Mitochondrial DNA analysis of Bronze Age horses recovered from Chifeng region, Inner Mongolia, China

In this study, mitochondrial DNA (mtDNA) analysis was carried out on 9 Bronze Age horses recovered from Dashanqian and Jinggouzi archaeological sites in Chifeng region, Inner Mongolia. China to explore the origin of Chinese domestic horses. Both mtDNA 16S rRNA gene and control region (D-loop) fragments of ancient horses were amplified and sequenced. The analysis of the highly conservative 16S rRNA gene sequences indicated that the burial environment of Chifeng region is suitable for the preservation of ancient DNA (aDNA). Combing 465 mtDNA D-loop sequences representing different breeds from East Asia, Central Asia, Near East and Europe, we constructed a phylogenetic network to investigate the relationship between ancient and modern horses. The phylogenetic network showed that the 9 horses were distributed into different modern horse clusters which were closely related to them representing a certain geographical distribution. Our results showed that the maternal genetic line of the ancient horses in Chifeng region was highly diversified, which contributed to the gene pool of modern domestic horses and suggested a complex origin of domestic horses in China.     

西藏马线粒体DNA D loop区的遗传多样性

对西藏拉萨和泽当两个地区23匹西藏马的线粒体DNA控制区(mtDNA D-loop)部分片段进行序列分析, 检测出16个单倍型, 包括32个核苷酸多态性位点(其中转换位点31个, 缺失位点1个), 占所分析位点总数的9.27%. 单倍型多样性(h)和核苷酸多样性(π)分别为0.93±0.04和2.51%±0.16%, 表明西藏马的遗传多样性较丰富. 基于23匹西藏马序列以及现代欧亚马群的mtDNA序列, 进行了系统发育分析和多维尺度分析. 结果表明, 西藏马在母系遗传关系上与近东、 中亚以及欧洲家马有较近的亲缘关系, 与东亚的蒙古马以及韩国马亲缘关系较远.     

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.     

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.     

淡水鱼类线粒体DNA D-loop基因的引物设计和应用

 线粒体DNA测序已广泛应用于鉴定和区分种类以及解决系统进化关系问题。本文选取已测定的主要淡水鱼类的线粒体DNA D-loop基因序列进行同源性比较,寻找保守序列,利用简并性原则设计一对通用的简并引物。利用设计的引物对广东省珠江流域主要的淡水鱼类线粒体DNA D-loop控制区基因进行扩增,均能获得单一的目的DNA片断,特异性扩增产物大小为1 kb左右。经测序及与GenBank同源序列的比较,证实为包含线粒体控制区全序列的扩增产物。本研究所设计的引物和应用的方法可以快速地同时对多种鱼类进行大规模的遗传背景分析,鉴定某些难于鉴别的近缘物种,为我国鱼类的种类鉴定、地理种群鉴别及种质资源的评估提供重要的工具。     

Molecular biological analysis of remains from Jiangjungou Cemetery in Inner Mongolia

The 364-bp nucleotide sequence in hypervariable region I (HVRI) of mitochondrial DNA is successfully amplified from 9 out of 11 individuals of an ancient population buried in the Jiangjungou Cemetery in Inner Mongolia dated back to the Warring States Period in China. Nine fragments with different variations are obtained. A phylogenetic tree and a multidimensional scaling (MDS) plot are constructed using mtDNA sequences from the ancient population and several modern Asian populations. The results show that ancient population shares a closer genetic relationship with East Asian populations than with North and Central Asian populations. The genetic and historical evidence raise the possibility that the population might be the immigrants from Zhongyuan area, sent by the King Wuling of Zhao State to guard the nation against the attack from Huns.     

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.     

Pitfalls in the analysis of ancient human mtDNA

The retrieval of DNA from ancient human specimens is not always successful owing to DNA deterioration 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 Xinjiang, China) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylogeny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demonstrated that many mtDNAs reported are more or less problematic.Startim, 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.     

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.     

中国部分地方牛种mtDNA D-loop区全序列的遗传多样性与系统进化分析

利用PCR测序及生物信息学分析技术,对我国5个地方黄牛品种、5个地方水牛品种及2个地方牦牛品种的mtDNA D-loop区全序列进行PCR扩增以及核苷酸多样度、单倍型多样度分析,发现中国地方黄牛、水牛与牦牛具有丰富的遗传多样性.对试验牛mtDNA D-loop区全序列与牛亚科代表性物种黄牛、水牛、家牦牛、野牦牛、欧洲普通牛、印度瘤牛以及摩拉水牛相应序列进行系统发育分析.结果显示:黄牛与牦牛的亲缘关系较近,它们与水牛的亲缘关系较远;中国水牛属于沼泽型水牛,也有少量江河型水牛渐渗入中国水牛群体;中国黄牛为普通牛和瘤牛的混合母系起源;进化树显示高原牦牛与野牦牛的亲缘关系较近,环湖牦牛与家牦牛的亲缘关系较近.     

