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Positive Darwinian selection in human population:A review

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Chinese Science Bulletin 2008年第10期53卷 1457-1467页

作者： WU DongDong1,3.& ZHANG YaPing1,2 1 State Key laboratory of Genetic resources and Evolution, kunming Institute of Zoology, Chinese Academy of Sciences, kunming 650223. china 2 laboratory for conservation and utilization of bio-resource, Yunnan University, kunming 650091, china 3.Graduate University of Chinese Academy of Sciences, Beijing 100049, china State Key laboratory of Genetic resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China laboratory for conservation and utilization of {3.-resource Yunnan University Kunming 650091 China Graduate University of Chinese Academy of Sciences Beijing 100049 China

This paper reviews a large number of genes under positive Darwinian selection in modern human populations, such as brain development genes, immunity genes, reproductive related genes, perception receptors. The research on the evolutionary property of these genes will provide important insight into human evolution and disease mechanisms. With the increase of population genetics and comparative genomics data, more and more evidences indicate that positive Darwinian selection plays an indispensable role in the origin and evolution of human beings. This paper will also summarize the methods to detect positive selection, analyze the interference factors faced and make suggestions for further research on positive selection.

关键词：自然选择积极选择达尔文进化论人类学种群遗传

Evolution of cd59 gene in mammals

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Science china(Life Sciences) 2007年第6期50卷 773-779页

作者： GONG YuanYing1,2, PENG MinSheng1,2, ZHOU WeiPing1,3.4 & ZHANG YaPing1,4 1 State Key laboratory of Genetic resources and Evolution, kunming Institute of Zoology, Chinese Academy of Sciences, kunming 650223. china 2 Graduate University of the Chinese Academy of Sciences, Beijing 100049, china 3.Molecular and Cell biology, University of Science and Technology of china, Hefei 23.026, china 4 laboratory for conservation and utilization of bio-resources, Yunnan University, kunming 650091, china State Key laboratory of Genetic resources Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China Graduate University of the Chinese Academy of Sciences Beijing 100049 China Molecular Cell biology University of Science Technology of china Hefei 230026 China laboratory for conservation utilization of bio-resources Yunnan University Kunming 650091 China

The CD59-coding sequences were obtained from 5 mammals by PCR and BLAST, and combined with the available sequences in GenBank, the nucleotide substitution rates of mammalian cd59 were calcu- lated. Results of synonymous and nonsynonymous substitution rates revealed that cd59 experienced negative selection in mammals overall. Four sites experiencing positive selection were found by using "site-specific" model in PAML software. These sites were distributed on the molecular surface, of which 2 sites located in the key functional domain. Furthermore, "branch-site-specific" model detected 1 positive site in cd59a and cd59b lineages which underwent accelerated evolution caused by positive selection after gene duplication in mouse.

关键词： cd59, evolution, positive selection

Application of the phylogenetic analysis in mitochondrial disease study

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Chinese Science Bulletin 2008年第18期53卷 2733-2738页

作者： WANG ChengYe1,2,3. KONG QingPeng1,2 & ZHANG YaPing1,2? 1 State Key laboratory of Genetic resources and Evolution, kunming Institute of Zoology, Chinese Academy of Sciences, kunming 650223. china 2 laboratory for conservation and utilization of bio-resource, Yunnan University, kunming 650091, china 3.Graduate University of Chinese Academy of Sciences, Beijing 100049, china Chinese Acad Sci Kunming Inst Zool State Key Lab Genet Resources and Evolut Kunming 650223 Peoples R China.

Mitochondrial disease currently received an increasing concern. However, the case-control design commonly adopted in this field is vulnerable to genetic background, population stratification and poor data quality. Although the phylogenetic analysis could help solve part of these problems, it has not received adequate attention. This paper is a review of this method as well as its application in mito- chondrial disease study.

