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Floristics and Plant Biogeography in China

Journal of Integrative Plant Biology 2008年第7期50卷 771-777页

作者： De-Zhu Li Key Laboratory of biodiversity and Biogeography Kunming Institute of Botany the Chinese Academy of Sciences and Plant Germplasm and Genomics Center Germplasm Bank of Wild Species Kunming 650204 China

In 1998, a revolutionary system of angiosperm classification, the Angiosperm Phylogeny Group system was published. Meanwhile, another new system of classification of angiosperms, the eight-class system was proposed by C.Y. Wu and colleagues based on long term work on the flora of China. The Flora Reipublicae Popularis Sinicae project was initiated in 1959 and completed by 2004. It is the largest Flora so far completed in the world, including 31 228 species of vascular plants, or one-eighth of the global plant diversity. The English-language and updated Flora of China （FOC） is an international joint effort initiated in 1988 and accelerated in 1998. Up to now, 15 of the 24 volumes of the FOC have been published. Based on the floristic data, the composition, characteristics, floristic divisions and affinities of the flora of China have been studied by Wu and colleagues since 1965. In the past 10 years, analyses of the available floristic data have been very productive. The East Asiatic Floristic Kingdom was proposed in 1998. All 346 families of angiosperms in China, according to the eight-class system of classification, were comprehensively discussed by using knowledge of current and historical distribution of seed plants in the world, together with some morphological and molecular data. A scheme of distribution patterns or areal-types of families and genera of seed plants in China was modified and elucidated, together with a proposed scheme of areal-types of the world. Molecular phylogenetic and biogeographical studies of angiosperms in China in the past 10 years also witnessed a progressive development. Integration of morphological and molecular data and fossil evidence revealed some significant results. Eastern Asia, which used to be regarded as an important center of survival during the ice age, is likely an important center of diversification of angiosperms.

关键词： biogeography center of diversification eastern Asia floristics phylogenetics.

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Genetic Characterization of Indigenous Rice Varieties in Eastern Himalayan Region of Northeast India

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Rice science 2014年第2期21卷 90-98页

作者： Baharul Islam CHOUDHURY Mohammed Latif KHAN Selvadurai DAYANANDAN Forest and Evolutionary genomics Laboratory and Centre for Structural and Functional GenomicsBiology DepartmentConcordia University Québec centre for biodiversity Sciences 1205 Dr.Penfield Avenue MontréalQC Department of Forestry North Eastern Regional Institute of Science & Technology Department of Botany Dr.Harisingh Gour Central University

The eastern Himalayan region of Northeast （NE） India is home to a large number of indigenous rice varieties, which are traditionally classified as Oryza sativa subspecies indica, japonica or intermediate types. The classification based on traditional Cheng’s index is often inconclusive due to phenotypic plasticity of morphological characters, which are influenced by environmental conditions. We used molecular markers specific for indica and japonica subspecies to assess the degree of genetic relatedness of indigenous rice varieties in NE India. The results revealed that majority of upland （jum） and glutinous rice varieties, traditionally considered as japonica, were genetically close to the subspecies indica. All varieties of boro ecotype were found to be indica type, and only a few varieties cultivated in lowland and upland areas were japonica type. Some of the lowland varieties of the sali ecotype were intermediate between indica and japonica, and they showed a closer genetic affinity to O. rufipogon.

关键词： classification genetic characterization insertion and deletion marker indica japonica O. sativa

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DNA barcoding of Gaultheria L. in China(Ericaceae:Vaccinioideae)

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Journal of Systematics and Evolution 2011年第5期49卷 411-424页

作者： 1~He REN 1,2~Lu LU 1,2~Hong WANG 1,2~De-Zhu LI 1(Laboratory of biodiversity and Biogeography,Kunming Institute of Botany,Chinese Academy of Sciences,Kunming 650204,China) 2(Plant Germplasm and genomics Center,Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences,Kunming 650204,China) (Laboratory of biodiversity and Biogeography Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China) (Plant Germplasm and genomics Center Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China)

