沉积物古DNA探秘灭绝古人类演化

古DNA领域首次从世界不同洞穴遗址的沉积物里提取古核基因组以揭示相关物种演化的突破性进展,标志着沉积物古DNA研究正式进入全基因组时代。近期,一种新的沉积物古核DNA富集方法成功从西班牙Estatuas洞穴沉积物里捕获多个尼安德特人的核DNA,揭示该灭绝古人类群体此前未知的人口更替的历史。沉积物古核DNA富集突破了古DNA研究依赖化石材料的限制,为深入探究远古不同人类群体在更宏大时空框架下迁徙、演化与适应的历史提供了更多可能。由此,本文将着重解读该研究带来的对尼安德特人遗传历史的新认识及其方法创新的重要意义;此外还将结合人类化石DNA及其他沉积物研究所发现的灭绝古人类线粒体DNA证据,厘清尼安德特人的种群多样性及其种群间分离或替代的历史。     

人源化小鼠人源细胞检测方法

目的人源化小鼠在人类疾病与再生医学研究中具有广泛应用,为获得一种理想的人源化小鼠检测方法,研究人特异性线粒体序列扩增作为人源化动物模型中人类DNA检测方法的可行性。方法设计人线粒体DNA特异性引物,并用该引物对人脐血造血干细胞嵌合体小鼠进行了检测。结果在人源化动物模型的人类DNA检测中,这种人线粒体DNA的PCR检测方法能够达到理想的特异性与灵敏性,是一种理想的嵌合体小鼠检测方法。结论获得了一种理想的人源化小鼠人源细胞检测方法。     

动物线粒体遗传系统理论与应用研究进展

随着线粒体与人类疾病之间关系研究的不断深入,线粒体DNA及其编码的13个多肽的功能和进化引起了众多研究者的关注。作为有氧呼吸的后生动物主要的产能系统——线粒体电子传递系统(ETS)由线粒体和核基因组共同编码,自然选择被认为偏爱那些增强ETS功能的突变,此类突变可发生在线粒体或核编码的ETS蛋白中并引起积极的基因组间的相互作用,即"共适应"。线粒体DNA进化通常被认为遵循一种稳定的突变速率平衡中性模型,但有证据表明该假设可能并不可靠。对线粒体遗传系统研究的最新进展进行了综述,这对科学和合理地使用线粒体DNA分析技术具重要意义。     

线粒体不完整的自然历史

线粒体DNA在分子生态和系统地理方面的应用已经有25年了。很多重要的信息都是通过它得到的,而现在是从这个细胞器自身和它的生态,生物化学和生理学来研究它的进化历史,考虑线粒体自身的生物学问题的时候了。这篇综述分为4个部分。首先,文章对线粒体的自然历史和线粒体DNA作为一个区别于核DNA,具有特殊性状的独特分子作了评论。     

一种有效分离沙冬青线粒体基因组DNA的方法

线粒体作为重要的细胞器,在植物进化适应过程中起着不可忽视的作用。抗旱耐寒常绿阔叶灌木沙冬青主要分布在我国西北荒漠地区,是第三纪孑遗植物,研究该植物线粒体基因组与长期进化适应的关系具有重要意义。然而,用常规的方法难以分离纯化获得沙冬青线粒体基因组DNA,限制了沙冬青线粒体功能基因组研究。该研究利用不连续蔗糖梯度密度离心和DNase I消化技术,成功获得了高纯度沙冬青线粒体DNA,该线粒体DNA的纯度和完整性满足建库的要求,为沙冬青线粒体基因组研究提供了技术支持,对其他植物线粒体基因组学研究也具有参考价值。     

卵胞质移植的研究进展

许多研究表明,线粒体对卵母细胞的受精和胚胎发育有显著影响,卵胞质中线粒体DNA含量和ATP含量的减少,以及线粒体DNA缺失均能降低卵母细胞的受精和胚胎发育,是老龄妇女和老龄动物生育率下降的重要原因之一。卵胞质移植技术能有效改善老龄卵母细胞的受精能力和早期胚胎的发育能力,在人类已有健康后代出生,它已成为人类辅助生殖生物技术和动物克隆研究的新热点。但是,卵胞质转移也可能会导致线粒体DNA异质,即供体和受体的线粒体DNA同时存在于后代体内。目前,人们对于转入的异质卵胞质中对胚胎的发生和发育造成影响的因素并不完全了解。通过卵胞质移植研究概况、卵胞质与受精和胚胎发育、异种线粒体DNA遗传方式和卵胞质转移遗传物质的检测4个方面对卵胞质移植技术进行讨论。     