关键词：线粒体疾病分析单元型种群分布

Pitfalls in the analysis of ancient human mtDNA

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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 650223.{3. 2. laboratory for conservation and utilization of bio-resource, Yunnan University, kunming 650091,{3. 3. Graduate School of the Chinese Academy of Sciences, Beijing 10003.,{3. 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 {3.-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

Molecular evolution of stress-response gene Leptin in high-altitude Chinese snub-nosed monkeys (Rhinopithecus genus)

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Chinese Science Bulletin 2010年第36期55卷 4132-4135页

作者： WANG XiaoPing1,2, JIN Wei1,2, YU Li1,2 & ZHANG YaPing1,2 1 laboratory for conservation and utilization of {3.-resource, Yunnan University,{3., china 2 State Key laboratory of Genetic resources and Evolution, kunming Institute of Zoology, Chinese Academy of Sciences, kunming 650223. china laboratory for conservation and utilization of {3.-resource Yunnan University Kunming 650091 China State Key laboratory of Genetic resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China

Chinese snub-nosed monkeys (genus Rhinopithecus, subfamily Colobinae), including R. bieti, R. brelichi and R. roxellana, are well-known as the non-human primates with the highest known altitudinal distribution. They represent an interesting model organism of adaptation to the extreme environmental stresses. However, no study at the molecular level has yet been reported for the high-altitude adaptation in Chinese snub-nosed monkeys. Leptin, as an adipocyte-derived hormone, is believed to play an important role in energy homeostasis in adaptation to high altitude environments. In the present study, we sequenced and compared leptin sequences of the Chinese snub-nosed monkeys (R. bieti and R. roxellana) with their lowland close relative R. avunculus and other Colobines. Unexpectedly, no amino acid changes were observed in the 7 Colobinae species examined, including the 2 Chinese snub-nosed monkeys, indicating no difference in the evolutionary pattern of the Leptin gene between high-altitude monkeys and their lowland counterparts. In contrast to a previous finding of adaptive evolution of Leptin gene in plateau pikas, our study suggests that this gene may not have an important role in high-altitude adaptation of Chinese snub-nosed monkeys. Other nuclear genes associated with energy metabolism, or mitochondrial genes, are most likely to be involved the molecular mechanism underlying adaptation of these monkeys to cold and hypoxia associated with the highland environment.

关键词： Leptin基因金丝猴属瘦素基因压力反应分子进化高空鼻极端环境

Regulation of eight avr genes by hrpG and hrpX in Xanthomonas campestris pv. campestris and their role in pathogenicity

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Progress in Natural Science:Materials International 2006年第12期16卷 1288-1294页

作者： XU Rongqi~ 1,3., LI Xianzhen~3. WEI Hongyu~3. JIANG Bole~2, LI Kai~3. HE Yongqiang~ 2,3., FENG Jiaxun~ 1,3.and TANG Jiliang~ 1,2 **(1. Guangxi Key laboratory of Subtropical bioresources {3. and {3. 2. The Key laboratory of Ministry of Education for Microbial and Plant Genetic Engineering 3. College of Life Science and Technology, Guangxi University, Nanning 53.004, china) Guangxi Key laboratory of Subtropical bioresources {3. and {3. Guangxi University Nanning 530004 China College of Life Science and Technology Guangxi University Nanning 530004 China The Key laboratory of Ministry of Education for Microbial and Plant Genetic Engineering Guangxi University Nanning 530004 China

Eight putative avirulence genes in Xanthomonas campestris pv. campestris (Xcc) strain 8004 were characterized by Tn5gusA5 mutagenesis and gene expression analysis. The virulence test of mutants on Chinese radish showed that all mutants in individual avr genes except avrBs2 mutant were not significantly different from the wild type in virulence. The avrBs2 mutant showed reduced virulence and bacterial growth in planta. Gene expression analysis using β-glucuronidase as reporter indicated that avrBs1.1,avrBs1,avrXccB,avrXccC,avrXccE1 were regulated by hrpG, whereas avrXccA1, avrXccA2 and avrBs2 were not. RT-PCR analysis showed that all hrpG-regulated genes except avrBs1 were also regulated by hrpX. In addition, it was demonstrated that avrBs1 was responsible for elicitation of a type III dependent hypersensitive reaction (HR) on nonhost plant pepper ECW-10R, and wild type Xcc 8004 was unable to cause HR on pepper ECW-20R.

关键词： Xanthomonas campestris pv. campestris avirulence gene virulence expression analysis.