Four DNA barcoding loci,chloroplast loci rbcL,matK,trnH-psbA,and nuclear locus internal transcribed spacer(ITS),were tested for the accurate discrimination of the Chinese species of Gaultheria by using intraspecific and interspecific pairwise P-distance,Wilcoxon signed rank test,and tree-based *** study included 186 individuals from 89 populations representing 30 *** all individuals,single locus markers showed high levels of sequencing universality but were ineffective for species *** chain reaction amplification and sequencing were successful for all four *** ITS and matK showed significantly higher levels of interspecific species delimitation than rbcL and trnH-psbA.A combination of matK and ITS was the most efficient DNA barcode among all studied regions,however,they do not represent an appropriate candidate barcode for Chinese Gaultheria,by which only 11 out of 30 species can be *** rbcL,matK,and trnH-psbA,which were recently proposed as universal plant barcodes,have a very poor capacity for species separation for Chinese *** barcodes may be reliable tools to identify the evolutionary units of this group,so further studies are needed to develop more efficient DNA barcodes for Gaultheria and other genera with complicated evolutionary histories.

关键词： DNA barcoding Ericaceae Gaultheria species discrimination taxonomy Vaccinioideae.

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Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering

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Synthetic and Systems Biotechnology 2022年第1期7卷 631-647页

作者： Sebastian L.Wenski Sirinthra Thiengmag Eric J.N.Helfrich Institute for Molecular Bio Science Goethe University Frankfurt60438Frankfurt am MainGermany LOEWE Center for Translational biodiversity genomics(TBG) 60325Frankfurt am MainGermany

Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical *** a result,many peptides have entered the clinics for various *** main routes for the biosynthesis of complex peptides have evolved in nature:ribosomally synthesized and post-translationally modified peptide(RiPP)biosynthetic pathways and non-ribosomal peptide synthetases(NRPSs).Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two *** universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural *** this review,we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide *** addition,the influence of the fundamentally different biosynthetic principles on past,current and future engineering ap-proaches is *** the different biosynthetic principles of both peptide biosynthetic routes,the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely *** continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.

关键词： Peptide natural products Non-ribosomal peptide synthetases Ribosomally synthesized and post-translationally modified peptides Biosynthesis Modification Engineering

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genomics of plant speciation

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Plant Communications 2023年第5期4卷 112-133页

作者： Dan G.Bock Zhe Cai Cassandra Elphinstone Eric Gonza lez-Segovia Kaede Hirabayashi Kaichi Huang Graeme L.Keais Amy Kim Gregory L.Owens Loren H.Rieseberg Department of Botany and biodiversity Research centre University of British ColumbiaVancouverBCCanada Department of Biology University of VictoriaVictoriaBCCanada

Studies of plants have been instrumental for revealing how new species *** several decades,botanical research has complemented and,in some cases,challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can ***,the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation ***,we review these recent genome-enabled developments in plant *** discuss complications related to identification of reproductive isolation(RI)loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation,as increasingly revealed by new sequencing ***,we review how genomics has advanced what we know of some routes to new species formation,like hybridization or whole-genome duplication,while casting doubt on others,like population bottlenecks and genetic *** genomics can fast-track identification of genes and mutations that confer RI,we emphasize that follow-up molecular and field experiments remain ***,genomics has clarified the outsized role of ancient variants rather than new mutations,particularly early during *** conclude by highlighting promising avenues of future *** include expanding what we know so far about the role of epigenetic and structural changes during speciation,broadening the scope and taxonomic breadth of plant speciation genomics studies,and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.