东海野生灰鲳mtDNA D-loop序列遗传变异分析

以东海区野生灰鲳背部肌肉的线粒体DNA为模板,采用PCR技术对7个个体的D-loop序列进行了扩增,通过对PCR产物进行双向测序,最终得到了471 bp的核苷酸片断(除去两端部分序列)。用DNAMAN6.0软件进行了排序比较发现,东海野生灰鲳的D-loop序列同源性高达99.48%;用DNASP4.0软件分析得知,7个序列共有6个单倍型(在GenBank登录号:GU970085-GU970087,GU970089-GU970091),在7个个体中,共检测到14个变异位点,包括13个转换和1个颠换位点。运用MEGA4.0软件计算出了不同个体间的遗传距离,并据此构建了MP和NJ系统树。用DNASP4.0软件计算出的多态位点数为14,核苷酸多样性指数和平均核苷酸差异数分别为0.009 71和4.571。研究结果表明,东海野生灰鲳的D-loop序列个体变异程度并不丰富。     

High genetic diversity of Tibetan Mastiffs revealed by mtDNA sequences

Many studies have been reported the origin and evolution of domesticated animals, particularly dogs, however, few have system-atically examined the Tibetan Mastiff (TM), a dog that lives primarily in the Qing-Tibet Plateau. Here, we study the origin and evolution of TM based on the population comparison of mtDNA D-loop sequences from TM and other dogs across the world. Intriguingly, non-simultaneous arrivals of Tibetan Mastiffs ancestors to Tibet occurred, which may result from continuous Tibetans’ settlement on Qing-Tibet Plateau supported by archaeological and genetic evidence. High genetic and haplotype diversity and robust haplotypes sharing with other dogs unique to East Asia are observed in Tibetan Mastiff, supporting that it is a very archaic breed derived probably from East Asia.     

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.     

线粒体D-Loop区全序列分析A2a基因敲除小鼠生产扩大群的遗传稳定性

目的采用线粒体D-Loop全序列测定法对A2a基因敲除小鼠近交系生产扩大群中的小鼠进行了遗传稳定性分析。方法对5个子代A2a杂合子50只小鼠的线粒体DNA D-Loop区进行了PCR扩增,产物纯化后测序,其结果与小鼠线粒体标准序列比对,分析50只小鼠之间的序列差异。结果发现检测的50只小鼠的D-Loop基因序列完全一致,且与小鼠线粒体标准序列完全一致。结论 A2a基因敲除小鼠扩大繁殖群具有较好的遗传稳定性,同时为进一步研究A2a小鼠提供遗传学资料。     

Analysis of RAPD and mitochondrial 16S rRNA gene sequences from Trichiurus lepturus and Eupleurogrammus muticus in the Yellow Sea

Random amplified polymorphic DNA (RAPD) technique is applied to 12 individuals from each species of the hairtail fishes Trichiurus lepturus and Eupleurogrammus muticus in the Yellow Sea. The percentage of polymorphic sites, degree of genetic polymorphism and genetic distance are compared and the phylogenetic tree is constructed by Neighbor-joining method. The partial mitochondrial 16S rRNA gene is amplified by polymerase chain reaction (PCR) and the PCR products are directly sequenced after being purified. These sequences, together with the homologous sequences of another Trichiuridae species Lepidopus caudatus obtained from GenBank, are used to analyze nucleotide difference and to construct a UPGMA phylogenetic tree by means of biological informatics. Analysis shows: (1) the RAPD technique is a highly sensitive method for investigating genetic diversity in T. lepturus, and E. muticus. T. lepturus exhibits a lower polymorphism and genetic diversity than E. muticus; (2) according to the analysis of the partial mitochondrial 16S rRNA gene sequences, a very low intraspecific variation and considerably high divergence among species were found, which reveals a dual nature of conservatism and variability in mitochondrial 16S rRNA gene; (3) five primers generate the species-specific RAPD sites and these sites can be served as the molecular markers for species identification and (4) it can be proved at DNA variation level that T. lepturus and E. muticus are of two species respectively pertaining to different genera, which supports the Nelson taxonomic conclusion.     

Genetic evidence for Near-Eastern origins of European cattle

The limited ranges of the wild progenitors of many of the primary European domestic species point to their origins further east in Anatolia or the fertile crescent. The wild ox (Bos primigenius), however, ranged widely and it is unknown whether it was domesticated within Europe as one feature of a local contribution to the farming economy. Here we examine mitochondrial DNA control-region sequence variation from 392 extant animals sampled from Europe, Africa and the Near East, and compare this with data from four extinct British wild oxen. The ancient sequences cluster tightly in a phylogenetic analysis and are clearly distinct from modern cattle. Network analysis of modern Bos taurus identifies four star-like clusters of haplotypes, with intra-cluster diversities that approximate to that expected from the time depth of domestic history. Notably, one of these clusters predominates in Europe and is one of three encountered at substantial frequency in the Near East. In contrast, African diversity is almost exclusively composed of a separate haplogroup, which is encountered only rarely elsewhere. These data provide strong support for a derived Near-Eastern origin for European cattle.     

