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Genetic structure and recent population demographic history of Taihangshan macaque(Macaca mulatta tcheliensis),North China

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Integrative Zoology 2023年第3期18卷 530-542页

作者： Yanyan ZHOU Jundong TIAN Jiqi LU School of Life Sciences Zhengzhou UniversityZhengzhouChina Institute of Biodiversity and Ecology Zhengzhou UniversityZhengzhouChina

Massive actions have been and are being taken into protecting the world’s primates from extinction,while the study of the properties of genetic diversity,demographic history,and ecological relationships will beneﬁt the understand-ing of the long-term survival of a species.The Taihangshan macaque(Macaca mulatta tcheliensis),a subspecies of rhesus macaque(Macaca mulatta),is endemic to China and currently restricted to southern Mt.Taihangshan area.Herein,we evaluated the genetic diversity,population structure,and demographic history of this subspecies using mitochondrial(Cytb and high variable region I:HVR I)and nuclear markers(microsatellite loci)of 131 in-dividuals collected from 9 localities covering the distribution range of this subspecies.Both phylogenetic analyses and genetic assignment revealed that the wild populations of Taihangshan macaques could be divided into 2 major highly divergent clades,THS-east and THS-west.Low genetic diversity(π:0.00266±0.00016)but high haplotype diversity(Hd:0.80352±0.015)were detected in the Taihangshan macaques,particularly in THS-east.Analyses of demographic history suggested that the Taihangshan macaques experiencedﬁrst a stable historical population size from Holocene to early 19th century but a subtle decline and then slight growth in the recent 200 years.We suggest that bridging the neighbor populations(i.***.setting corridors)would facilitate the male-mediated geneﬂow and subsequently increase the genetic diversity of the Taihangshan macaque populations.

关键词： conservation demographic history genetic diversity Genetic structure Taihangshan macaque(Macaca mulatta tcheliensis)

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Comparative Study of Genetic structure and genetic Diversity betweenWild and Cultivated Populations of Taxus cuspidata,Northeast China

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Phyton-International Journal of Experimental Botany 2024年第2期93卷 355-369页

作者： Dandan Wang Xiaohong Li Yanwen Zhang School of Science Liaodong UniversityDandong118003China

Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and Genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(pgenetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of

关键词： T.cuspidata SLAF-seq SNP wild population cultivated population Genetic structure

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genetic diversity and structure of the endemic and endangered species Aristolochia delavayi growing along the Jinsha River

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Plant Diversity 2021年第3期43卷 225-233页

作者： Yu-Long Yu Hui-Chun Wang Zhi-Xiang Yu Johann Schinnerl Rong Tang Yu-Peng Geng Gao Chen School of Ecology and Environmental Science Yunnan UniversityKunming650091China Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations Kunming Institute of BotanyChinese Academy of SciencesKunming650201China University of Chinese Academy of Sciences Beijing100049China Sichuan Panzhihua Cycas National Nature Reserver Bureau Panzhihua617000China Department of Botany and Biodiversity Research University of ViennaRennweg 14A-1030ViennaAustria CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming650201China

The traditional medicinal plant,and endangered species Aristolochia delavayi(Aristolochiaceae)is an endemic species in China and occurs in the warm and dry areas along the Jinsha river.It is also a specific host of the larvae of Byasa daemonius,a vulnerable butterfly.In this study,15 pairs of polymorphic microsatellite primers of A.delavayi were designed and screened based on the Simple Sequence Repeats(SSR)loci found by using the results of genome skimming.Based on these 15 SSR markers,the genetic diversity and structure of 193 individuals from ten natural populations were analyzed in detail.In comparison to other endemic and endangered plants in the region,the population of A.delavayi possess a relatively high genetic diversity(He=0.550,I=1.112).AMOVA analysis showed that 68.4%of the total genetic diversity was within populations and 31.6%of the variation occurred among populations.There was a significant genetic differentiation among natural populations of A.delavayi detectable,with low gene flow(Nm=0.591).This might be attributed to geographical barriers and limited seed dispersal.To test the isolation by distance(IBD),we performed Mantel test,which showed a significant correlation between the geographic and genetic distances.In order to cope with the possible biases caused by IBD,we additionally performed Bayesian genetic cluster analyses and principal coordinate analysis(PCoA).The final cluster analysis revealed three groups with distinct geographical distribution.Habitat fragmentation and limited gene flow between these populations may be the main reasons for the current Genetic structure.For conservation of this species,we suggest to divide its populations into three protection management units,with subsequent focus on the Yongsheng and Luquan populations which experienced a genetic bottleneck event in the past.

