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Pitfalls in the analysis of ancient human mtDNA

chinese Science Bulletin 2003年第8期48卷 826-830页

作者： yao yonggang1,3 & zhang yaping1,2.1. laboratory of molecular evolution and genome diversity, kunming institute of zoology, chinese academy of sciences, kunming 6502.3, china 2. laboratory for Conservation and Utilization of Bio-resource, Yunnan University, kunming 650091, china 3. Graduate School of the chinese academy of sciences, Beijing 100039, china Correspondence should be addressed to zhang yaping (e-mail: zhang- yp1@***) laboratory of molecular evolution and genome diversity Kunning Institute of Zoology Chinese Academy of Sciences China Graduate School of the chinese academy of sciences China laboratory for Conservation and Utilization of Bio-resource Yunnan University China

The retrieval of DNA from ancient human specimens is not always successful owing to DNA deteriora-tion and contamination although it is vital to provide new insights into the genetic structure of ancient people and to reconstruct the past history. Normally, only short DNA fragments can be retrieved from the ancient specimens. How to identify the authenticity of DNA obtained and to uncover the information it contained are difficult. We employed the ancient mtDNAs reported from Central Asia (including Xin-jiang, china) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylog-eny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demon-strated that many mtDNAs reported are more or less prob-lematic. Starting from a reliable mtDNA phylogeney and combining the available modern data into analysis, one can ascertain the authenticity of the ancient DNA, distinguish the potential errors in a data set, and efficiently decipher the meager information it harbored. The reappraisal of the mtDNAs with the age of more than 2000 years from Central Asia gave support to the suggestion of extensively (pre)historical gene admixture in this region.

关键词：古代人类遗传构造 DNA 脱氧核糖核酸

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Ambient Temperature is A Strong Selective Factor Influencing Human Development and Immunity

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Genomics, Proteomics & Bioinformatics 2020年第5期18卷 489-500页

作者： Lindan Ji Dongdong Wu Haibing Xie Binbin yao Yanming Chen David M.Irwin Dan Huang Jin Xu Nelson L.S.Tang yaping zhang State Key laboratory of Genetic Resources and evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Department of Biochemistry Medical School of Ningbo UniversityNingbo 315211China Department of Preventive Medicine Medical School of Ningbo UniversityNingbo 315211China Department of laboratory Medicine and Pathobiology University of TorontoTorontoON M5S 1A8Canada Banting and Best Diabetes Centre University of TorontoTorontoON M5S 1A8Canada Department of Chemical Pathology and Laboratory for Genetics of Disease SusceptibilityLi Ka Shing Institute of Health SciencesFaculty of MedicineThe Chinese University of Hong KongHong Kong Special Administrative RegionChina KIZ/CUHK Joint laboratory of Bioresources and molecular Research in Common Diseases Kunming 650223China laboratory for Conservation and Utilization of Bio-resource Yunnan UniversityKunming 650091China

Solar energy,which is essential for the origin and evolution of all life forms on Earth,can be objectively recorded through attributes such as climatic ambient temperature(CAT),ultraviolet radiation(UVR),and sunlight duration(SD).These attributes have specific geographical variations and may cause different adaptation ***,the adaptation profile of each attribute and the selective role of solar energy as a whole during human evolution remain ***,we performed a genome-wide adaptation study with respect to CAT,UVR,and SD using the Human genome diversity Project-Centre Etude Polymorphism Humain(HGDP-CEPH)panel *** singled out CAT as the most important driving force with the highest number of adaptive loci(6 SNPs at the genome-wide 1×10^(-7)level;401 at the suggestive 1×10^(-5)level).Five of the six genomewide significant adaptation SNPs were successfully replicated in an independent chinese population(N=1395).The corresponding 316 CAT adaptation genes were mostly involved in development and *** addition,265(84%)genes were related to at least one genome-wide association study(GWAS)-mapped human trait,being significantly enriched in anthropometric loci such as those associated with body mass index(χ^(2);P<0.005),immunity,metabolic syndrome,and cancer(χ^(2);P<0.05).For these adaptive SNPs,balancing selection was evident in Euro-Asians,whereas obvious positive and/or purifying selection was observed in *** together,our study indicates that CAT is the most important attribute of solar energy that has driven genetic adaptation in development and immunity among global human *** also supports the non-neutral hypothesis for the origin of disease-predisposition alleles in common diseases.