黄瓜生殖细胞分离及其线粒体DNA的观察与拷贝数定量分析

该研究以6～8月上午10点左右摘取的新鲜黄瓜花朵为材料,采用渗透压冲击的方法分离黄瓜生殖细胞,并应用竞争型定量PCR技术测定其线粒体DNA数量,分析生殖细胞在发育过程中线粒体DNA的变化,以明确高丰度线粒体DNA的来源,为进一步研究被子植物调控线粒体DNA扩增的分子机制奠定基础。结果显示:(1)DAPI染色观察发现,黄瓜生殖细胞的细胞核周围存在大量的细胞器DNA荧光点,表明黄瓜生殖细胞的细胞质中存在大量的线粒体DNA。(2)成熟黄瓜生殖细胞平均包含(1 037±126)个线粒体DNA拷贝。(3)成熟生殖细胞内线粒体DNA含量为早期生殖细胞的14.5倍,表明成熟生殖细胞中的线粒体DNA主要来自于生殖细胞形成后其内活跃的线粒体DNA扩增。研究认为,黄瓜生殖细胞内活跃的线粒体DNA是黄瓜线粒体父系遗传的基础。     

中国西藏拉托唐古墓地古代居民线粒体全基因组研究

目前青藏高原高海拔地区古DNA研究匮乏.拉托唐古墓地位于青藏高原西南高海拔区域,本文对该墓地出土距今约700年的人骨进行古DNA提取,捕获了高质量线粒体全基因组数据,结合东亚线粒体基因组数据库,运用遗传统计方法开展分析.研究结果表明,距今3000年以内青藏高原西南部人群的遗传历史具有连续性,距今700年左右的拉托唐古墓...     

线粒体微卫星DNA不稳定性与肿瘤关系的研究进展

线粒体DNA直接控制细胞氧化磷酸化过程,其基因组序列发生突变尤其是微卫星DNA 不稳定性会严重降低线粒体产生能量的功能,诱发细胞程序性死亡和癌细胞形成。目前,有关人类线粒体微卫星DNA不稳定性与肿瘤关系的研究越来越受到关注。仅就微卫星DNA的特点和不稳定性形成的机理以及与肿瘤关系的研究进展作以概述。     

外源性线粒体DNA在细胞内的重建(简报)

近年来发现人类多种神经肌肉疾病存在线粒体电子传递链(electron transport chain,ETC)缺陷。由于线粒体在遗传上受核基因和线粒体基因双重控制,给确定ETC缺陷的来源造成困难。转线粒体DNA技术是线粒体同无线粒体DNA的细胞(ρ°cells)融合,形成转线粒体DNA细胞系(mtDNA-transferred cell line,也称cytoplasmic hybrids,简称cybrids),使病人的线粒体DNA(mito-     

A "Copernican" reassessment of the human mitochondrial DNA tree from its root

Mutational events along the human mtDNA phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence, a contemporary European sequence published in 1981. This historical choice is a continuous source of inconsistencies, misinterpretations, and errors in medical, forensic, and population genetic studies. Here, after having refined the human mtDNA phylogeny to an unprecedented level by adding information from 8,216 modern mitogenomes, we propose switching the reference to a Reconstructed Sapiens Reference Sequence, which was identified by considering all available mitogenomes from Homo neanderthalensis. This “Copernican” reassessment of the human mtDNA tree from its deepest root should resolve previous problems and will have a substantial practical and educational influence on the scientific and public perception of human evolution by clarifying the core principles of common ancestry for extant descendants.     

Origin and differentiation of human mitochondrial DNA.