New ancient DNA sequences suggest high genetic diversity for the woolly mammoth (Mammuthus primigenius)

Partial DNA sequences of cytochrome b gene (mtDNA) were successfully retrieved from Late Pleistocene fossil bone of Mammuthus primigenius collected from the Xiguitu County ( Yakeshi), Inner Mongolia Autonomous Region and from Zhaodong, Harbin of Heilongjiang Province in northern China. Two ancient DNA fragments (109 bp and 124 bp) were authenticated by reproducible experiments in two different laboratories and by phylogenetic analysis with other Elephantidae taxa. Phylogenetic analysis using these sequences and published data in either separate or combined datasets indicate unstable relationship among the woolly mammoth and the two living elephants, Elephas and Loxodonta . In addition to the short sequences used to attempt the long independent evolution of Elephantidae terminal taxa, we suggest that a high intra-specific diversity existed in Mammuthus primigenius crossing both spatial and temporal ranges, resulting in a complex and divergent genetic background for DNA sequences so far recovered. The high genetic diversity in the extinct woolly mammoth can explain the apparent instability of Elephantidae taxa on the molecular phylogenetic trees and can reconcile the apparent paradox regarding the unresolved Elephantidae trichotomy.     

New ancient DNA sequences suggest high genetic diversity for the woolly mammoth (Mammuthus primigenius)

Partial DNA sequences of cytochrome b gene (mtDNA) were successfully retrieved from Late Pleistocene fossil bone of Mammuthus primigenius collected from the Xiguitu County (Yakeshi), Inner Mongolia Autonomous Region and from Zhaodong, Harbin of Heilongjiang Province in northern China. Two ancient DNA fragments (109 bp and 124 bp) were authenticated by reproducible experiments in two different laboratories and by phylogenetic analysis with other Elephantidae taxa. Phylogenetic analysis using these sequences and published data in either separate or combined datasets indicate unstable relationship among the woolly mammoth and the two living elephants, Elephas and Loxodonta. In addition to the short sequences used to attempt the long independent evolution of Elephantidae terminal taxa, we suggest that a high intra-specific diversity existed in Mammuthus primigenius crossing both spatial and temporal ranges, resulting in a complex and divergent genetic background for DNA sequences so far recovered. The high genetic diversity in the extinct woolly mammoth can explain the apparent instability of Elephantidae taxa on the molecular phylogenetic trees and can reconcile the apparent paradox regarding the unresolved Elephantidae trichotomy.     

New ancient DNA sequences suggest high genetic diversity for the woolly mammoth (Mammuthus primigenius)

Partial DNA sequences of cytochrome b gene (mtDNA) were successfully retrieved from Late Pleistocene fossil bone of Mammuthus primigenius collected from the Xiguitu County (Yakeshi), Inner Mongolia Autonomous Region and from Zhaodong, Harbin of Heilongjiang Province in northern China. Two ancient DNA fragments (109 bp and 124 bp) were authenticated by reproducible experiments in two different laboratories and by phylogenetic analysis with other Elephantidae taxa. Phylogenetic analysis using these sequences and published data in either separate or combined datasets indicate unstable relationship among the woolly mammoth and the two living elephants, Elephas and Loxodonta. In addition to the short sequences used to attempt the long independent evolution of Elephantidae terminal taxa, we suggest that a high intra-specific diversity existed in Mammuthus primigenius crossing both spatial and temporal ranges, resulting in a complex and divergent genetic background for DNA sequences so far recovered. The high genetic diversity in the extinct woolly mammoth can explain the apparent instability of Elephantidae taxa on the molecular phylogenetic trees and can reconcile the apparent paradox regarding the unresolved Elephantidae trichotomy.     

Complete mitochondrial DNA sequence of Chinese alligator,Alligator sinensis, and phylogeny of crocodiles

The 16746-neueleotide (nt) sequence of mitochondrial DNA(mtDNA) of Chinese alligator,Alligator sinensis,was determined using the Long-PCR and primer walking methods.As is typical in vertebrates,the mtDNA encodes 13 proteins,2 rDNA,22 tRNA genes,and a noncoding control region.The Composition of bases is respectively 29.43%A,24.59%T,14.86%G,31.12% C.The gene arrangement differs from the common vertebrate gene arrangement,but is similar to that of other crocodiles,DNA sequence data from 12S rRNA,168 rRNA,protein-coding genes and combined sequence data were used to reconstruct the phylogeny of reptiles with the MP and ML methods.With this large data set and an appropriate range of outgroup taxa,the authors demonstrate that Chinese alligator is most closely related to American alligator among three crocodilian species,which suppors the traditional viewpoint.According to the branch lengths of ML tree from the combined data set,the primary divergence between Alligator and Caiman genus was dated at about 74.9 Ma,the split between Chinese alligator and American alligator was dated at 50.9Ma.