The emerging limbs and twigs of the East Asian mtDNA tree

High prevalence of m.1555A > G in patients with hearing loss in the Baikal Lake region of Russia as a result of founder effect

Mitochondrial forms account approximately 1-2% of all nonsyndromic cases of hearing loss (HL). One of the most common causative variants of mtDNA is the m.1555A > G variant of the MT-RNR1 gene (OMIM 561000). Currently the detection of the m.1555A > G variant of the MT-RNR1 gene is not included in all research protocols. In this study this variant was screened among 165 patients with HL from the Republic of Buryatia, located in the Baikal Lake region of Russia. In our study, the total contribution of the m.1555A > G variant to the etiology of HL was 12.7% (21/165), while the update global prevalence of this variant is 1.8% (863/47,328). The m.1555A > G variant was notably more prevalent in Buryat (20.2%) than in Russian patients (1.3%). Mitogenome analysis in 14 unrelated Buryat families carrying the m.1555A > G variant revealed a predominant lineage: in 13 families, a cluster affiliated with sub-haplogroup A5b (92.9%) was identified, while one family had the D5a2a1 lineage (7.1%). In a Russian family with the m.1555A > G variant the lineage affiliated with sub-haplogroup F1a1d was found. Considering that more than 90% of Buryat families with the m.1555A > G variant belong to the single maternal lineage cluster we conclude that high prevalence of this variant in patients with HL in the Baikal Lake region can be attributed to a founder effect.

Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses

Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease.

The maternal phylogenetic insights of Yunnan Miao group revealed by complete mitogenomes

The Miao group is one of the representative Hmong-Mien-speaking populations and primarily scattered in southern China and Southeast Asia, which has experienced massive migrations in history and thus forms distinctive evolutionary genetics. Yet, the genetic explorations of Miao group are relatively limited based on complete mitochondrial genome (mitogenome), especially for the Miao group from Yunnan Province (YNM). Here, we sequenced complete mitogenomes of 132 Miao individuals from Yunnan Province using massively parallel sequencing method. Total 132 Miao individuals could be allocated to 119 various haplotypes, which were mainly dominated by haplogroups prevalent in southern East Asia (B, F, M7 and R9), and rarely occupied by northern lineages (A, D, G and M8). In order to dissect the genetic background of YNM more comprehensively, we introduced 99 published population data with 7135 complete mitochondrial sequences for population genetic comparisons. YNM exhibited closer genetic relationships with Hmong-Mien, Tai-Kadai, Sino-Tibetan and Austroasiatic populations, especially for Hmong-Mien populations; we further speculated that Miao group might have certain direct or indirect gene exchanges with ancient Baiyue groups. Several maternal lineages, such as B5a1c1a, F1g1, B4a5 and D4e1a3, were found to be specifically shared by YNM and other Hmong-Mien populations, and these matrilineal expansions occurred roughly during the Neolithic period. Eventually, according to the population dynamic analyses of YNM, the population size began to emerge recovery ∼1-0.5 kya after a long-term population reduction ∼1-5 kya, during which the B5a1c1a haplogroup manifested relatively apparent lineage expansion.

Genomic insights into the genetic structure and population history of Mongolians in Liaoning Province

The Mongolian population exceeds six million and is the largest population among the Mongolic speakers in China. However, the genetic structure and admixture history of the Mongolians are still unclear due to the limited number of samples and lower coverage of single-nucleotide polymorphism (SNP). In this study, we genotyped genome-wide data of over 700,000 SNPs in 38 Mongolian individuals from Fuxin in Liaoning Province to explore the genetic structure and population history based on typical and advanced population genetic analysis methods [principal component analysis (PCA), admixture, F_ST, f₃-statistics, f₄-statistics, qpAdm/qpWave, qpGraph, ALDER, and TreeMix]. We found that Fuxin Mongolians had a close genetic relationship with Han people, northern Mongolians, other Mongolic speakers, and Tungusic speakers in East Asia. Also, we found that Neolithic millet farmers in the Yellow River Basin and West Liao River Basin and Neolithic hunter–gatherers in the Mongolian Plateau and Amur River Basin were the dominant ancestral sources, and there were additional gene flows related to Eurasian Steppe pastoralists and Neolithic Iranian farmers in the gene pool of Fuxin Mongolians. These results shed light on dynamic demographic history, complex population admixture, and multiple sources of genetic diversity in Fuxin Mongolians.