A recent study of mitochondrial DNA (mtDNA) polymorphism has generated much debate about modern human origins by proposing the existence of an "African Eve" living 200,000 years ago somewhere in Africa. In an attempt to synthesize information concerning human mtDNA genetic polymorphism, all available data on mtDNA RFLP have been gathered. A phylogeny of the mtDNA types found in 10 populations reveals that all types could have issued from a single common ancestral type. The distribution of shared types between continental groups indicates that caucasoid populations could be the closest to an ancestral population from which all other continental groups would have diverged. A partial phylogeny of the types found in five other populations also demonstrates that the myth of an African Eden was based on an incorrect "genealogical tree" of mtDNA types. Two measures of molecular diversity have been computed on all samples on the basis of mtDNA type frequencies, on one hand, and on the basis of the number of polymorphic sites in the samples, on the other. A large discrepancy is found between the two measures except in African populations; this suggests the existence of some differential selective mechanisms. The lapse of time necessary for creating the observed molecular diversity from an ancestral monomorphic population has been calculated and is found generally greater in Oriental and caucasoid populations. Implications concerning human mtDNA evolution are discussed.     

Human mitochondrial DNA types in two Israeli populations--a comparative study at the DNA level.

Variations in human mtDNA restriction endonuclease fragment patterns were investigated in a sample number of 81 Israelis--Jews and Arabs--using total blood cell DNA. Eight new morphs were observed using five enzymes: HpaI, BamHI, HaeII, MspI, and AvaII. Of the 18 different combinations of fragment patterns (mtDNA types), only three were shared by both groups, but with striking frequency differences. The Arab sample disclosed "African" characteristics and was found to be slightly more polymorphic than the Israeli sample. One of the new types filled a "missing link" originally postulated in a phylogeny of mtDNA human types.     

Palm-Pitviper (Bothriechis) Phylogeny, mtDNA, and Consilience

The phylogeny of the neotropical palm-pitviper genus Bothriechis has been previously inferred from morphology and allozymes. These nuclear-based data sets were found to be congruent and also consilient with the geologic history of the region. We present mtDNA sequence data as an additional data set in the inference of Bothriechis phylogeny and analyze it separately and combined with previous data. The mtDNA phylogeny is incongruent with the nuclear data sets. Based on a number of factors, we hypothesize that the incongruence is due to both mtDNA introgression and lineage sorting. We argue that mtDNA represents extrinsic data and as such should be used as a consilient data set.     

The dawn of human matrilineal diversity

The quest to explain demographic history during the early part of human evolution has been limited because of the scarce paleoanthropological record from the Middle Stone Age. To shed light on the structure of the mitochondrial DNA (mtDNA) phylogeny at the dawn of Homo sapiens, we constructed a matrilineal tree composed of 624 complete mtDNA genomes from sub-Saharan Hg L lineages. We paid particular attention to the Khoi and San (Khoisan) people of South Africa because they are considered to be a unique relic of hunter-gatherer lifestyle and to carry paternal and maternal lineages belonging to the deepest clades known among modern humans. Both the tree phylogeny and coalescence calculations suggest that Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool 90,000-150,000 years before present (ybp) and that at least five additional, currently extant maternal lineages existed during this period in parallel. Furthermore, we estimate that a minimum of 40 other evolutionarily successful lineages flourished in sub-Saharan Africa during the period of modern human dispersal out of Africa approximately 60,000-70,000 ybp. Only much later, at the beginning of the Late Stone Age, about 40,000 ybp, did introgression of additional lineages occur into the Khoisan mtDNA pool. This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations.     

蚕类昆虫线粒体DNA研究及其在起源与进化研究中的应用

线粒体DNA(mtDNA)属母系遗传,进化速率较核基因快且基因组结构相对简单,已作为理想的分子标记广泛应用于昆虫群体遗传学及分子系统学等研究。本文对蚕类昆虫线粒体DNA在分子水平上的最新研究进展进行了较详细的阐述,重点介绍了蚕类昆虫线粒体基因组的组成及特征、mtDNA克隆与多态性及在蚕类昆虫分子系统学研究中的应用等。     

Free from mitochondrial DNA: Nuclear genes and the inference of species trees among closely related darter lineages (Teleostei: Percidae: Etheostomatinae)