关键词： Aristolochia delavayi Conservation biology genetic diversity Genetic structure Microsatellites Genome skimming

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Analysis of genetic diversity and structure across a wide range of germplasm reveals genetic relationships among seventeen species of Malus Mill,native to China

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Journal of Integrative Agriculture 2021年第12期20卷 3186-3198页

作者： GAO Yuan WANG Da-jiang WANG Kun CONG Pei-hua LI Lian-wen PIAO Ji-cheng Research Institute of Pomology Chinese Academy of Agricultural Sciences/Key Laboratory of Horticultural Crops Germplasm Resources UtilizationMinistry of Agriculture and Rural AffairsXingcheng 125100P.R.China

China is a center of diversity for Malus Mill,with 27 native species including 21 wild species and six domesticated species.We applied a set of 19 simple sequence repeat markers to genotype 798 accessions of 17 species(12 wild species and five cultivated species)of Malus originating from 14 provinces in China.A total of 500 alleles were detected.Diversity statistics indicated a high level of genetic variation as quantified by the average values of the effective allele number(N_(e)).expected heterozygosity(H_(e)),and Shannon's Information Index(I)(10.309,0.886,and 2.545,respectively).Malus sieversii(MSR;H_(e)=0.814,I=2.041,N_(e)=6.054),M.baccata(MBB;H_(e)=0.848,/=2.350,N_(e)=8.652),M.toringoides(MTH;He=0.663,I=1.355,N_(e)=3.332),and M.hupehensis(MHR;H_(e)=0.539,I=0.912,N_(e)=0.579)showed a higher level of genetic diversity in this study than the previous studies.MSR and MBB contributed to the origin and evolution of some accessions of M.domestica subsp.chinensis(MDC).However,other accessions of MDC showed a closer genetic distance with MBB and cultivated species,especially M.robusta(MRB),M.asiatica(MAN),and M.prunifolia(MPB).Not all accessions of MDC were descended from MSR in Xinjiang Uygur Autonomous Region of China.This research provides novel insights into the genetic relationships of Malus native to China,which will be useful for genetic association studies,germplasm conservation,and breeding programs.

关键词： genetic diversity Genetic structure genetic relationship microsatellite Malus Mill

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High levels of genetic diversity and an absence of Genetic structure among breeding populations of the endangered Rufous-backed Bunting in Inner Mongolia,China:implications for conservation

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Avian Research 2021年第1期12卷 52-62页

作者： Shi Li Dan Li Lishi Zhang Weiping Shang Bo Qin Yunlei Jiang College of Animal Science and Technology Jilin Agricultural University

Background:The Rufous-backed Bunting,Emberiza jankowskii,is an endangered species that is primarily distributed in Inner Mongolia,China.The main threats to the continued persistence of this species are habitat loss and degradation.However,the impact of population loss on genetic diversity remains unclear.To support future conservation and management efforts,we assessed the genetic diversity and population structure of E.jankowskii using mitochondrial DNA and microsatellites.Methods:Blood samples were collected from 7-8-day-old nestlings in Inner Mongolia,China between May and August of 2012 and 2013.Mitochondrial DNA sequences and microsatellite markers were used to assess the genetic diversity,Genetic structure and inbreeding of E.jankowskii.The results of genetic diversity and inbreeding were compared to other avian species.Results:We found an unexpectedly high level of genetic diversity in terms of mitochondrial DNA and microsatellite compared to other avian species.However,there were high levels of gene flow and minimal genetic structuring,among the fragmented breeding populations of E.jankowskii in Inner Mongolia.These findings suggest that E.jankowskii in Inner Mongolia is a metapopulation.Despite the high genetic diversity of E.jankowskii,local populations in each small patch remain at risk of extinction due to habitat loss.In addition,the E.jankowskii population has a high risk of inbreeding.Conclusions:To minimize further loss of genetic diversity of this endangered species,we suggest that the E.jankowskii in Inner Mongolia should be considered as a protected species for management purposes.Conservation efforts should concentrate on E.jankowskii habitat management.This may be most effectively achieved by protecting the current breeding habitats and prohibiting over-grazing.