关键词： genomic islands of speciation structural variation hybrid speciation polyploid speciation reproductive isolation standing genetic variation

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Capturing the value of biosurveillance“big data”through natural capital accounting

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Big Earth Data 2021年第3期5卷 352-367页

作者： David Castle Paul D.N.Hebert Elizabeth L.Clare Ian D.Hogg Crystal Tremblay School Public Administration and Gustavason School of Business University of VictoriaCanada centre for biodiversity genomics University of GuelphGuelphCanada Ecology and Evolutionary Biology York UniversityTorontoCanada Ecosystem Science Polar Knowledge CanadaOttawa and Cambridge BayCanada Department of Geography University of VictoriaCanada

Global biodiversity is in *** of the scale and pace of biodiversity loss is leading to rapid technological development in biodiversity science to identify species,their interactions,and eco-system *** and international policy developments to stimulate mitigation and remediation actions are escalating to meet the biodiversity *** can take advantage of biosurveil-lance“big data”as evidence for more sweeping and impactful policy *** critical factor is translating biosurveillance data into the value-based frameworks underpinning new policy *** approach to this integration process,using natural capital accounting frameworks is developed.

关键词： biodiversity biosurveillance big data SDGs policy natural capital accounting digital twins modelling

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Potential and progress of studying mountain biodiversity by means of butterfly genetics and genomics

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Journal of Genetics and genomics 2024年第3期51卷 292-301页

作者： Shuting Wang Marco Girardello Wei Zhang State Key Laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China cE3c-centre for Ecology Evolution and Environmental Changes/Azorean Biodiversity GroupFaculdade de Ciencias Agrarias e do AmbienteUniversidade dos Açores9700-042 Angra do HeroísmoTerceiraPortugal

Mountains are rich in biodiversity,and butterflies are species-rich and have a good ecological and evolutionary research *** review addresses the potential and progress of studying mountain biodiversity using butterflies as a *** discuss the uniqueness of mountain ecosystems,factors influencing the distribution of mountain butterflies,representative genetic and evolutionary models in butterfly research,and evolutionary studies of mountain biodiversity involving butterfly genetics and ***,we demonstrate the necessity of studying mountain butterflies and propose future *** review provides insights for studying the biodiversity of mountain butterflies as well as a summary of research methods for reference.

关键词： Mountain ecosystem Butterfly biodiversity Adaptation genomics Genetics

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Patterns of geographic variation between mitochondrial and nuclear markers in Heaviside’s(Benguela)dolphins(Cephalorhynchus heavisidii)

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Integrative Zoology 2019年第5期14卷 506-526页

作者： Keshni GOPAL Leszek KARCZMARSKI Krystal A.TOLLEY Mammal Research Institute University of PretoriaPretoriaSouth Africa South African National biodiversity Institute Kirstenbosch Research CentreCape TownSouth Africa School of Biological Sciences University of Hong KongHong KongChina Cetacean Ecology Lab Cetacea Research InstituteHong KongChina centre for Ecological genomics and Wildlife Conservation Department of ZoologyUniversity of JohannesburgJohannesburgSouth Africa

The Heaviside’s(or Benguela)dolphin(Cephalorhynchus heavisidii)is endemic to the west coast of southern *** present study investigated the population genetic structure across a large portion of the species distribution using mitochondrial control region and nuclear(microsatellite)markers.A total of 395 biopsy skin samples were analyzed;they were collected from free-ranging Heaviside’s dolphins in 7 locations along 1650 km of coast between Table Bay,South Africa and Walvis Bay,*** genetic markers rejected the hypothesis of 1 homogenous population but revealed contrasting results in the genetic structuring of putative pop*** DNA suggested either 2 populations or a fine-scale division with 6(sub)populations,while microsatellite markers were indicative of 2 widespread populations with measurable gene flow between *** tests and mismatch distribution of the mitochondrial sequences indicated a departure from mutation-drift equilibrium due to a population expansion at the 2 extremes of the geographic range,but not towards the middle of the *** results highlight the importance of evaluating multiple genetic markers to gain reliable insights into population processes and structure.