Investigations into the phylogenetics of closely related animal species are dominated by the use of mitochondrial DNA (mtDNA) sequence data. However, the near-ubiquitous use of mtDNA to infer phylogeny among closely related animal lineages is tempered by an increasing number of studies that document high rates of transfer of mtDNA genomes among closely related species through hybridization, leading to substantial discordance between phylogenies inferred from mtDNA and nuclear gene sequences. In addition, the recent development of methods that simultaneously infer a species phylogeny and estimate divergence times, while accounting for incongruence among individual gene trees, has ushered in a new era in the investigation of phylogeny among closely related species. In this study we assess if DNA sequence data sampled from a modest number of nuclear genes can resolve relationships of a species-rich clade of North American freshwater teleost fishes, the darters. We articulate and expand on a recently introduced method to infer a time-calibrated multi-species coalescent phylogeny using the computer program ^*BEAST. Our analyses result in well-resolved and strongly supported time-calibrated darter species tree. Contrary to the expectation that mtDNA will provide greater phylogenetic resolution than nuclear gene data; the darter species tree inferred exclusively from nuclear genes exhibits a higher frequency of strongly supported nodes than the mtDNA time-calibrated gene tree.     

Congruence of Microsatellite and Mitochondrial DNA Variation in Acrobat Ants (Crematogaster Subgenus Decacrema,Formicidae: Myrmicinae) Inhabiting Macaranga (Euphorbiaceae) Myrmecophytes

A previously reported mitochondrial DNA (mtDNA) phylogeny of Crematogaster (subgenus Decacrema) ants inhabiting Macaranga myrmecophytes indicated that the partners diversified synchronously and their specific association has been maintained for 20 million years. However, the mtDNA clades did not exactly match morphological species, probably owing to introgressive hybridization among younger species. In this study, we determined the congruence between nuclear simple sequence repeat (SSR, also called microsatellite) genotyping and mtDNA phylogeny to confirm the suitability of the mtDNA phylogeny for inferring the evolutionary history of Decacrema ants. Analyses of ant samples from Lambir Hills National park, northeastern Borneo, showed overall congruence between the SSR and mtDNA groupings, indicating that mtDNA markers are useful for delimiting species, at least at the local level. We also found overall high host-plant specificity of the SSR genotypes of Decacrema ants, consistent with the specificity based on the mtDNA phylogeny. Further, we detected cryptic genetic assemblages exhibiting high specificity toward particular plant species within a single mtDNA clade. This finding, which may be evidence for rapid ecological and genetic differentiation following a host shift, is a new insight into the previously suggested long-term codiversification of Decacrema ants and Macaranga plants.     

Distilling artificial recombinants from large sets of complete mtDNA genomes

Background

Large-scale genome sequencing poses enormous problems to the logistics of laboratory work and data handling. When numerous fragments of different genomes are PCR amplified and sequenced in a laboratory, there is a high immanent risk of sample confusion. For genetic markers, such as mitochondrial DNA (mtDNA), which are free of natural recombination, single instances of sample mix-up involving different branches of the mtDNA phylogeny would give rise to reticulate patterns and should therefore be detectable.

Methodology/Principal Findings

We have developed a strategy for comparing new complete mtDNA genomes, one by one, to a current skeleton of the worldwide mtDNA phylogeny. The mutations distinguishing the reference sequence from a putative recombinant sequence can then be allocated to two or more different branches of this phylogenetic skeleton. Thus, one would search for two (or three) near-matches in the total mtDNA database that together best explain the variation seen in the recombinants. The evolutionary pathway from the mtDNA tree connecting this pair together with the recombinant then generate a grid-like median network, from which one can read off the exchanged segments.

Conclusions

We have applied this procedure to a large collection of complete human mtDNA sequences, where several recombinants could be distilled by our method. All these recombinant sequences were subsequently corrected by de novo experiments – fully concordant with the predictions from our data-analytical approach.     

DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals

Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up‐to‐date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high‐resolution mtDNA haplogroup trees based on 1240 complete or near‐complete mtDNA genome sequences are available in open resource DomeTree ( http://www.dometree.org ). In addition, we offer the software MitoToolPy ( http://www.mitotool.org/mp.html ) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy.