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genetic diversity and population structure of the endangered species Monimopetalum chinense revealed by AFLP

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Genetic diversity and population structure of the endangered...

后植物志时代的系统与进化植物学——2011年全国系统与...

作者：谢国文 Michael J.Blum South China Biodiversity Institute Guangzhou UniversityGuangzhou 510006China Department of Ecology and Evolutionary Biology Tulane UniversityNew OrleansLA 70118USA

Monimopetalum chinense Rehd.is an endangered woody vine endemic to eastern China.Using amplified fragment length polymorphism(AFLP) markers,we examined levels of genetic variation within and among eleven populations located across the species’ distribution.Although modest levels of heterozygosity were detected,other measures of genetic diversity registered relatively high levels of variability,both at the species level(P 1/4 91.0%,HE 1/4 0.232,IS 1/4 0.365) and at the population level(P 1/4 53.0%,HE 1/4 0.155,IS 1/4 0.239).populations also exhibited high levels of genetic differentiation(Nei’s genetic diversity analysis,GST 1/4 0.330),corresponding to isolation-by-distance and hierarchical population structure.These results indicate that,despite low levels of gene flow,populations of M.chinense still harbor substantial amounts of genetic diversity.Management plans for the species should include measures that ensure genetic diversity remains high within and among extant populations.

关键词： Monimopetalum chinense genetic diversity population genetic structure AFLP species conservation

Molecular phylogenetics and population demographic history of Amphioctopus fangsiao,inferred from mitochondrial and microsatellite DNA markers

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Acta Oceanologica Sinica 2023年第6期42卷 39-48页

作者： Jian Zheng Yan Tang Ran Xu Xiaoying Zhang Xiaodong Zheng Institute of Evolution&Marine Biodiversity Ocean University of ChinaQingdao 266003China Key Laboratory of Mariculture of Ministry of Education Ocean University of ChinaQingdao 266003China

Amphioctopus fangsiao(Cephalopoda:Octopodidae)is an important commercial species in the coastal waters of China.In recent years,however,the resource of A.fangsiao have declined because of habitat destruction and overfishing.To analyze the genetic variations of A.fangsiao caused by the fluctuation of resources,the population genetic structure of nine sampling locations collected from the Bohai Sea to the South China Sea were investigated,using mtDNA COI fragments and microsatellite DNA.The results of F-statistics,AMOVA,structure and PCA analyses showed three phylogeographic clades(Clades A,B and C),revealing limited genetic exchange between north and south populations.These clades diverged in 2.23(Clades A and B)and 3.67(Clades A,B and C)million years ago,during the dramatic environmental fluctuations,such as sea level and temperature changes,have exerted great influence on the survival distribution pattern of global organisms.Our results for low genetic connectivity among A.fangsiao populations provide insights into the development of management strategies,that is,to manage this species as separate management unit.

关键词： genetic diversity population genetic structure Amphioctopus fangsiao mitochondrial DNA microsatellite DNA

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 Africa.The 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,Namibia.Both genetic markers rejected the hypothesis of 1 homogenous population but revealed contrasting results in the genetic structuring of putative populations.Mitochondrial 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 them.Neutrality 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 distribution.These 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

High regional genetic differentiation of an endangered relict plant Craigia yunnanensis and implications for its conservation

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Plant Diversity 2016年第5期38卷 221-226页

作者： Jing Yang Zerui Gao Weibang Sun Changqin Zhang Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of Sciences Yunnan Tobacco Industrial Hi-tech Material CO. LTD Kunming Botanical Garden Kunming Institute of BotanyChinese Academy of Sciences

Of the genus Craigia,widespread in the Tertiary,only two relict species survived to modern times.One species is now possibly extinct and the other one,Craigia yunnanensis,is severely endangered.Extensive surveys have located six C.yunnanensis populations in Yunnan province,southwest China.Using fluorescent amplified fragment length polymorphism(AFLP),the genetic diversity and population structure of these populations were examined.It was found that genetic diversity of C.yunnanensis was moderate at the species level,but low at regional and population levels.Analysis of population structure showed significant genetic differentiation between Wenshan and Dehong regions,apparently representing two geographically isolated for long time refuges.There are also clear indications of isolation between populations,which,together with anthropogenically caused decline of population size,will lead to general loss of the species genetic variation with subsequent loss of adaptive potential.To conserve the genetic integrity of C.yunnanensis,we recommend that ex-situ conservation should include representative samples from every population of the two differentiated regions(e.g.Wenshan and Dehong).The crosses between individuals originated from different regions should be avoided because of a high risk of outbreeding depression.As all the extant populations of C.yunnanensis are in unprotected areas with strong anthropogenic impact,there is no alternative to reintroduction of C.yunnanensis into suitable protected locations.