Whole mitochondrial genome analysis of Tai-Kadai-speaking populations in Southwest China

As a single matrilineal gene, human mitochondrial DNA plays a very important role in the study of population genetics. The whole mitogenome sequences of 287 individuals of the Tai-Kadai-speaking population in Guizhou were obtained. It was discovered that there were 82, 104, and 94 haplotypes in 83 Bouyei individuals, 107 Dong individuals, and 97 Sui individuals, respectively; and the haplotype diversity in Bouyei, Dong, and Sui groups was 1.000 ± 0.02, 0.9993 ± 0.0015, and 0.999 ± 0.002, respectively. The result of neutrality tests of the Tai-Kadai-speaking population in Guizhou showed significant negative values, and the analysis of mismatch distribution showed an obvious unimodal distribution. The results implied that Guizhou Tai-Kadai-speaking populations had high genetic diversities and may have experienced recent population expansion. In addition, the primary haplogroups of studied populations were M*, F, B, D, and R*, implying that they may origin from Southern China. The matrilineal genetic structure of the Tai-Kadai-speaking populations in Guizhou was analyzed by merging the mitogenome data of 79 worldwide populations as reference data. The results showed that there were close relationships between studied populations and other Tai-Kadai as well as some Austronesian populations in East and Southeast Asia. Overall, the mitogenome data generated in this study will provide important data for the study of genetic structure of Tai-Kadai speaking populations.

Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago

Archaeological and ancient DNA studies revealed that Shandong, a multi-culture center in northern coastal China, was home to ancient populations having ancestry related to both northern and southern East Asian populations. However, the limited temporal and geographical range of previous studies have been insufficient to describe the population history of this region in greater detail. Here, we report the analysis of 86 complete mitochondrial genomes from the remains of 9500 to 1800-year-old humans from 12 archaeological sites across Shandong. For samples older than 4600 years before present (BP), we found haplogroups D4, D5, B4c1, and B5b2, which are observed in present-day northern and southern East Asians. For samples younger than 4600 BP, haplogroups C (C7a1 and C7b), M9 (M9a1), and F (F1a1, F2a, and F4a1) begin to appear, indicating changes in the Shandong maternal genetic structure starting from the beginning of the Longshan cultural period. Within Shandong, the genetic exchange is possible between the coastal and inland regions after 3100 BP. We also discovered the B5b2 lineage in Shandong populations, with the oldest Bianbian individual likely related to the ancestors of some East Asians and North Asians. By reconstructing a maternal genetic structure of Shandong populations, we provide greater resolution of the population dynamics of the northern coastal East Asia over the past nine thousand years.

Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences

The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

Mitochondrial haplogroup G is associated with nonalcoholic fatty liver disease, while haplogroup A mitigates the effects of PNPLA3

Objectives

Mitochondrial dysfunction plays a pivotal role in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). We hypothesized that mitochondrial DNA (mtDNA) haplogroups affect the risk of NAFLD in Han Chinese patients and interact with PNPLA3 genotypes.

Design

NAFLD and control patients were recruited from a tertiary care centre. The mitochondrial genome was amplified in overlapping segments and sequenced. Mitochondrial haplogroups were determined using Mitomaster. PNPLA3 rs738409 genotyping was performed using restriction fragment length polymorphism analysis.

Patients

We enrolled 655 NAFLD patients and 504 controls.

