allium.

关键词： Chloroplast genome SNP Phylogeny Chloroplast capture

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How little is known about “the little brown frogs”:description of three new species of the genus Leptobrachella(Anura:Megophryidae)from yunnan Province, China

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Zoological Research 2020年第3期41卷 292-313页

作者： Jin-Min Chen Kai Xu Nikolay A.Poyarkov Kai Wang Zhi-Yong Yuan Mian Hou Chatmongkon Suwannapoom Jian Wang Jing Che State Key laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Southeast asia biodiversity Research Institute Chinese Academy of SciencesYezinNay Pyi Taw 05282Myanmar Kunming College of Life Science University of the Chinese Academy of SciencesKunmingYunnan 650204China Department of Vertebrate Zoology Biological FacultyLomonosov Moscow State UniversityMoscow 119991Russia joint Russian-Vietnamese Tropical Research and Technological Center Nghia DoCau GiayHanoiVietnam Sam Noble Oklahoma Museum of Natural History&Department of Biology University of oklahomaNormanOklahoma 73072USA Key laboratory for Conserving Wildlife with Small Populations in yunnan Southwest Forestry UniversityKunmingYunnan 650224China College of Continuing(Online)Education Sichuan Normal UniversityChengduSichuan 610068China School of Agriculture and Natural Resources University of PhayaoPhayao 56000Thailand College of Life Science and Technology Honghe UniversityMengziYunnan 661199China

asian leaf-litter toads of the genus Leptobrachella represent a great anuran diversification in asia.Previous studies have suggested that the diversity of this genus is still underestimated. During herpetological surveys from 2013 to 2018, a series of Leptobrachella specimens were collected from the international border areas in the southern and western parts of yunnan Province, China.Subsequent analyses based on morphological and molecular data revealed three distinct and previously unknown lineages, which we formally describe as three new species herein. Among them, we describe a new species that occurs at the highest known elevation for Leptobrachella in China. Four species of Leptobrachella, including two new species, are found in the same reserve. Furthermore, our results suggest that the population from Longchuan County,yunnan, may represent an additional new species of Leptobrachella, although we tentatively assigned it to Leptobrachella cf. yingjiangensis due to the small sample size examined. Lastly, we provide the first description of females of L. yingjiangensis. Our results further highlight that both micro-endemism and sympatric distributions of species are common patterns in Leptobrachella, that contribute to taxonomic and conservation challenges in these frogs. We provide an identification key for Leptobrachella known to occur in yunnan. Given the lack of knowledge on species diversity of Leptobrachella along international border areas, we recommend that future studies include transboundary collaborative surveys.

关键词： biodiversity hotspot Conservation Cryptic diversity Micro-endemism National border Speciation Taxonomy

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Plant endemism in the Nepal Himalayas and phytogeographical implications

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Plant Diversity 2019年第3期41卷 174-182页

作者： Achyut Tiwari Yadav Uprety Santosh Kumar Rana Department of Botany Tri-Chandra Campus Tribhuvan University Kathmandu Nepal central Department of Botany Tribhuvan University Kirtipur Kathmandu Nepal Research Centre for Applied Science and Technology Tribhuvan University Kathmandu Nepal IUCN (international Union for Conservation of Nature) Kathmandu Nepal Key laboratory for Plant Diversity and Biogeography of East asia Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China University of Chinese Academy of Sciences Beijing 100049 China

Nepal is located in the central part of the greater Himalayan range with a unique series of mountain chains formed by recent mountain building geological events. As one of the youngest mountains in the world it contributes to diversity of plants and also provided barriers to and corridors through which plants migrated during the ice ages. The higher altitudinal variation with the high mountains, deep river valleys and lowland plains combine with the effects of the summer monsoon and dry winter result with an extraordinary diversity of ecosystems including flora and fauna in a relatively small land area. The existing checklists for Nepal record some 6000 species of flowering plants and about 530 ferns. However, the botanical experts estimate that numbers may go up to 7000 when the poorly known remote regions are fully explored. The information on plant endemism in Nepal Himalaya is not adequately known as Nepal is still struggling to complete long awaited Flora of Nepal project. Endemic species are confined to specific areas and are the first to be affected by land use and other global changes. We sought to explore the spatial distribution of endemic plant species in Nepal in relation to the consequences associated with climatic and geologic changes over time in the region with the help of published literature. It was found that the endemism showed marked spatial variation between open moist habitat and dry inner valleys, the former with higher endemism. The updated records showed 312 flowering plant species to be endemic to Nepal with higher endemism around the elevation of 3800e4200 m at sea level. The recent human population explosion, intensified deforestation, habitat fragmentation and modern day environmental changes are posing greater threats to endemic plant in Nepal. The conservation status and threats to these peculiar species are unknown. Nevertheless, environmental degradation and high poverty rates create a potent mix of threats to biodiversity in this landscape.