The role of MC1R gene in buffalo coat color

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Science china(Life Sciences) 2010年第2期53卷 267-272页

作者： MIAO YongWang1,2,WU GuiSheng3.WANG Lei2,LI DaLin4,TANG ShouKun5,LIANG JianPing2,MAO HuaMing2,LUO HuaiRong3.& ZHANG YaPing1,6 1 laboratory for conservation and utilization of {3.-resource,Yunnan University,{3. 650091,china 2 Faculty of Animal Science and Technology,Yunnan Agricultural University,{3. 650201,china 3.{3. Institute of Botany,Chinese Academy of Sciences,{3. 650204,china 4 Yunnan Institute of Buffalo Science and Technology,{3. 650021,china 5 Animal Husbandry and Veterinary Station of Luxi city,Luxi 678400,china 6 State Key laboratory of Genetic resources and Evolution,{3. Institute of Zoology,Chinese Academy of Sciences,{3. 650223.china 1. laboratory for conservation and utilization of {3.-resource Yunnan University Kunming 650091 China2. Faculty of Animal Science and Technology Yunnan Agricultural University Kunming 650201 China3. Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China4. Yunnan Institute of Buffalo Science and Technology Kunming 650021 China5. Animal Husbandry and Veterinary Station of Luxi city Luxi 678400 China6. State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China

Melanocortin-1 receptor (MC1R) plays a major role in pigmentation in many *** investigate if the MC1R gene is associated with coat color in water buffalo,the coding region of MC1R gene of 216 buffalo samples was sequenced,which included 49 black river buffalo (Murrah and Nili-Ravi),13. swamp buffalo (Dehong,Diandongnan,Dechang,Guizhou,and Xilin) with white and gray body,and 3. hybrid offspring of river buffalo Nili-Ravi (or Murrah) and swamp *** the three variation sites found,SNP684 was synonymous,while SNP3.0 and SNP3.4 were nonsynonymous,leading to p.S104G and p.I128M changes,*** Individuals carrying homozygote EBR/EBR were *** genotype and phenotype analysis of the hybrid offspring of black river buffalo and gray swamp buffalo further revealed that the river buffalo type allele EBR or the allele carrying the amino acid p.104S was important for the full function of *** in silico functional analysis showed that the amino acid substitutions p.G104S and p.M128I had significant impact on the function of *** results indicate that the allele EBR or the allele carrying the amino acid p.104S was associated with the black coat color in buffalo.

关键词： Buffalo coat color MC1R

Gene admixture in ethnic populations in upper part of Silk Road revealed by mtDNA polymorphism

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Science china(Life Sciences) 2008年第5期51卷 435-444页

作者： YANG LiuQi, TAN SiJie, YU HaiJing, ZHENG BingRong, QIAO EnFa, DONG YongLi, ZAN RuiGuang & XIAO ChunJie Key laboratory of bioresources {3. and {3. & Human Genetics Center, Yunnan University, kunming 650091, china Key laboratory of bioresources {3. utilization & Human Genetics Center Yunnan University Kunming 650091 China

To evaluate the gene admixture on the current genetic landscape in Gansu Corridor (GC) in china, the upper part of the ancient Silk Road which connects the Eastern and Central Asia, we examined mitochondrial DNA (mtDNA) polymorphisms of five ethnic populations in this study. Using PCR-RFLP and sequencing, we analyzed mtDNA haplotypes in 242 unrelated samples in three ethnic populations from the GC region and two ethnic populations from the adjacent Xinjiang Uygur Autonomous Region of china. We analyzed the data in comparison with the previously reported data from Eastern, Central and Western Asia and Europe. We found that both European-specific haplogroups and Eastern Asian-specific haplogroups exist in the Gansu Corridor populations, while a modest matrilineal gene flow from Europeans to this region was revealed. The Gansu Corridor populations are genetically located between Eastern Asians and Central Asians, both of who contributed significantly to the maternal lineages of the GC populations. This study made the landscape of the gene flow and admixture along the Silk Road from Europe, through Central Asia, to the upper part of the Silk Road more complete.

关键词： polymorphism mtDNA gene admixture Gansu Corridor

Molecular diversity of arbuscular mycorrhizal fungi colonizing the valley-type savanna,southwest china

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Molecular diversity of arbuscular mycorrhizal fungi colonizi...