Results

More NAFLD patients encoded haplogroup G; odds ratio (OR) 1.85 (95% confidence interval [CI] 1.16, 2.80). Subhaplogroup G3 was present more frequently in NAFLD patients (25.8% vs 6.5%). The PNPLA3 CG genotype resulted in an OR of 1.66 (95% CI 1.25, 2.21), and the GG genotype resulted in an OR of 2.33 (95% CI 1.72, 3.17) for NAFLD. Patients with mitochondrial haplogroup A had a significantly higher frequency of genotype GG. Among patients with haplogroup A, no PNPLA3 genotype was associated with increased NAFLD risk (CG: OR 1.17, 95% CI 0.55, 2.34; GG: OR 1.04 95% CI 0.66, 2.65). Excluding haplogroup A, the OR for CG was 1.58 (95% CI 1.18, 2.12), and the OR for GG was 1.81 (95% CI 1.30, 2.51).

Conclusion

Haplogroup G was associated with an increased risk of NAFLD PNPLA3 GG genotype was overrepresented among patients encoding haplogroup A and was not associated with NAFLD risk among haplogroup A patients. Mitochondrial genetics influence NAFLD risk and interact with PNPLA3 genotypes.

The Genetic Structure of Chinese Hui Ethnic Group Revealed by Complete Mitochondrial Genome Analyses Using Massively Parallel Sequencing

Mitochondrial DNA (mtDNA), coupled with maternal inheritance and relatively high mutation rates, provides a pivotal way for us to investigate the formation histories of populations. The Hui minority with Islamic faith is one of the most widely distributed ethnic groups in China. However, the exploration of Hui's genetic architecture from the complete mitochondrial genome perspective has not been detected yet. Therefore, in this study, we employed the complete mitochondrial genomes of 98 healthy and unrelated individuals from Northwest China, as well as 99 previously published populations containing 7274 individuals from all over the world as reference data, to comprehensively dissect the matrilineal landscape of Hui group. Our results demonstrated that Hui group exhibited closer genetic relationships with Chinese Han populations from different regions, which was largely attributable to the widespread of haplogroups D4, D5, M7, B4, and F1 in these populations. The demographic expansion of Hui group might occur during the Late Pleistocene. Finally, we also found that Hui group might have gene exchanges with Uygur, Tibetan, and Tajik groups in different degrees and retained minor genetic imprint of European-specific lineages, therefore, hinting the existence of multi-ethnic integration events in shaping the genetic landscape of Chinese Hui group.

Munda languages are father tongues, but Japanese and Korean are not

Over two decades ago, it was observed that the linguistic affinity of the language spoken by a particular population tended to correlate with the predominant paternal, i.e. Y-chromosomal, lineage found in that population. Such correlations were found to be ubiquitous but not universal, and the striking exceptions to such conspicuous patterns of correlation between linguistic and genetic phylogeography elicit particular interest and beg for clarification. Within the Austroasiatic language family, the Munda languages are a clear-cut case of father tongues, whereas Japanese and Korean are manifestly not. In this study, the cases of Munda and Japanese are juxtaposed. A holistic understanding of these contrasting cases of ethnolinguistic prehistory with respect to the father tongue correlation will first necessitate a brief exposition of the phylogeography of the Y chromosomal lineage O. Then triangulation discloses some contours and particulars of both long lost episodes of ethnolinguistic prehistory.