关键词： Himalaya Topography Endemism

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A new species of the genus Xenophrys(Anura:Megophryidae) from northern Thailand

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Zoological Research 2019年第6期40卷 564-574页

作者： Yun-He Wu Chatmongkon Suwannapoom Nikolay A. Poyarkov,Jr. Parinya Paawangkhanant Kai Xu Jie-Qiong Jin Robert W. Murphy Jing Che State Key laboratory of Genetic Resources and Evolution State Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Kunming College of Life Science University of the Chinese Academy of SciencesKunming Yunnan 650204China Southeast asia biodiversity Research Institute Chinese Academy of SciencesYezin Nay Pyi Taw 05282Myanmar School of Agriculture and Natural Resources University of PhayaoPhayao 56000Thailand Department of Vertebrate Zoology Biological FacultyLomonosov Moscow State UniversityMoscow 119991Russia joint Russian-Vietnamese Tropical Research and Technological Center 63 Nguyen Van Huyen RoadNghia DoCau GiayHanoiVietnam Centre for biodiversity and Conservation Biology Royal Ontario MuseumToronto M5S 2C6Canada

DEAR EDITOR,Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein we report the collection of specimens from Doi Inthanon, Chiang Mai Province, northern Thailand, which were identified previously as X. minor. Molecular and morphological analyses find that these specimens differ significantly from other known congeners, and therefore we describe a new species. Further, our phylogenetic analyses indicate that X. latidactyla is a junior synonym of X. palpebralespinosa.

关键词： genus Xenophrys Megophryidae Thailand

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Plant diversity in yunnan:Current status and future directions

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Plant Diversity 2020年第4期42卷 281-291页

作者： Li-Shen Qian Jia-Hui Chen Tao Deng Hang Sun CAS Key laboratory for Plant Diversity and Biogeography of East asia Kunming Institute of BotanyChinese Academy of SciencesKunming650201China University of Chinese Academy of Sciences Beijing100049China School of Life Science Yunnan UniversityKunming650091China

yunnan,located in southwestern China,harbors more than 19,000 higher plants,which represents the highest plant diversity in the country.However,plant diversity in yunnan faces enormous threats today,including habitat destruction and fragmentation,environmental pollution,and over-exploitation of natural resources.Despite recent efforts to protect biodiversity,there are still thousands of threatened species,some of which have become extinct.We analyzed available data to gain a greater understanding of plant diversity and the status of plant conservation in yunnan.We found that southern,southeastern,and northwestern yunnan are hotspots of total species,endemic species,specimens,new species and threatened species,whereas southeastern yunnan is a hotspot for plant species with extremely small populations.Moreover,we found that there are still conservation gaps and poorly protected areas in central,eastern,and northeastern yunnan.We conclude that conservation of plant diversity in yunnan requires modern field investigation,systematic research,the development of comprehensive databases,and government support.We recommend that conservationists pay more attention to building and improving functional protection systems and popularizing science.

关键词： biodiversity Conservation status Protection yunnan Province Hotspot

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Molecular phylogeny,biogeography and character evolution of the montane genus Incarvillea Juss.(Bignoniaceae)

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Plant Diversity 2021年第1期43卷 1-14页

作者： Santosh Kumar Rana Dong Luo Hum Kala Rana Shaotian Chen Hang Sun CAS Key laboratory for Plant Diversity and Biogeography of East asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China University of the Chinese Academy of Sciences Beijing 100049China College of Pharmaceutical Science Yunnan University of Chinese MedicineKunming 650500China

The complex orogeny of the Himalaya and the Qinghai-Tibet Plateau(QTP)fosters habitat fragmentation that drives morphological differentiation of mountain plant species.Consequently,determining phylogenetic relationships between plant subgenera using morphological characters is unreliable.Therefore,we used both molecular phylogeny and historical biogeographic analysis to infer the ancestral states of several vegetative and reproductive characters of the montane genus Incarvillea.We determined the taxonomic position of the genus Incarvillea within its family and inferred the biogeographical origin of taxa through Bayesian inference(BI),maximum likelihood(ML)and maximum parsimony(MP)analyses using three molecular data sets(trnL-trnF sequences,nr ITS sequences,and a data set of combined sequences)derived from 81%of the total species of the genus Incarvillea.Within the genus-level phylogenetic framework,we examined the character evolution of 10 key morphological characters,and inferred the ancestral area and biogeographical history of the genus.Our analyses revealed that the genus Incarvillea is monophyletic and originated in central asia during mid-Oligocene ca.29.42 Ma.The earliest diverging lineages were subsequently split into theWestern Himalaya and Sino-Himalaya during the early Miocene ca.21.12 Ma.These lineages resulted in five re-circumscribed subgenera(Amphicome,Olgaea,Niedzwedzkia,Incarvillea,and Pteroscleris).Moreover,character mapping revealed the ancestral character states of the genus Incarvillea(e.g.,suffruticose habit,cylindrical capsule shape,subligneous capsule texture,absence of capsule wing,and loculicidal capsule dehiscence)that are retained at the earliest diverging ancestral nodes across the genus.Our phylogenetic tree of the genus Incarvillea differs from previously proposed phylogenies,thereby recommending the placement of the subgenus Niedzwedzkia close to the subgenus Incarvillea and maintaining two main divergent lineages.

关键词： biodiversity hotspots Biogeography Incarvillea Molecular phylogeny Phytools Stochastic character mapping

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