关键词： Solar radiation Ambient temperature Natural selection Development Immunity

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人类群体环境适应的古DNA研究进展

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科学通报 2017年第9期62卷 880-887页

作者：季林丹姚彬彬励佶佚徐进张亚平宁波大学医学院生物化学与分子生物学系宁波315211 中国科学院昆明动物研究所遗传资源与进化国家重点实验室昆明650223 宁波大学医学院预防医学系宁波315211 宁波大学医学院临床医学系宁波315211 云南大学生物资源保护与利用国家重点实验室昆明650091

人类(Homo sapiens)起源、迁徙和进化对现代人类遗传多样性具有重要的塑造作用,一直是多学科研究热点.分子遗传学通过现有人群的遗传数据和表型特征来推导、演绎历史事件,提出了"走出非洲完全替换"人类起源模型.在走出非洲迁居世界各地... 详细信息

人类(Homo sapiens)起源、迁徙和进化对现代人类遗传多样性具有重要的塑造作用,一直是多学科研究热点.分子遗传学通过现有人群的遗传数据和表型特征来推导、演绎历史事件,提出了"走出非洲完全替换"人类起源模型.在走出非洲迁居世界各地的过程中,不同环境对人类表型和遗传多样性具有重要的选择作用,如人群肤色、身高等外形特征以及乳糖耐受、淀粉代谢、免疫应答和低氧适应等生理特征的表型和遗传多态性演化过程.近年来兴起的人类古DNA研究,通过采集对应事件前、中、后不同时期的古DNA样本,进行全基因组测序,同时系统比较古DNA和现今人群遗传多态性,补充和完善了经典分子遗传学研究结果,可以更全面地分析人类演化历史.基于古基因组研究,学者提出了人类起源的"走出非洲基因渗透"模型,并对上述重要人类表型和遗传多态性的演化史提出了新的证据和观点.本文将对现有人类环境适应的古DNA研究进展进行综述,并据此对自然选择如何塑造人类遗传和表型多态性展开新的讨论,为今后同类研究提供线索.

关键词：人类群体环境适应古DNA 遗传多样性

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The Chromosome-Based Rubber Tree genome Provides New Insights into Spurge genome evolution and Rubber Biosynthesis

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molecular Plant 2020年第2期13卷 336-350页

作者： Jin Liu Cong Shi Cheng-Cheng Shi Wei Li Qun-Jie zhang Yun zhang Kui Li Hui-Fang Lu Chao Shi Si-Tao Zhu Zai-Yun Xiao Hong Nan yao Yue Xun-Ge Zhu Yu Wu Xiao-Ning Hong Guang-Yi Fan Yan Tong Dan zhang Chang-Li Mao Yun-Long Liu Shi-Jie Hao Wei-Qing Liu Mei-Qi Lv Hai-Bin zhang Yuan Liu Ge-Ran Hu-tang Jin-Peng Wang Jia-Hao Wang Ying-Huai Sun Shu-Bang Ni Wen-Bin Chen Xing-Cai zhang Yuan-Nian Jiao Evan E.Eichler Guo-Hua Li Xin Liu Li-Zhi Gao Yunnan institute of Tropical Crops Jinghong 666100China Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern ChinaKunming Institute of BotanyChinese Academy of SciencesKunming 650204China University of chinese academy of sciences Beijing 100049China BGI-Qingdao Qingdao 266555China lnstitution of Genomics and Bioinformatics South China Agricultural UniversityGuangzhou 510642China Asia-Pacific Tropical Forestry Germplasm Institution Southwest China Forestry UniversityKunming 650224China School of Life sciences Nanjing UniversityNanjing 210023China Novogene Bioinformatics institute Beijing 100083China BGI-Shenzhen Shenzhen 518083China State Key laboratory of Systematic and evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China John A.Paulson School of Engineering and Applied sciences Harvard UniversityCambridgeMA 02138USA Howard Hughes Medical institute University of WashingtonSeattleWA 98195USA

The rubber tree,Hevea brasiliensis,produces natural rubber that serves as an essential industrial raw ***,we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing(SMRT)and Hi-C technologies to anchor the～1.47-Gb genome assembly into 18 *** chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution,since the common paleopolyploid event occurred before the split of Hevea and *** show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years,leading to the massive expansion by～65.88%(～970 Mbp)of the whole rubber tree genome since the divergence from *** identify large-scale expansion of genes associated with whole rubber biosynthesis processes,such as basal metabolic processes,ethylene biosynthesis,and the activation of polysaccharide and glycoprotein lectin,which are important properties for latex production.A map of genomic variation between the cultivated and wild rubber trees was obtained,which contains～15.7 million high-quality single-nucleotide *** identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree,some of which are involved in rubber *** genome assembly represents key resources for future rubber tree research and breeding,providing novel targets for improving plant biotic and abiotic tolerance and rubber production.

关键词： rubber tree rubber biosynthesis chromosome evolution whole-genome duplication domestication

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