关键词： Heaviside’s(Benguela)dolphins microsatellite loci mitochondrial DNA population genetic structure southern Africa

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Functional trait and community phylogenetic analyses reveal environmental filtering as the major determinant of assembly of tropical forest tree communities in the Western Ghats biodiversity hotspot in India

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Forest Ecosystems 2018年第4期5卷 345-360页

作者： K.Nagaraju Shivaprakash B.R.Ramesh Ramanan Umashaanker Selvadurai Dayanandan centre for Structural and Functional genomics Biology Department Concordia University7141 Sherbrooke WestMontrealQC H4BIR6Canada Quebec centre for biodiversity Sciences 1205Dr.Penfield AvenueMontreal QC H3A1B1Canada Suri Sehgal centre for biodiversity and Conservation Ashoka Trust for Research In Ecology and the EnvironmentRoyal Enclave SriramapuraJakkur PostBangaloreKarnataka 560064India French Institute of Pondicherry 11 Saint Louis StreetP.O.Box 33Pondicherry 605001India Department of Crop Physiology University of Agricultural SciencesBangalore India.

Background: Improved understanding of the processes shaping the assembly of tropical tree communities is crucial for gaining insights into the evolution of forest communities and biological diversity. The climate is thought to be the first order determinant of abundance and distribution patterns of tree species with contrasting traits such as evergreen and deciduous leaf phenology. However, the relative role of neutral, and niche-based processes in the evolution of these patterns remain poorly ***: Here, we perform an integrated analysis of the data on tree species abundance, functional traits and community phylogeny from a network of 96 forest plots, each 1 ha in size, distributed along a broad environmental gradient in the central Western Ghats, India. Then, we determine the relative importance of various process in assembly and structuring of tropical forest communities with evergreen and deciduous leaf ***: The deciduous leaf phenological trait has repeatedly evolved among multiple distantly related lineages. Tree communities in dry deciduous forests were phylogenetically clustered and showed a low range and variance of functional traits related to light harvesting, reproduction, and growth suggesting niche-based processes such as environmental filtering play a vital role in the assembly of tree communities in these forests. The external factors such as human-mediated disturbance also significantly, but to a lesser extent, influences the species and phylogenetic ***: These findings revealed that the environmental filtering plays a significant role in assembly of tree communities in the biologically diverse tropical forests in the Western Ghats biodiversity hotspot.

关键词： Functional traits Phylogenetic turnover Deciduous Evergreen Niche-based processes Human disturbance

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Speciation with gene flow via cycles of isolation and migration:insights from multiple mangrove taxa

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National Science Review 2019年第2期6卷 275-288页

作者： Ziwen He Xinnian Li Ming Yang Xinfeng Wang Cairong Zhong Norman C.Duke Chung-I Wu Suhua Shi State Key Laboratory of Biocontrol Guangdong Key Lab of Plant Resources Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education InstitutesSchool of Life Sciences Sun Yat-Sen University Department of Ecology and Evolution University of Chicago CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences Hainan Dongzhai Harbor National Nature Reserve Administration centre for Tropical Water and Aquatic Ecosystem Research James Cook University

Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a well-delineated geographical barrier are necessary. The Strait of Malacca,narrowly connecting the Pacific and Indian Ocean coasts, serves at different times either as a geographical barrier or a conduit of gene flow for coastal/marine species. We surveyed 1700 plants from 29 populations of 5 common mangrove species by large-scale DNA sequencing and added several whole-genome assemblies. Speciation between the two oceans is driven by cycles of isolation and gene flow due to the fluctuations in sea level leading to the opening/closing of the Strait to ocean currents. Because the time required for speciation in mangroves is longer than the isolation phases, speciation in these mangroves has proceeded through many cycles of mixing-isolation-mixing, or MIM, cycles. The MIM mechanism, by relaxing the condition of no gene flow, can promote speciation in many more geographical features than strict allopatry can. Finally, the MIM mechanism of speciation is also efficient, potentially yielding mn(m > 1) species after n cycles.

关键词： speciation gene flow allopatry geographical isolation mangrove

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