关键词： Conservation Emberiza jankowskii genetic diversity Genetic structure Habitat fragmentation

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The roles of calving migration and climate change in the formation of the weak Genetic structure in the Tibetan antelope(Pantholops hodgsonii)

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Integrative Zoology 2019年第3期14卷 248-258页

作者： Jiarui CHEN Gonghua LIN Wen QIN Jingyan YAN Tongzuo ZHANG Jianping SU Qinghai Provincial Key Laboratory of Animal Ecological Genomics Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina University of Chinese Academy of Sciences BeijingChina

Geographical barriers and distance can reduce gene exchange among animals,resulting in genetic divergence of geographically isolated populations.The Tibetan antelope(Pantholops hodgsonii)has a geographical range of approximately 1600 km across the Qinghai-Tibet Plateau,which comprises a series of tall mountains and big rivers.However,previous studies indicate that there is little genetic differentiation among their geographically delineated populations.To better understand the Genetic structure of P.hodgsonii populations,we collected 145 samples from the 3 major calving regions,taking into consideration their various calving grounds and migration routes.We used a combination of mitochondrial sequences(Cyt b,ATPase,D-loop and COX I)to investigate the Genetic structure and the evolutionary divergence of the populations.Significant,albeit weak,genetic differentiation was detected among the 3 geographical populations.Analysis of the genetic divergence process revealed that the animals gradually entered a period of rapid genetic differentiation approximately 60000 years ago.The calving migration of P.hodgsonii cannot be the main cause of their weak Genetic structure because this cannot fully homogenize the genetic pool.Instead,the geological and climatic events as well as the coupling vegetation succession process during this period have been suggested to greatly contribute to the genetic structure and the expansion of genetic diversity.

关键词： calving migration climate change Genetic structure Tibetan antelope vegetation succession

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The Impact of Stream Landscape on Genetic structure and Dispersal Patterns in Stream Salamander(Pachyhynobius shangchengensis)

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Asian Herpetological Research 2020年第3期11卷 205-218页

作者： Tao PAN Hui WANG Peng YAN Chenling ZHANG Wenliang ZHOU Xiaobing WU Baowei ZHANG School of Life Sciences Anhui UniversityHefei 230601AnhuiChina Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource School of Life SciencesAnhui Normal UniversityWuhu 241000AnhuiChina Jiangsu Key Laboratory of Biofunctional Molecule Chemistry and Chemical Engineering School of Life SciencesJiangsu Second Normal UniversityNanjing 210013JiangsuChina

Compared with other terrestrial environments,the stream environment generally presents a linear spatial structure and relatively simple environment.In a stream landscape,the dispersal direction of stream-type organisms usually presents a linear structure along the stream,which results in the limited dispersal and the genetic differentiation of stream-type organisms across different stream sections.The Shangcheng Stout Salamander(Pachyhynobius shangchengensis)is a narrowly distributed stream salamander in Dabie Mountains of East China.In the present study,we tested for the impact of stream landscape(i.***.waterfalls and underground river)on Genetic structure and dispersal pattern in P.shangchengensis based on 12 nuclear microsatellite loci from 195 individuals in 3 populations(A,B and C)from three closely connected sections within one stream.genetic diversity results suggested that Population B contains relatively high genetic diversity for P.shangchengensis when compared to the other populations(A and C).Detectable genetic differentiation was found(FST=0.008,P=0.007)among three populations,which was also supported by the structure,FCA analysis and relatedness estimates of each pair of individuals among populations.The assignment test suggested that P.shangchengensis has philopatric males and female-biased dispersal(mean female Alc=.0.031,SE=0.225;mean male Alc=0.026,SE=0.198).Female-biased dispersal was also supported by analyses for each sex(i.e.Spatial autocorrelation,genetic distance,Relatedness analysis).Our study indicated that small and isolated populations(A and C)had relatively low genetic diversity due to the limited population size.For stream salamanders,landscape features(i.***.waterfalls and underground river)can influence the ability of an individual to disperse through the landscape,and consequently influence the formation of strong genetic differentiation of P.shangchengensis.

关键词： Dabie Mounta ins Genetic structure landscape features Pachyhynobius shangchengensis sexbiased dispersal

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Role of seed size, phenology, oogenesis and host distribution in the specificity and Genetic structure of seed weevils (Curculio spp.) in mixed forests

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Integrative Zoology 2018年第3期13卷 267-279页

作者： Harold ARIAS-LECLAIRE Raúl BONAL Daniel GARCÍA-LÓPEZ Josep Maria ESPELTA CREAF Centre for Ecological Research and Forestry ApplicationsCerdanyola del Vallès08193Spain Exact and Natural Sciences School State Distance University of Costa RicaUNEDMercedes de Montes de OcaSan JoséCosta Rica Forest Research Group INDEHESAUniversity of ExtremaduraPlasenciaSpain DITEG Research Group University of Castilla-La ManchaToledoSpain Zoology Department Autonomous University of BarcelonaCerdanyola del VallèsSpain

Synchrony between seed growth and oogenesis is suggested to largely shape trophic breadth of seed-feeding insects and ultimately to contribute to their co-existence by means of resource partitioning or in the time when infestation occurs.Here we investigated:(i)the role of seed phenology and sexual maturation of females in the host specificity of seed-feeding weevils(Curculio spp.)predating in hazel and oak mixed forests;and(ii)the consequences that trophic breadth and host distribution have in the Genetic structure of the weevil populations.DNA analyses were used to establish unequivocally host specificity and to determine the population Genetic structure.We identified 4 species with different specificity,namely Curculio nucum females matured earlier and infested a unique host(hazelnuts,Corylus avellana)while 3 species(Curculio venosus,Curculio glandium and Curculio elephas)predated upon the acorns of the 2 oaks(Quercus ilex and Quercus pubescens).The high specificity of C.nucum coupled with a more discontinuous distribution of hazel trees resulted in a significant Genetic structure among sites.In addition,the presence of an excess of local rare haplotypes indicated that C.nucum populations went through genetic expansion after recent bottlenecks.Conversely,these effects were not observed in the more generalist Curculio glandium predating upon oaks.Ultimately,co-existence of weevil species in this multi-host-parasite system is influenced by both resource and time partitioning.To what extent the restriction in gene flow among C.nucum populations may have negative consequences for their persistence in a time of increasing disturbances(e.***.drought in Mediterranean areas)deserves further research.

关键词： Corylus avellana Curculio spp. Genetic structure Quercus spp. trophic breadth

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Genetic structure of needle morphological and anatomical traits of Pinus yunnanensis

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Journal of Forestry Research 2016年第1期27卷 13-25页

作者： Yujie Huang Jianfeng Mao Zhiqiang Chen Jingxiang Meng Yulan Xu Anan Duan Yue Li National Engineering Laboratory for Forest Tree Breeding Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Key Laboratory for Forest Resources Conservation and the Southwest Mountains of China Ministry of Education Southwest Forestry University

Pinus yunnanensis Franch. is an particular conifer tree species in Yunnan-Guizhou plateau in south- west China. The morphological and anatomical traits of needles are important to evaluate geographic variation and population dynamics of conifer species. Seedlings from seven populations of P. yunnanensis were analyzed, look- ing at 22 morphological and anatomical needle traits. The results showed that variations among and within popula- tions were significantly different for all traits and the variance components within populations were generally higher than that among populations in the most tested needle traits. The proportions of three-needle fascicle were significantly different among populations. The traits related to needle size in both morphology and anatomy were positive with latitude and negative with annual temperature and precipitation. Ratio indices, including mesophyllarea/vascular bundle area, mesophyll area/resin canals area, vascular bundle area/resin canals area and mesophyU area/（resin canals area and vascular bundle area）, were negatively correlated with elevation and positively corre- lated with the annual mean temperature, showing some fitness feature for the populations. Needle traits were more significantly correlated with longitude than with other four environmental factors. Needle length was significantly correlated with almost all environmental factors. First four principal components accounted for 81.596 % of the variation with eigenvalues 〉1; the differences among populations were mainly dependent on needle width, stomatal density, section areas of vascular bundle, total resin canals, and mesophyll, as well as area ratio traits. Seven populations were divided into three categories by Euclidean distance. Variations in needle traits among the populations have shown systematic microevolution in terms of geographic impact on P. yunnanensis. This study would provide empirical data to characterize adaptation and genetic variation of P. yunnanensis, which would be helpful for management of gen

关键词： Genetic structure Needle Morphologicaland anatomical traits Geographic population Pinusyunnanensis

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Genetic structure and Indica/Japonica Component Changes in Major Inbred Rice Varieties in China

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Rice science 2013年第1期20卷 39-44页

作者： YU Ping YUAN Xiao-ping XU Qun WANG Cai-hong YU Han-yong WANG Yi-ping TANG Sheng-xiang WEI Xing-hua State Key Laboratory of Rice Biology China National Rice Research Institute

We used 39 SSR markers to analyze the Genetic structure of 304 major Chinese inbred rice varieties, and to compare changes in the indica or japonica components in these varieties that have been widely cultivated from the 1950s to the 1990s in China. The Genetic structure analysis showed that these rice varieties were distinctly divided into two populations,＇ indica and japonica. The sub-structure of indica varieties was more complex than that of japonica ones. Among the various lines, late-season indica and early season japonica varieties had simpler genetic backgrounds. The seasonal ecotypes were not quite consistent with the subtypes of Genetic structure. Twelve SSR loci with specific differentiation between indica and japonica were used to calculate the indica/japonica components. The differences in indica/japonica components among the five decades were not significant, except for late-season indica varieties in the 1990s, which had a significantly higher japonica component. These results will help to understand the Genetic structure of the major Chinese inbred rice varieties and will be useful for indica-japonica hybrid breeding in China.

关键词： rice major variety Genetic structure indica/japonica component

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