基于DNA分子的现代人起源研究35年回顾与展望

1983年,有学者首次发表现代人线粒体DNA进化树,认为现代人可能起源自亚洲。1987年,又有学者按照分子钟假说得到线粒体在10-20万年前出自非洲的推论。随后,以分子钟为前提的Y染色体和常染色体DNA研究也支持了出非洲的结论,该结论逐渐成为分子进化领域的主流理论。2010年,对尼安德特人常染色体基因组的研究指出其对现代人有遗传贡献,这颠覆了人们先前关于现代人只来源自非洲,其他大洲的当地古人被完全取代的认知。目前,单地区起源说已经被修正为同化说。尽管学界对非洲人遗传多样性最高这一现象有共识,但是对该现象的不同解读却可以得出两种迥然不同的结果,现代人出亚洲说和出非洲说。大量研究证实基因组的大部分序列是有功能的,并处在遗传变异水平的饱和态,这质疑了中性理论以及由它推导的现代人出非洲说的合理性,而中性理论的提出恰恰是用来解释并非普遍存在的分子钟的。近年来已经有研究者从新理论的角度解读遗传多样性的饱和态和线性态,人们对现代人起源的认识将会进一步加深完善。     

东亚现代人的起源

古遗传学过去十年的发展表明, 现代人在全新物种——智人的出现过程中并没有一个系统发育学意义上的起源, 因此, 解剖学、行为学和遗传学方面的现代性并不是一个相同且单一事件的结果。本文研究了东亚解剖学、行为学和遗传学方面的证据,现代性在每个方面都可以被理解为多地区进化过程的一个片段, 而不是一个整体。三个方面的现代性在某种程度上是相互独立的, 而且各自都是在不同的时间发展出来, 直到晚更新世的人口变化才使三者相互关联起来; 人类存活率的提高和不断扩张改变了人类的进化行程。     

中国山羊mtDNA D-loop遗传多样性及其起源研究

采用DNA测序技术分析了中国9个山羊品种（板角山羊、成都麻羊、贵州黑山羊、贵州白山羊、黔北麻羊、马头山羊、陕南白山羊、黄淮山羊和雷州山羊）共计128个个体的mtDNA D-loop全序列。结果表明：山羊mtDNA D-loop全序列长度为1212-1213bp,检测到102个变异位点,约占分析位点总数的8．42％,可变位点中转换占99个,颠换2个,1个转换/颠换共存;界定了92种单倍型,有78种为各品种独享单倍型,另外14种为群体内或群体间共享单倍型。9个山羊品种单倍型多样度为0．9333-1．0000,核苷酸多样度为0．7062％-1．8265％,表明中国山羊品种遗传多样性丰富。根据92种mtDNA单倍型构建了中国山羊的NJ分子系统树,聚类表明,中国山羊mtDNA D-loop序列单倍型分为支系A和支系B两大类。支系A包括75种单倍型,代表95个样本,占总数的74．22％;支系B包括17种单倍型,代表33个样本,占总数的25．78％,说明中国山羊存在支系A和支系B两大母系起源。对中国山羊mtDNA D-loop的支系A和支系B进行核苷酸不配对分布曲线分析和Fu的Fs中性检验,分析表明,支系A的分布曲线呈单峰形,Fs值为-24．6491,P值为0．0000,显著偏离中性,表明山羊支系A曾经历群体扩张;支系B呈近似双峰分布,Fs值为-3．3947,P值为0．0980,中性检验差异不显著,表明山羊支系B没有经历群体扩张,群体大小保持相对稳定。山羊支系B可能起源于中国。     

浅谈现代人类的起源

对目前争论不休的关于现代人类起源的2种主要学说的观点和依据进行综述和适当的比较。同时引进了这2种主流观点之外的第3方观点。     

我们从哪里来？

目前人类的数量超过了60亿,有人预测到2050年会超过92亿,逼近100亿。人类几百万年的进化史中,存在的人口总数量估计在1000亿左右。假如达尔文是对的,我们都是由猴子变来的,那么我们已经不是传统意义上的猴子,而是主宰这个地球的超级生灵了。从猴子变成人有一系列枯燥的数据,尽管科学家们还在不断地努力着,     

