Reconstructing the evolutionary history of China: A caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modem data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (similar to 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modem populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

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. 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.

东亚现代人群起源与史前迁移的群体遗传学和古DNA研究

现代人起源和史前迁移问题的遗传学研究是一个受到广泛关注的研究领 域。首先，它可以解答人类所关心的关于自身的起源以及我们祖先的史前活动问 题；其次，现代人祖先分开并扩散到世界各地，由于受到不同的外界环境和不同 的历史事件的影响，遗传上发生相应的变化，形成现有人群之间不仅在外表上存 在差异，同时在对疾病的易感性方面也存在差异。近年来的研究还发现，不同人 群之间在对药物的反应上也存在差异。 因此，人群起源与史前迁移研究对生物 医学研究也至关重要。目前，世界各地人群的起源和史前迁移问题的研究已经取 得很多进展，东亚之外的其它各个地区现有人群的起源和迁移已经相当清楚，东 亚现代人的起源对完整回答现代人的起源问题至关重要。 东亚现代人史前早期迁移的问题还存在很大争议，对现有研究结果的解释 甚至存在冲突。通过对东亚地区现有人群展开系统采样，并对东亚特有的Y 单 倍型遗传标记进行扫描，以东亚现代人特有的单倍型组O3-M122 下的各个特征 位点为遗传标记，我们对来自东亚地区的2332 份男性样本进行了研究。结果发 现，O3-M122 单倍型组为东亚现代人群的主导单倍型，其平均频率是44.3％。 以SNPs 突变特征为背景，展开SNPs-STRs 相结合的研究，通过大量的分析和统 计检验，从STRs 数据上可以看出东亚现代人南部人群的O3-M122 单倍型组的 多样性比北方人群高。这一证据揭示出东亚现代人特有单倍型O3-M122 突变为 东亚南部起源，然后随着东亚现代人早期的由南向北迁移活动而扩散到北方。利 用SNPs-STRs 相结合的遗传学分析手段，推导出东亚特有单倍型组O3-M122 伴 随人群由南向北的早期迁移事件发生于距今约25000～30000 年以前，这一结论 与东亚现代人的化石证据推断的结论相一致。O3-M122 单倍型组的史前早期迁 移事件有助于从遗传学角度透视东亚现代人早期迁移的路线和起源问题。 东亚地区现代人史前迁移活动遗留下神秘的悬棺文化一直令人费解，考古学的推论存在很大争议。我们利用遗传学手段对现存悬棺文化的保留人群展开研 究，采用父系和母系遗传标记相结合的方法探讨悬棺文化的传播人群的族源。从 遗传上看，悬棺葬俗的拥有人群不论从母系还是父系遗传学证据都为典型的东亚 南方人群。 为最终解决东亚现代人起源和史前迁移问题，我们对考古发掘出来的东亚 地区现代人化石展开古DNA（ancient DNA, aDNA）研究。目前，aDNA 分析的 技术和手段已经建立并逐步成熟，并且积累了一定量的东亚现代人的aDNA 数 据，这一研究还在继续。aDNA 最终会为解答东亚现代人起源和史前迁移问题提 供强有力的遗传学证据。

Analysis of mitochondrial DNA polymorphisms in Guangdong Han Chinese

Previous investigations on Chinese mitochondrial DNA (mtDNA) variation revealed that the matrilineal gene pool of southern Han Chinese is rather complex, with much higher genetic diversity and more basal/ancient lineages than the northern Hans. The extrem

Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages

The four species of "river dolphins" are associated with six separate great river systems on three subcontinents and have been grouped for more than a century into a single taxon based on their similar appearance. However, several morphologists recently questioned the monophyly of that group. By using phylogenetic analyses of nucleotide sequences from three mitochondrial and two nuclear genes, we demonstrate with statistical significance that extant river dolphins are not monophyletic and suggest that they are relict species whose adaptation to riverine habitats incidentally insured their survival against major environmental changes in the marine ecosystem or the emergence of Delphinidae.

Molecular Dynamics Simulation of Peeling a DNA Molecule on Substrate

Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

Metric representation of DNA sequences

A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.

Ancient Chinese algorithm: The Ying Buzu Shu (method of surplus and deficiency) vs Newton iteration method

Air exploratory discussion of an ancient Chinese algorithm, the Ying Buzu Shu, in about 2nd century BC, known as the rule of double false position in the West is given. In addition to pointing out that the rule of double false position is actually a translation version of the ancient Chinese algorithm, a comparison with well-known Newton iteration method is also made. If derivative is introduced, the ancient Chinese algorithm reduces to the Newton method. A modification of the ancient Chinese algorithm is also proposed, and some of applications to nonlinear oscillators are illustrated.

Recurrence plot analysis of DNA sequences

Recurrence plot technique of DNA sequences is established on metric representation and employed to analyze correlation structure of nucleotide strings. It is found that, in the transference of nucleotide strings, a human DNA fragment has a major correlation distance, but a yeast chromosome's correlation distance has a constant increasing. (C) 2004 Elsevier B.V All rights reserved.

Origin of Chinese ancient glasses;study on the earliest Chinese ancient glasses

The earliest Chinese ancient glasses before the West Han Dynasty (200 BC) from different regions are studied. The glass samples were unearthed from Hunan, Hubei, Yunnan, Sichuan, Guizhou, Guangdong and Xinjiang of China. The chemical composition of these glasses samples is analyzed by proton induced X-ray emission (PIXE) technique, energy dispersive X-ray fluorescence (EDXRF) method and inductively coupled plasma atomic emission spectrometry (ICP-AES). It is shown that the glass chemical compositions belong to barium-lead silicate BaO-PbO-SiO2, potash soda lime silicate K2O (Na2O)-CaO-SiO2 (K2O/Na2O > 1), soda potash lime silicate Na2O (K2O)-CaO-SiO2 (K2O/Na2O < 1) and potash silicate K2O-SiO2 glass systems, respectively. The origins of the earliest Chinese ancient glasses are discussed from the archaeological and historical points of view. These four types of Chinese ancient glasses were all made in Chinese territory using local raw materials. The glass preparation technology was related to the Chinese ancient bronze metallurgy and proto-porcelain glaze technology. The glass technology relationship between the East and the West is analyzed at the same time.