关键词： Craigia yunnanensis Isolation AFLP genetic diversity population genetic structure Conservation genetics

genetic boundary and gene flow between 2 parapatric subspecies of brown rats

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Current Zoology 2020年第6期66卷 677-688页

作者： Lei ZHAO Jian-Xu Zhang Yao-Hua Zhang State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture Institute of ZoologyChinese Academy of SciencesBeichen West Road 1-5Chaoyang DistrictBeijing 100101China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing100049China

Two parapatric Rattus norvegicus subspecies,R.n.humiliatus(RNH)and R.n.caraco(RNC),are classified accordi ng to morphological diverge nee and are mainly distributed in North and Northeast China.Here,we aimed to explore the population genetic structure,genetic boundary,and gene flow in these rats using 16 microsatellite loci.structure analysis and principal component an alysis revealed 3 ancestral clusters.We found that the in termediate cluster exhibited higher genetic diversity and a lower in breeding coefficie nt tha n the other 2 clusters.The genetic differentiation between the 3 clusters was significant but weak,with a higher FST value being observed betwee n the clusters on both sides.The subspecies bou ndary inf erred from microsatellite markers may indicate the existence of an admixture or hybridization area covering Liaoning,Inner Mongolia,and Jilin Provinces,rather than corresponding to the administrative provincial boundaries between Liaoning and Jilin.The RNH and RNC subspecies presented moderate gene exchange and an asymmetric bidirectional gene flow pattern,with higher gene flow from the RNH subspecies to the RNC subspecies,constraining speciation.Such genetic characteristics might be explained by biological processes such as dispersal ability,mate choice,and dynamic lineage boundaries.

关键词： genetic boundary gene flow population genetic structure Rattus norvegicus

Resolving the taxonomy of emerging zoonotic pathogens in the Trichophyton benhamiae complex

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Fungal Diversity 2020年第5期104卷 I0001-I0055页

作者： AdélaČmoková Miroslav Kolařík Radim Dobiáš Lois L.Hoyer Helena Janouškovcová Rui Kano Ivana Kuklová Pavlína Lysková Lenka Machová Thomas Maier Naďa Mallátová Matěj Man Karel Mencl Pietro Nenoff Andrea Peano Hana Prausová Dirk Stubbe Silke Uhrlaß TomášVětrovský Cornelia Wiegand Vit Hubka Department of Botany Faculty of ScienceCharles UniversityPragueCzech Republic Laboratory of Fungal genetics and Metabolism Institute of MicrobiologyCzech Academy of SciencesPragueCzech Republic Public Health Institute in Ostrava OstravaCzech Republic Department of Biomedical Sciences Institute of Microbiology and ImmunologyFaculty of MedicineUniversity of OstravaOstravaCzech Republic Department of Pathobiology University of Illinois at Urbana-ChampaignUrbanaILUSA Faculty of Medicine in Pilsen Biomedical CenterCharles UniversityPilsenCzech Republic Department of Veterinary Dermatology Nihon University College of Bioresource SciencesFujisawaJapan Department of Dermatology and Venereology First Faculty of MedicineGeneral University Hospital in PragueCharles University and General University Hospital in PraguePragueCzech Republic Public Health Institute inÚstíNad Labem PragueCzech Republic Microbiological Laboratory/R&D Bioanalytics Bruker Daltonik GmbHBremenGermany Laboratory of Medical Parasitology and Mycology HospitalČeskéBudějoviceČeskéBudějoviceCzech Republic Institute of Botany Czech Academy of SciencesPrůhoniceCzech Republic Pardubice Regional Hospital PardubiceCzech Republic Laboratory of Medical Microbiology MölbisGermany Department of Veterinary Sciences University of TurinTurinItaly Clinical Veterinary Laboratory Labvet PragueCzech Republic Mycology and Aerobiology Service SciensanoBrusselsBelgium Laboratory of Environmental Microbiology Institute of MicrobiologyCzech Academy of SciencesPragueCzech Republic Department of Dermatology University Hospital JenaJenaGermany

Species of the Trichophyton benhamiae complex are predominantly zoophilic pathogens with a worldwide distribution.These pathogens have recently become important due to their epidemic spread in pets and pet owners.Considerable genetic and phenotypic variability has been revealed in these emerging pathogens,but the species limits and host spectra have not been clearly elucidated.In this study,we used an approach combining phylogenetic analysis based on four loci,population-genetic data,phenotypic and physiological analysis,mating type gene characterization and ecological data to resolve the taxonomy of these pathogens.This approach supported the inclusion of nine taxa in the complex,including three new species and one new variety.Trichophyton benhamiae var.luteum var.nov.(“yellow phenotype”strains)is currently a major cause of zoonotic tinea corporis and capitis in Europe(mostly transmitted from guinea pigs).The isolates of the“white phenotype”do not form a monophyletic group and are segregated into three taxa,T.benhamiae var.benhamiae(mostly North America;dogs),T.europaeum sp.nov.(mostly Europe;guinea pigs),and T.japonicum sp.nov.(predominant in East Asia but also found in Europe;rabbits and guinea pigs).The new species T.africanum sp.***.is proposed for the“African”race of T.benhamiae.The introduction to new geographic areas and host jump followed by extinction of one mating type gene have played important roles in the evolution of these pathogens.Due to considerable phenotypic similarity of many dermatophytes and phenomena such as incomplete lineage sorting or occasional hybridization and introgression,we demonstrate the need to follow polyphasic approach in species delimitation.Neutrally evolving and noncoding DNA regions showed significantly higher discriminatory power compared to conventional protein-coding loci.Diagnostic options for species identification in practice based on molecular markers,phenotype and MALDI-TOF spectra are presented.A microsatellite typing scheme developed in this study is a powerful

关键词： Epizootic fungal infections Microsatellite typing scheme Multigene phylogeny population genetic structure Superficial skin infections Zoophilic dermatophytes

Spatial distribution of sensitivity to difenoconazole in the pathogenic fugus Alternaria alternata from potato

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Spatial distribution of sensitivity to difenoconazole in the...