新证据下的现代人起源模型

解剖结构上的现代人是指具有近圆球形头骨、短而平的面颅、纤细的骨骼等特征的区别于其他古老人类的化石和现今的人群。支持多地区演化模型和支持近期非洲起源模型的学者,在“解剖结构上的现代人”的应用范围方面是不同的,前者以连续演化为基本思想,认为这一名词只包括智人中较进步的类群;而后者以分支系统学思想为基础,认为包括所有智人。分子古生物学研究显示,尼人、丹人和智人在遗传学水平上属于不同的人种。新近的以标本-种群为单元的系统分析,因为不是以属、种等分类学阶元进行的,因此与分类学的阶元划分无关。该系统分析的结果显示智人属于单系类群,哈尔滨人、大荔人等组成其姊妹群。尼人与智人的分异早于1百万年,与基因组水平的谱系分析相符合。多次多向的穿梭扩散是统计学上符合系统关系的模型。     

分子人类学与现代人的起源*

1953年Watson & Crick 对于DNA双螺旋结构模型的提出及对其遗传机理的解释,标志着现代分子生物学的诞生。其后短短50年的时间里,分子生物学在各个学科之间广泛渗透,相互促进,不断深入和发展。在以研究人类的起源和进化为首要任务的人类学领域,由于现代分子生物学理论和方法的应用,诞生了分子人类学这一全新的结合型分支学科,为人类学的发展提供了科学可信的研究方法和具发展前景的研究方向。系统地介绍了分子人类学的发展历史、研究方法及原理;另外,结合分子人类学在古人类学研究中的应用,讨论了关于现代人起源的“非洲起源说”和“多地区连续演化说”。Abstract: Since Watson & Crick put forward the double-helix model of DNA structure and hereditary mechanism in 1953, it is generally accepted that this event marks the birth of modern molecular biology. This new field of biology has experienced a flourishing development in the past 50 years. On one hand, the development of molecular biology has been deeply influencing many relative fields; on the other hand, its own proceeding pace has been accelerated by the reaction from the other fields. Anthropology is one of the fields most deeply impacted by the theory and method of molecular biology. Most importantly, molecular anthropology was born as a result of combination of molecular biology, anthropology as well as paleoanthropology. This new branch provides reliable method and vital direction for paleoanthropology. This paper systematically reviews the history, principle and method of molecular anthropology. Two hypotheses on the origin of modern human, which include “out-of-African theory” and “theory of multiregional evolution” are also discussed for the purpose of showing how molecular anthropology is applied in paleoanthropology.     

广东省地方鸡线粒体遗传多样性与母系起源

系统评估地方鸡的遗传变异水平并追溯其母系起源, 可为保护利用优质家禽种质资源库提供科学依据。本研究测定了广东省和邻省共12个地方鸡品种的线粒体DNA D-loop序列, 分析品种间的遗传距离与系统关系, 并构建单倍型系统发生树和中介网络图。360份样品共检测到60个突变位点, 均为转换。定义了85种单倍型, 归属于单倍型类群A、B、C和E, 在12个鸡品种中均有分布, 其中B是优势单倍型类群(187个, 51.94%), E次之(76个, 21.11%)。B02 和C01是优势单倍型(85个, 23.61%; 48个, 13.33%), 为12个鸡品种共有; E03位居第三(35个, 9.72%), 杏花鸡、黄郎鸡和宁都三黄鸡未见此单倍型。杏花鸡集中分布在单倍型类群B, 惠阳胡须鸡和中山沙栏鸡则主要分布在单倍型类群E; 怀乡鸡的单倍型数量最多, 中山沙栏鸡的最少。广东地方鸡品种间遗传距离为0.012-0.015, 单倍型多样性0.805 ± 0.047至0.949 ± 0.026, 核苷酸多样性0.0102 ± 0.0017至0.0138 ± 0.0009。邻接树和中介网络图将85种单倍型划分为进化枝A、B、C和E, 广东省与邻省地方鸡单倍型的地理分布模式相似。中性检验显示广东地方鸡未经历明显的群体历史扩张。结果表明广东地方鸡处于较好的保护状态, 遗传多样性水平较高, 品种的形成受到邻省和北方家鸡的影响, 东南亚红原鸡对广东地方鸡也有重要的遗传贡献。     

雪豹的微卫星DNA遗传多样性

利用微卫星DNA标记,对来自青海囊谦县、治多县以及甘肃阿克塞县3个地区的36份雪豹(Panthera uncia)粪便DNA样品进行了遗传多样性研究。结果显示,在8个微卫星位点上共检测到57个等位基因,有效等位基因数为2.190~5.488,平均每个位点的等位基因数为7.130,基因频率分布不均匀;期望杂合度为0.543~0.847,平均0.759;多态信息含量为0.458~0.829,平均0.722;表明这8个微卫星位点均为高度多态性位点,有较丰富的遗传多样性。3个样地雪豹居群之间的遗传距离与地理距离相关,地理距离最近的青海省囊谦县和治多县的雪豹居群遗传距离最小。根据雪豹平均遗传分化度Fst(0.053)、平均基因流(4.488)以及STRUCTURE聚类分析结果(当K=1时,ln P(D)值最大),推测3个居群间虽然有一定的遗传距离,但均来自同一个种群,暂无分化现象。     

