Can the occurrence of rare insertion/deletion polymorphisms in human mtDNA be verified from phylogeny?

Due to its specific characteristics, such as maternal inheritance and absence of recombination, each mtDNA belongs to certain monophyletic clade in the rooted mtDNA tree (haplogroup) according to the mutations it harbors. Rare mutation (excluding parallel mutation) occurring at multiple times in different haplogroups could thus be a potential reading error according to the mtDNA phylogeny. This experience has been widely used in double-checking the credibility of the rare mutations in human mtDNA sequences. However, no test has been performed so far for the feasibility of applying this strategy to the rare insertion/deletion (indel) events in mtDNA sequences. In this study, we attempted to relate the rare indels in mtDNAs to their haplogroup status in a total of 2352 individuals from 50 populations in China. Our results show that the insertion of A at position 16259 is restricted to a subclade of haplogroup C and can be verified. The other indel polymorphisms, which occur in the repeat of the deleted or inserted nucleotide(s), may not be distinguished from phantom mutations from a phylogenetic point of view. Independently and multiply sequencing the fragment with the indel is the best and the most reliable way for confirmation.

mtDNA mutation C1494T, haplogroup A, and hearing loss in Chinese

Mutation C1494T in mitochondrial 12S rRNA gene was recently reported in two large Chinese families with aminoglycoside-induced and nonsyndromic hearing loss (AINHL) and was claimed to be pathogenic. This mutation, however, was first reported in a sample f

Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A

The penetrance of Leber's hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in d

mtDNA Data Indicate a Single Origin for Dogs South of Yangtze River, Less Than 16,300 Years Ago, from Numerous Wolves

There is no generally accepted picture of where, when, and how the domestic dog originated. Previous studies of mitochondrial DNA (mtDNA) have failed to establish the time and precise place of origin because of lack of phylogenetic resolution in the so fa

Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations

Knowledge about the world phylogeny of human mitochondrial DNA (mtDNA) is essential not only for evaluating the pathogenic role of specific mtDNA mutations but also for performing reliable association studies between mtDNA haplogroups and complex disorder

Reply to van Oven: Suggestions and caveats for naming mtDNA haplogroup

The authors thank all subjects for their participation and Mr. Wen-Zhi Wang for helpful assistance with the data analysis. This study was supported in part by grants (30725044) from the National Natural Science Foundation of China.

Lack of mtDNA control region variation in Hainan Eld's deer: Consequence of a recent population bottleneck?

We find no genetic variation at 550bp of mtDNA control region among 55 Hainan Eld's deer in an island population that has suffered recent population contractions. Congeneric species show high levels of variation at this locus. We use a simulation approach to test the likelihood of various bottleneck scenarios, and show, in the context of what is known about the recent demographic history of this population, that there are credible scenarios for a bottleneck driven by hunting pressure in the 1960s that could account for the lack of variation at this locus.

The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes

Many efforts based on complete mitochondrial DNA (mtDNA) genomes have been made to depict the global mtDNA landscape, but the phylogeny of Indian macrohaplogroup M has not yet been resolved in detail. To fill this lacuna, we took the same strategy as in o

The Acquisition of an Inheritable 50-bp Deletion in the Human mtDNA Control Region Does Not Affect the mtDNA Copy Number in Peripheral Blood Cells

The mitochondrial DNA (mtDNA) control region is believed to play an important biological role in mtDNA replication. Large deletions in this region are rarely found, but when they do occur they might be expected to interfere with the replication of the molecule, thus leading to a reduction of mtDNA copy number. During a survey for mtDNA sequence variations in 5,559 individuals from the general Chinese population and 2,538 individuals with medical disorders, we identified a 50-bp deletion (m.298_347del50) in the mtDNA control region in a member of a healthy Han Chinese family belonging to haplogroup B4c1b2, as suggested by complete mtDNA genome sequencing. This deletion removes the conserved sequence block II (CSBII; region 299-315) and the replication primer location (region 317-321). However, quantification of the mtDNA copy number in this subject showed a value within a range that was observed in 20 healthy subjects without the deletion. The deletion was detected in the hair samples of the maternal relatives of the subject and exhibited variable heteroplasmy. Our current observation, together with a recent report for a benign 154-bp deletion in the mtDNA control region, suggests that the control of mtDNA replication may be more complex than we had thought. Hum Mutat 31:538-543, 2010. (C) 2010 Wiley-Liss, Inc.

Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups

Background: It is widely accepted that the ancestors of Native Americans arrived in the New World via Beringia approximately 10 to 30 thousand years ago (kya). However, the arrival time(s), number of expansion events, and migration routes into the Western

银额果蝇自然群体中的mtDNA多态性研究──Ⅱ．银额果蝇的起源和分化

本文以８种限制性内切酶对８个银额果蝇群体进行了ｍｔＤＮＡ的限制性片段长度多态性（ＲＦＬＰ）分析。发现现生银额果蝇种群可以分成三个相对独立的群体，即东部、中部和西部群体。结合其它有关资料，我们推测，银额果蝇可能起源于马来半岛南部和加里曼丹岛一带。起初分成东西两支向北扩散。东支发展成现在的东部群体；西支则在中南半岛北部又分成两个支系；从而形成了现生银额果蝇群体的东部、中部和西部的地理分布模式。

银额果蝇自然群体中的mtDNA多态性

采用mtDNA RFLP技术, 探讨了银额果蝇自然群体中的mtDNA多态性及其与银额果蝇起源、扩 散的关系。图4表3参9(梁嘉)

银额果蝇自然群体中的mtDNA多态性研究 I: 银额果蝇自然群体内存在丰富的mtDNA多态性

运用限制性内切酶对银额果蝇自然群体进行了mtDNA的限制性片段长度多态性(RFLP)分析。 发现银额果蝇自然群体中存在极为丰富的mtDNA多态性, 从82个单雌系中, 共检测到34种限 制性类型。对这一现象的效应和成因进行了探讨。图3表7参19

西南地区家猪和野猪mtDNA遗传多样性研究

用20种限制性内切酶分析来自中国西南地区的家猪和野猪的mtDNA群体遗传多样性。结果表 明: 在全部28只个体中, 共检出26种限制性态型, 归结为6种不同的限制性类型, 限制性类 型的差异主要来源于少数几个限制性位点的偶然突变。利用现代分子群体遗传学方法, 对这些猪的遗传多样性进行评估, 结果表明中国西南地区猪的mtDNA变异度很低, 遗传多样性贫 乏, 提示西南地区的猪起源于一个共同的祖先, 在品种形成的早期可能受到创立者效应的制约。图1表3参11