内蒙古和林格尔东周时期古代人群的分子遗传学分析

对10个古代个体的线粒体DNA高可变Ⅰ区进行了扩增和测序. 基于和林格尔古代人群与现今相关欧亚人群的mtDNA序列， 进行了系统发育分析和多维尺度分析. 研究结果表明, 和林格尔古代人群在母系遗传上与现在北亚人群的亲缘关系最近. 结合考古学、 人类学以及分子生物学的研究， 推断这个古代人群是从蒙古高原以及外贝加尔地区南下迁移至今天的内蒙古和林格尔地区的游牧人.     

新疆锡伯族人群线粒体DNA的遗传学分析

分析48个锡伯人线粒体DNA高可变Ⅰ区的遗传多态性, 并与已发表的相关人群线粒体DNA数据进行比较. 结果表明, 在48个序列中共检测出43个突变位点, 界定了35种单倍型, 其线粒体DNA1序列多态性为0.982, 核苷酸多态性为0.018, 而其平均核苷酸差异为5.922. 人群比较分析表明, 锡伯人与古代拓跋鲜卑人有最近的亲缘关系, 同时也表现出与中国北方游牧民族有较近的亲缘关系, 推断锡伯人可能是拓跋鲜卑的后裔.     

饮牛沟墓地古人骨线粒体DNA的研究

对内蒙古饮牛沟战国时期墓地的古代人群（Yng古代人群）进行分子生物学研究, 获得了线粒体高可变一区DNA序列, 初步确定了单倍型归属并搜寻其共享序列, 与现代人群对比构建系统发育树和多维尺度分析. 结果表明, 饮牛沟古代人群与现代东亚人群在母系遗传关系上较近.     

新疆扎滚鲁克古代人群的线粒体DNA分析

从15例扎滚鲁克古代人牙齿样本中提取扩增线粒体DNA, 确定其单倍型归属, 并结合相关现代人群进行了系统发育分析和多维尺度分析. 结果表明,扎滚鲁克古代人群与现代中亚人群有较近的母系遗传关系, 是欧亚混合人群. 与以前的新疆古代人群研究相比, 该人群东部欧亚序列的成分明显增多, 这可能与人群所处的地理及历史时代相关.     

内蒙古砧子山墓地古人的线粒体DNA多态性分析

为了研究内蒙古元上都遗址砧子山墓地古代人群的遗传结构及其可能来源,对该墓地古人的DNA进行了抽提、扩增和测序,获得了10个个体的线粒体DNA高可变一区序列.结合现代东亚、北亚、中亚和欧洲人的线粒体DNA数据进行了系统发育分析和多维尺度分析.研究结果表明:埋藏在砧子山墓地的元代居民为汉族人,主要是来自中国北方地区的汉族.本研究为揭示元代的复杂社会结构和人群历史动态提供了新的方法.     

Analysis of the matrilineal genetic structure of population in the early Iron Age from Tarim Basin, Xinjiang, China

Ancient mtDNA data of human remains were analyzed from four early Iron Age Tarim Basin sites （Yuansha, Zaghunluq, Sampula and Niya） in the southern Silk Road region. Haplogroup distributions show that ancient Tarim Basin population was comprised of well-differentiated Western and Eastern matrilineal lineages. Some West lineage of Tarim Basin population originated from Near East and Iran region. Of the East lineages, North and Northeast Asia originated lineages were the main components, and a few Southeast Asian lineages also existed, which indicated a more extensive origin and a more complex admixture. The genetic structure of ancient Tarim Basin population is relatively close to the modern populations of Xinjiang, which implied that the early Iron Age is an important period during the formation of the modern Xinjiang population.     

Low gene copy number shows that arbuscular mycorrhizal fungi inherit genetically different nuclei

Arbuscular mycorrhizal fungi (AMF) are ancient asexually reproducing organisms that form symbioses with the majority of plant species, improving plant nutrition and promoting plant diversity. Little is known about the evolution or organization of the genomes of any eukaryotic symbiont or ancient asexual organism. Direct evidence shows that one AMF species is heterokaryotic; that is, containing populations of genetically different nuclei. It has been suggested, however, that the genetic variation passed from generation to generation in AMF is simply due to multiple chromosome sets (that is, high ploidy). Here we show that previously documented genetic variation in Pol-like sequences, which are passed from generation to generation, cannot be due to either high ploidy or repeated gene duplications. Our results provide the clearest evidence so far for substantial genetic differences among nuclei in AMF. We also show that even AMF with a very large nuclear DNA content are haploid. An underlying principle of evolutionary theory is that an individual passes on one or half of its genome to each of its progeny. The coexistence of a population of many genomes in AMF and their transfer to subsequent generations, therefore, has far-reaching consequences for understanding genome evolution.     

野生和人工选育黄河鲤遗传多样性的ISSR分析

利用ISSR分子标记技术,对采集于长垣天然文岩渠(野生群体)、河南省水产科学研究院(黄河品系Ⅰ群体)、小浪底水库(野生群体)、河南黄河鲤鱼良种场(豫选黄河鲤群体)的4个群体黄河鲤的120个个体的遗传多样性进行了分析.8个ISSR引物共获得64个扩增位点,其中多态位点31个,多态位点比例为48.44%.4个群体的多态位点比例分别为14.06%,32.81%,34.38%和20.31%,遗传距离分别为0.0576、0.1657、0.1674和0.0800,Nei基因多样性分别为0.0538、0.1099、0.1308和0.0723,Shannon信息指数分别为0.0784、0.1669、0.1923和0.1072.文岩渠群体与黄河品系Ⅰ群体遗传距离最远(0.1717),与小浪底水库群体遗传距离最近(0.0558).表明这些群体间发生了较弱的遗传分化.UPGMA聚类结果为文岩渠群体与小浪底群体先聚在一起,其次是与豫选黄河鲤,最后与黄河鲤品系Ⅰ相聚.用AMOVA进行遗传变异方差分析得到遗传变异固定指数(Φst=0.0179,P0.05),显示黄河鲤大部分变异(98.21%)发生在群体内,群体间变异较小(1.79%).说明人工选育群体的遗传结构尚未发生明显变化.     

岛屿地理隔离对红楠种群遗传结构的影响

利用简单重复序列间扩增(ISSR)分子标记对舟山群岛红楠(Machilus thunbergii)8个种群91个个体进行了遗传结构分析,9条随机引物扩增出可分析条带75条,多态位点百分比(PPL)为61.3%。POPGENE分析结果表明:红楠种群平均水平多态位点百分比(PPL)为52.3%,Nei′s基因多样度(HE)为0.186,较台湾岛红楠种群(PPL为71.1%)具有偏低的遗传多样性;而种群间遗传分化程度较高(GST=0.311)。地理距离与遗传距离具有显著相关性(r=0.655,P=96.1%),岛屿地理隔离对红楠种群间遗传分化产生显著影响。UP-GMA聚类分析表明:朱家尖岛与普陀岛红楠种群间遗传相似度较高,桃花岛与大猫岛可能存在较近的亲缘关系。基于舟山群岛红楠种群遗传结构分析,建议在其自然生长地实施就地保护的同时,建立红楠种质资源库,促进基因交流。     

Inference of human population history from individual whole-genome sequences

The history of human population size is important for understanding human evolution. Various studies have found evidence for a founder event (bottleneck) in East Asian and European populations, associated with the human dispersal out-of-Africa event around 60 thousand years (kyr) ago. However, these studies have had to assume simplified demographic models with few parameters, and they do not provide a precise date for the start and stop times of the bottleneck. Here, with fewer assumptions on population size changes, we present a more detailed history of human population sizes between approximately ten thousand and a million years ago, using the pairwise sequentially Markovian coalescent model applied to the complete diploid genome sequences of a Chinese male (YH), a Korean male (SJK), three European individuals (J. C. Venter, NA12891 and NA12878 (ref. 9)) and two Yoruba males (NA18507 (ref. 10) and NA19239). We infer that European and Chinese populations had very similar population-size histories before 10-20?kyr ago. Both populations experienced a severe bottleneck 10-60?kyr ago, whereas African populations experienced a milder bottleneck from which they recovered earlier. All three populations have an elevated effective population size between 60 and 250?kyr ago, possibly due to population substructure. We also infer that the differentiation of genetically modern humans may have started as early as 100-120?kyr ago, but considerable genetic exchanges may still have occurred until 20-40?kyr ago.     

多辐溲疏居群过氧化物酶同工酶分化的研究

运用聚丙烯酰胺凝胶电泳，测试了采自四川南川县金佛山不同生境的多辐溲疏５个居群５０株个体的过氧化物酶同工酶，对酶谱带位置进行了二态编码，然后采用Ｒｏｇｅｒｓ－Ｔａｎｉｍｏｔｏ，Ｓｏｋａｌ－Ｍｉｃｈ－ｅｎｅｒ，Ｓｏｋａｌ－Ｓｎｅａｔｈ，Ｊａｃｃａｒｄ等结合系数用组平均法（ＵＰＧＭＡ）对各谱带位置进行了聚类分析．结果表明，相同生境同一居群内的个体间表现出较大的遗传同质性，而来源于不同生境的不同居群个体间却呈现出较大的遗传趋异性；同时，５个居群不但具有许多共同谱带，而且整体相聚的结合系数大多超过０．５，这表明５个居群在很早以前可能是属于同一大居群，在长期进化过程中，由于微生境的地理与气候因子选择，使得多辐溲疏现仅在金佛山海拔６００～１２００ｍ的约ｋｍ２范围内呈岛状分布；又由于其特殊的繁殖方式——居群内个体虽能杂交，但因该种仅能正常开花传粉，大部分种子败育，使得居群内个体遗传变异性不能通过有性生殖方式固定下来，仅能通过营养繁殖方式繁殖后代，而正是营养繁殖导致了居群内较大遗传同质性以及居群间的遗传趋异性．在整个进化过程中生境只不过是对那些遗传变异起到了选择固定作用     

Mitochondrial DNA analysis of ancient Sampula population in Xinjiang

The archaeological site of Sampula cemetery was located about 14 km to the southwest of the Luo County in Xinjiang Khotan, China, belonging to the ancient Yutian kingdom. ¹⁴C analysis showed that this cemetery was used from 217 B.C. to 283 A.D. Ancient DNA was analyzed by 364 bp of the mitochondrial DNA hypervariable region I (mtDNA HVR-I), and by six restriction fragment length polymorphism (RFLP) sites of mtDNA coding region. We successfully extracted and sequenced intact stretches of maternally inherited mtDNA from 13 out of 16 ancient Sampula samples. The analysis of mtDNA haplogroup distribution showed that the ancient Sampula was a complex population with both European and Asian characteristics. Median joining network of U3 sub-haplogroup and multi-dimensional scaling analysis all showed that the ancient Sampula had maternal relationship with Ossetian and Iranian.     

Craniometrical evidence for population admixture between Eastern and Western Eurasians in Bronze Age southwest Xinjiang

Xinjiang,the most northwest provincial administrative area of China,was the area where the oriental people met the occidental.The populations in Xinjiang exhibit very high genetic diversity.Previous study revealed that the eastern Xinjiang populations of the Bronze Age were mixed by the Eastern and the Western Eurasians.However,few studies have been performed to reveal when the population admixture started and how far to the west it reached.In this paper,we studied 148 craniofacial traits of 18 skulls from the Bronze Age Liushui graveyard in Khotan(Keriya County) in the southwest of Xinjiang.Seventeen craniometrical parameters of the Khotan samples were then compared with those of other ancient samples from around Xinjiang using dendrogram cluster analysis,principal components analysis,and multidimensional scaling.The results indicated that population sample of Liushui graveyard was mixed by the Western and Eastern Eurasians with about 79% contribution from the east.Therefore,we demonstrated that population admixture between east and west Eurasia can be traced back to as early as 1000 BC in southwest Xinjiang.     

Mitochondrial DNA analysis of ancient Sampula population in Xinjiang

The archaeological site of Sampula cemetery was located about 14 km to the southwest of the Luo County in Xinjiang Khotan,China,belonging to the ancient Yutian kingdom.~14C analysis showed that this cemetery was used from 217 B.C.to 283 A.D. Ancient DNA was analyzed by 364 bp of the mitochondrial DNA hypervariable region I (mtDNA HVR-I),and by six restriction fragment length polymorphism (RFLP) sites of mtDNA coding region.We successfully extracted and sequenced intact stretches of maternally inher- ited mtDNA from 13 out of 16 ancient Sampula samples.The analysis of mtDNA haplogroup distribution showed that the ancient Sampula was a complex population with both European and Asian characteristics.Median joining network of U3 sub-haplogroup and multi-dimen- sional scaling analysis all showed that the ancient Sampula had maternal relationship with Ossetian and Iranian.     

基于MHCⅡ类B基因的凹耳臭蛙(Odorrana tormota)种群遗传分化模式

利用II类MHC基因单基因座位Odto-A作为分子标记,对皖南山区凹耳臭蛙6个种群的遗传多样性和遗传分化进行研究.结果显示,皖南凹耳臭蛙总的基因多样性为0.812,核苷酸多样性为0.018.局域种群单倍型多样性变化范围为0.531-0.864,香溪种群单倍型多样性最高,最低的是漳河种群.与线粒体cyt b基因所揭示的单倍型多样性差别不大,但B基因的核苷酸多样性较之线粒体cyt b基因的高达一个数量级.暗示MHC基因丰富的核苷酸多态性可能与其病原体抗性多样性密切相关.分子变异分析结果显示,皖南山区凹耳臭蛙种群MHC II类B基因遗传变异主要来源于种群内,种群间发生了显著的遗传分化(Fst=0.05644,P=0.00391).成对种群间的遗传分化分析结果显示,直线距离最近的浮溪和香溪种群间也发生了显著的遗传分化,暗示这两个种群经历了不同的选择压力.受平衡选择的作用,MHC基因与基于中性分子标记所揭示的遗传格局不同,基于MHC基因的种群遗传分化与水系和直线地理距离均没有明显的相关性,而与种群所经历的选择压力密切相关.结果表明皖南凹耳臭蛙不同局域种群所经历的环境病原体的选择压力存在时空变异.     

Population Genetic Structure and Genetic Differentiation of the Pufferfish Takifugu Rubripes and Takifugu Pseudommus Revealed by RAPD Analysis

RAPD analysis is used to assay the population genetic structure and genetic differentiation of pufferfish T.rubripes and T.pseudommus.One hundred and twenty fragments are aplified with 21 random sequence 10-mer primers.The proportion of polymorphic fragments of T.rubripes populations from the coast of China(TRC),the coast of Japan(TRJ),general population of T.rubripes both from China and Japan(TRCJ),and the population of T.pseudommus are 31.7%,33.3%,35.0%and 39.2% respectively.The mean expected heterozygosities of the four populations are 0.116,0.125,0.126,and 0.144,respectively.Low genetic distances(ranging from 0.0118 to 0.0309)and Fst estimates(0.020 to 0.024) among the populations indicated that there is no significant differentiation between T.rubripes and T.pseudommus and suggested that only one species is involved.     

Migration and population genetics of the grain aphid Macrosiphum miscanti (Takahashi) in relation to the geographic distance and gene flow

The population genetics of the grain aphid Macrosiphum miscanti (Takahashi) is analyzed by microsatellite markers. Samples collected from 15 locations in China have been examined at 5 polymorphic microsatellite loci. Overall, genetic diversity displays a relation between the migration and gene flow in the grain aphid: a free and frequent gene flow is found in the eastern populations, and gene isolation occurs in the two western populations, especially Datong population and Guiyang population. The natural barriers may present an insurmountable obstacle preventing gene flow and aphid migration. However, a spatial genetic differentiation between populations is correlated with their geographical separation, indicating the geographic differentiation may play an important role in shaping the genetic structure of M. miscanti populations. In addition, most populations of grain aphids are out of Hardy-Weinberg equilibrium and there is heterozygote deficit. Based on F statistics, the average genetic differentiation among different geographical populations is relatively low. It seems that the long distance migration of the grain aphid may enhance gene flow and decrease genetic differentiation among different populations.     

南京椴群体遗传多样性和遗传结构分析

【目的】 南京椴(Tilia miqueliana)为江苏省重要的乡土树种,野外资源稀缺。南京椴野外群体遗传多样性和遗传结构的探索,可为资源保护、品种选育及遗传改良提供依据。【方法】 以南京椴5个天然群体[江苏宝华山(P1)、牛首山(P2)、安徽皇藏峪(P3)、安徽蜀山(P4)和浙江天台山(P5)]93个体为实验材料,选用15对多态性EST-SSR引物,进行遗传多样性及群体遗传结构分析。【结果】 ①用15对引物共检测等位基因数(A)总和为96,平均值为6.4,四倍体基因型(G)和四倍体特异基因型(G_i)总和分别为441和251,特异基因型比率(R₁)和种质鉴别率(R₂)均值分别为45.73%和17.99%。②在5个群体中,每个位点等位基因数(A_loc)和四倍体基因型丰富度均值(G_loc)分别为5.50±2.43和9.41±4.29;平均观测杂合度(H_o)和平均期望杂合度(H_e)为0.61±1.43和0.62±0.14。参考各群体G_loc和H_e值,确定遗传多样性较高的群体为P1和P3。③群体间遗传分化较小,遗传分化系数(G_st)仅为0.030;AMOVA分子变异分析显示,群体多样性水平变异来自于群体内(96%)。④聚类和遗传结构Structure分析显示,5个群体可划分为2组(组1包括P1、P2和P5;组2包括P3和P4)。Mental检验结果表明遗传距离与地理距离之间无显著相关。【结论】 南京椴群体均具有丰富的遗传多样性,其中宝华山群体和皇藏峪群体多样性较高,群体扩张可能是以这两个种群为中心,经人类活动迁移至其他区域。但南京椴群体间未形成明显分化,主要是由于植株寿命长,群体缺乏自然更新,加之群体间存在人为种子传播。因此,本研究提出通过建立隔离区,明确优先保护群体、加大植株异交,并采用人工繁育及种质回迁的方式保护南京椴野外群体。     

基于线粒体Cytb基因序列的褐石斑鱼种群遗传多样性分析

为评估种质资源状况被世界自然保护联盟(International Union for Conservation of Nature, IUCN)评定为易危物种的褐石斑鱼(Epinephelus bruneus)野生种群的遗传多样性和遗传分化水平，采用PCR方法测定褐石斑鱼西太平洋海区的中国海南岛(HN)、福建厦门(XM)和韩国济州岛(HG)3个地理群体的线粒体细胞色素b(Cytb)基因的部分序列，并对其基因序列遗传变异、谱系结构和群体扩张历史特征进行分析。结果显示，褐石斑鱼3个地理种群(88个个体)共检测出18个多态位点，共有7种单倍型；各地理群体遗传多样性水平较低，而且单倍型在群体间分布不均，韩国群体遗传多样性最高，中国海南和厦门群体遗传多样性较低。地理距离最远的韩国群体和中国海南群体遗传分化最高(F_ST=0.177 5),地理距离最近的中国海南群体和厦门群体的遗传分化最低(F_ST=0.013 4)。Mantel检验结果显示，3个褐石斑鱼群体间遗传距离和地理距离间存在显著相关，距离隔离(Isolation by Distance, IBD)...     

用45个SNP位点组合对国家啮齿类实验动物种子中心3个封闭群小鼠群体的遗传状况分析

摘要：目的 利用单核苷酸多态性位点对国家啮齿类实验动物种子中心3个封闭群小鼠群体进行群体遗传结构分析。方法 选取文献中45个SNP位点,采用基质辅助激光解吸电离飞行时间质谱(MALDI-TOF-MS)技术对来自国家啮齿类实验动物种子中心北京和上海分中心的ICR各1个群体,上海分中心的1个KM封闭群小鼠样本进行等位基因分型,分析群体遗传结构,并进行群体间遗传差异分析。结果 3个封闭群小鼠有效等位基因数(Ne)、观察杂合度(Ho)、期望杂合度(He)、平均杂合度(Ha)、多态信息含量(PIC)、香隆信息指数等遗传参数各不相同。同一群体的结果与微卫星DNA和生化位点的结果相比,SNP检测的参数值较低。但将3个群体中单态的SNP位点去除后参数值有所上升,尤其香隆指数值与STR检测结果接近。结论 所选SNP位点可用于封闭群小鼠遗传质量检测,所检测的3个群体遗传多样性用杂合度评价为SKM >BICR >SICR。