中国家驴的非洲起源研究

对我国13个家驴品种367条序列(其中引用文献资料241条)的mtDNA D-loop 区399 bp进行分析, 共检测到96种单倍型57个多态位点, 其单倍型多样度为0.767~0.967, 核苷酸多样度为0.014~0.032, 表明我国家驴的遗传多态性丰富。与3个努比亚野驴、3个索马里野驴和6个亚洲野驴的序列构建 NJ系统发育树, 证明我国家驴的母系起源为非洲野驴中的索马里驴和努比亚驴, 亚洲野驴不是中国家驴的母系祖先。     

Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: Heterogeneity among amino acid sites

The internal branch lengths estimated by distance methods such as neighbor joining are shown to be biased to be short when the evolutionary rate differs among sites. The variable-invariable model for site heterogeneity fits the amino acid sequence data encoded by the mitochondrial DNA from Hominoidea remarkably well. By assuming the orangutan separation to be 13 or 16 Myr old, a maximum-likelihood analysis estimates a young date of 3.6 ± 0.6 or 4.4 ± 0.7 Myr (±1 SE) for the human/chimpanzee separation, and these estimates turn out to be robust against differences in the assumed model for amino acid substitutions. Although some uncertainties still exist in our estimates, this analysis suggests that humans separated from chimpanzees some 4–5 Myr ago.Correspondence to: M. Hasewaga     

Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers

Unbiased readings of fossils are well known to contradict some of the popular molecular groupings among primates,particularly with regard to great apes and tarsiers.The molecular methodologies today are however flawed as they are based on a mistaken theoretical interpretation of the genetic equidistance phenomenon that originally started the field.An improved molecular method the ’slow clock’ was here developed based on the Maximum Genetic Diversity hypothesis,a more complete account of the unified changes in genotypes and phenotypes.The method makes use of only slow evolving sequences and requires no uncertain assumptions or mathematical corrections and hence is able to give definitive results.The findings indicate that humans are genetically more distant to orangutans than African apes are and separated from the pongid clade ～17.6 million years ago.Also,tarsiers are genetically closer to lorises than simian primates are.Finally,the fossil times for the radiation of mammals at the K/T boundary and for the Eutheria-Metatheria split in the Early Cretaceous were independently confirmed from molecular dating calibrated using the fossil split times of gorilla-orangutan,mouse-rat,and opossum-kangaroo.Therefore,the re-established primate phylogeny indicates a remarkable unity between molecules and fossils.     

The Rates of Molecular Evolution in Rodent and Primate Mitochondrial DNA

A higher rate of molecular evolution in rodents than in primates at synonymous sites and, to a lesser extent, at amino acid replacement sites has been reported previously for most nuclear genes examined. Thus in these genes the average ratio of amino acid replacement to synonymous substitution rates in rodents is lower than in primates, an observation at odds with the neutral model of molecular evolution. Under Ohta's mildly deleterious model of molecular evolution, these observations are seen as the consequence of the combined effects of a shorter generation time (driving a higher mutation rate) and a larger effective population size (resulting in more effective selection against mildly deleterious mutations) in rodents. The present study reports the results of a maximum-likelihood analysis of the ratio of amino acid replacements to synonymous substitutions for genes encoded in mitochondrial DNA (mtDNA) in these two lineages. A similar pattern is observed: in rodents this ratio is significantly lower than in primates, again consistent only with the mildly deleterious model. Interestingly the lineage-specific difference is much more pronounced in mtDNA-encoded than in nuclear-encoded proteins, an observation which is shown to run counter to expectation under Ohta's model. Finally, accepting certain fossil divergence dates, the lineage-specific difference in amino acid replacement-to-synonymous substitution ratio in mtDNA can be partitioned and is found to be entirely the consequence of a higher mutation rate in rodents. This conclusion is consistent with a replication-dependent model of mutation in mtDNA. Received: 24 September 1999 / Accepted: 18 September 2000     