中国植物病理学会2015年学术年会

作者： HE Meng-han ZHU Wen CHEN Feng-ping ZHAN Jia-sui Fujian Key Laboratory of Plant Virology Institute of Plant VirologyFujian Agriculture and Forestry University Key Lab of Biopesticide and Chemical Biology Ministry of EducationFujian Agriculture and Forestry University

Molecular markers combining with an experimental evolution approach were used to study the spatial distribution of difenoconazole sensitivity in the seven populations of Alternaria alternate sampled from potato.Sensitivity to difenoconazole displayed a continuous variation and difference in difenoconazole sensitivity was significant among the pathogen populations sampled from different regions.Furthermore,population differentiation in difenoconazole sensitivity(Q) was significantly lower than the corresponding population differentiation in neutral SSR markers(G).These results suggest that the evolution to difenoconazole resistance in A.alternate was under constraining selection,possibly due to high fitness costs and risk of developing difenoconazole resistance in A.alternate may be low.

关键词： Altemaria altemata fungicide resistance natural selection population genetic structure experimental evolution

genetic characteristics of Enterocytozoon bieneusi in fur animals and assessment of the potential for zoonotic transmission

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Genetic characteristics of Enterocytozoon bieneusi in fur an...

中国畜牧兽医学会兽医寄生虫学分会第一届青年科学家学术论...

作者： Zhu Weining Yang Yuqi Tao Wei Jiang Yanxue Wan Qiang Li Qiao Li Wei Heilongjiang Key Laboratory for Zoonosis Northeast Agricultural University

various ages by sequence analysis of the ITS locus.Genotypes CHN-DC1 and mixed CHN-DC1/WildBoar3 were detected in one adult raccoon dog each.We further explored the genotypic and phylogenetic characteristics of four mini-and microsatellites and performed a population genetic analysis of 39 E.bieneusi isolates of potentially zoonotic ITS genotype D from farmed foxes and raccoon dogs in China.Sequence polymorphisms facilitated determination of six,two,four,and five genotypes at markers MSI,MS3,MS4,and MS7,respectively.Patterns of phylogeny revealed different levels of diversity within and among the genetic markers.Clear genotypic and phylogenetic divergences between E.bieneusi isolates of ITS genotype D from fur animals and humans were observed at individual markers.Complete linkage disequilibrium and very limited recombination in subsequent population genetic analysis supported a clonal structure for E.bieneusi population from for animals(FID).Phylogenetic analysis,genetic network,and measures of F and gene flow demonstrated population differentiation of FID from two known human E.bieneusi populations HID(with a clonal structure) and HIA(with an epidemic structure).The data indicated an ideal resolving power of MLST compared to the previously widely used ITS genotyping and confirmed the clonal nature and population differentiation of E.bieneusi in various hosts.

关键词： Enterocytozoon bieneusi genotyping zoonotic transmission potential multilocus sequence typing population genetic structure host specificity

Deep intraspecific divergence in Lancea tibetica（Mazaceae） distributed over the Qinghai-Tibetan Plateau

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Deep intraspecific divergence in Lancea tibetica（Mazaceae）...

中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Mingze Xia Zunzhe Tian Faqi Zhang Gulzar Khan Qingbo Gao Rui Xing Yu Zhang Jingya Yu Shilong Chen Key Laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau BiologyChinese Academy of Sciences University of Chinese Academy of Sciences Qinghai Provincial Key Laboratory of Crop Molecular Breeding

Lancea tibetica,endemic to Qinghai-Tibetan Plateau（QTP）,is an important traditional Tibetan medicine,used in the treatment of leukaemia,intestinal angina,heart diseases and cough.Here we investigated genetic diversity and past population dynamics of L.tibetica,using 429 individuals distributed in 29 populations all over QTP.We generated chloroplast DNA（cpDNA） and nuclear ITS sequences for all the populations and analyzed.The results revealed a significant genealogical and geographical structure within the distribution range of L.tibetica.Chloroplast haplotypes divided all populations into two lineages: the north one and south.Tanggula and Bayangela mountains appear to act as a topological barrier,and probably played an important role towards the gene flow between both lineages.Divergence time between both lineages based on nuclear ITS sequences dated to 8.63 Mya,which corresponded well to the uplifting of QTP during Late Miocene and Pliocene.The ecological differences found between the two lineages,seem to represent species-specific characteristics and are sufficient to keep both lineages separated to a high degree.

关键词： Deep divergence Qinghai-Tibetan Plateau Lancea tibetica population genetic structure phylogeography demography