黑麂（Muntiacus crinifrons）3个种群的遗传多样性

黑麂,为我国特有动物,被公认为目前世界上最珍稀的鹿科动物之一.为了更好地保护黑麂这一珍稀的濒危野生动物,基于黑麂线粒体控制区序列对遂昌分布中心的3个黑麂种群的遗传多样性和基因流进行了研究.结果显示,3个种群的36个个体中有13个变异位点,占分析序列长度的2.71%,且这13个变异位点皆为碱基置换,并未出现碱基插入或缺失的现象,并由此定义了12个单倍型.遗传多样性检测结果显示遂昌种群具有最高的遗传多样性,应予以优先保护.从Tajima′s D和Fu and Li′s D值的估算结果来看,这3个黑麂种群相对于中性进化的歧异度并没有明显的偏离(P＞0.1),没有明显的证据显示这3个黑麂种群间存在很强的平衡选择.3个种群间基因流 Nm均大于1,这3个黑麂种群间存在着较为丰富的基因流.3个黑麂种群单倍型间的序列差异为0.009,这表明这3个黑麂种群的单倍型未出现分化.     

Molecular systematics of theDrosophila hydei subgroup as inferred from mitochondrial DNA sequences

The phylogeny of theDrosophila hydei subgroup, which is a member of theD. repleta species group, was inferred from 1,515 base pairs of mitochondrial DNA sequence of the cytochrome oxidase subunits I, II, and III. Four of the seven species in the subgroup were examined, which are placed into two taxonomic complexes: theD. bifurca complex (D. bifurca) andD. nigrohydei) and theD. hydei complex (D. hydei and (D. eohydei). Both complexes appear to be monophyletic, although theD. bifurca complex is only weakly supported. The evolution of chromosomal change, interspecific crossability, sperm gigantism, and divergence times of the subgroup is discussed in a phylogenetic context. Correspondence to: G. Spicer     

Phylogenetic Analysis of Different Breeds of Domestic Chickens in Selected Area of Peninsular Malaysia Inferred from Partial Cytochrome b Gene Information and RAPD Markers

The present investigation was carried out in an attempt to study the phylogenetic analysis of different breeds of domestic chickens in Peninsular Malaysia inferred from partial cytochrome b gene information and random amplified polymorphic DNA (RAPD) markers. Phylogenetic analysis using both neighbor-joining (NJ) and maximum parsimony (MP) methods produced three clusters that encompassed Type-I village chickens, the red jungle fowl subspecies and the Japanese Chunky broilers. The phylogenetic analysis also revealed that majority of the Malaysian commercial chickens were randomly assembled with the Type-II village chickens. In RAPD assay, phylogenetic analysis using neighbor-joining produced six clusters that were completely distinguished based on the locality of chickens. High levels of genetic variations were observed among the village chickens, the commercial broilers, and between the commercial broilers and layer chickens. In this study, it was found that Type-I village chickens could be distinguished from the commercial chickens and Type-II village chickens at the position of the 27th nucleotide of the 351 bp cytochrome b gene. This study also revealed that RAPD markers were unable to differentiate the type of chickens, but it showed the effectiveness of RAPD in evaluating the genetic variation and the genetic relationships between chicken lines and populations.     

Rates of molecular evolution and the fraction of nucleotide positions free to vary

Summary Selective constraints on DNA sequence change were incorporated into a model of DNA divergence by restricting substitutions to a subset of nucleotide positions. A simple model showed that both mutation rate and the fraction of nucleotide positions free to vary are strong determinants of DNA divergence over time.When divergence between two species approaches the fraction of positions free to vary, standard methods that correct for multiple mutations yield severe underestimates of the number of substitutions per site. A modified method appropriate for use with DNA sequence, restriction site, or thermal renaturation data is derived taking this fraction into account. The model also showed that the ratio of divergence in two gene classes (e.g., nuclear and mitochondrial) may vary widely over time even if the ratio of mutation rates remains constant.DNA sequence divergence data are used increasingly to detect differences in rates of molecular evolution. Often, variation in divergence rate is assumed to represent variation in mutation rate. The present model suggests that differing divergence rates among comparisons (either among gene classes or taxa) should be interpreted cautiously. Differences in the fraction of nucleotide positions free to vary can serve as an important alternative hypothesis to explain differences in DNA divergence rates.     

鲫鱼遗传多样性的初步研究

用１７种限制性内切酶对鲫属普通鲫鱼低背型,高背型,异育银鲫,日本白鲫及华南鲤的变种红鲤共１２４个个体的线粒体ＤＮＡ进行了ＲＦＬＰ分析,１４种酶具多态,共计４３种限制性态型,１１种单倍型。