Populations dynamics in Northern Eurasian forests: a long-term perspective from Northeast Asia

The 'Northern Eurasian Greenbelt' (NEG) is the northern forest zone stretching from the Japanese Archipelago to Northern Europe. The NEG has created highly productive biomes for humanity to exploit since the end of the Pleistocene. This research explores how the ecological conditions in northern Eurasia contributed to and affected human migrations and cultural trajectories by synthesizing the complimentary viewpoints of environmental archaeology, Geographic Information Science (GIS), genetics and linguistics. First, the environmental archaeology perspective raises the possibility that the NEG functioned as a vessel fostering people to develop diverse cultures and engage in extensive cross-cultural exchanges. Second, geographical analysis of genomic data on mitochondrial DNA using GIS reveals the high probability that population dynamics in the southeastern NEG promoted the peopling of the Americas at the end of the Pleistocene. Finally, a linguistic examination of environmental- and landscape-related vocabulary of the proto-Turkic language groups enables the outline of their original cultural landscape and natural conditions, demonstrating significant cultural spheres, i.e. from southern Siberia to eastern Inner Mongolia during Neolithization. All of these results combine to suggest that the ecological complex in the southern edge of the NEG in northeast Asia played a significant role in peopling across the continents during prehistory.

Japan considered from the hypothesis of farmer/language spread

Formally, the Farming/Language Dispersal hypothesis as applied to Japan relates to the introduction of agriculture and spread of the Japanese language (between ca. 500 BC-AD 800). We review current data from genetics, archaeology, and linguistics in relation to this hypothesis. However, evidence bases for these disciplines are drawn from different periods. Genetic data have primarily been sampled from present-day Japanese and prehistoric Jōmon peoples (14,000-300 BC), preceding the introduction of rice agriculture. The best archaeological evidence for agriculture comes from western Japan during the Yayoi period (ca. 900 BC-AD 250), but little is known about northeastern Japan, which is a focal point here. And despite considerable hypothesizing about prehistoric language, the spread of historic languages/ dialects through the islands is more accessible but difficult to relate to prehistory. Though the lack of Yayoi skeletal material available for DNA analysis greatly inhibits direct study of how the pre-agricultural Jōmon peoples interacted with rice agriculturalists, our review of Jōmon genetics sets the stage for further research into their relationships. Modern linguistic research plays an unexpected role in bringing Izumo (Shimane Prefecture) and the Japan Sea coast into consideration in the populating of northeastern Honshu by agriculturalists beyond the Kantō region.

Mitochondrial DNA Haplogroup N9a Negatively Correlates with Incidence of Hepatocellular Carcinoma in Northern China

Mitochondrial DNA (mtDNA) haplogroups are associated with various types of cancer; however, the molecular mechanisms by which mtDNA haplogroups affect primary hepatocellular carcinoma (HCC) are not known. In this study, we carried out a case-control study on 388 HCC patients and 511 geographically matched asymptomatic control subjects in northern China. We found that mtDNA haplogroup N9a and its diagnostic SNP, m.16257C > A, negatively correlated with the incidence of HCC in northern China (odds ratio [OR] 0.290, 95% confidence interval [CI] 0.123–0.685, p = 0.005), particularly in patients with infection of hepatitis B/C virus (HBV/HCV) (for haplogroup N9a: OR 0.213, 95% CI 0.077–0.590, p = 0.003; for m.16257C > A: OR 0.262, 95% CI 0.107–0.643, p = 0.003). However, mtDNA haplogroup N9a is not associated with clinical characteristics of HCC including serum alpha-fetoprotein (AFP) level and tumor size. In addition, cytoplasmic hybrid (cybrid) cells with N9a haplogroup (N9a10a and N9a1) had transcriptome profiles distinct from those with non-N9a (B5, D4, and D5) haplogroups. Gene set enrichment analysis (GSEA) showed that metabolic activity varied significantly between N9a and non-N9a haplogroups. Moreover, cells with haplogroup N9a negatively correlated with cell division and multiple liver cancer pathways compared with non-N9a cells. Although it is still unclear how N9a affects the aforementioned GSEA pathways, our data suggest that mtDNA haplogroup N9a is negatively correlated with the incidence and progression of HCC in northern China.

Whole Mitochondrial DNA Sequencing Analysis in 47 Han Populations in Southwest China

Background

Mitochondrial DNA (mtDNA) sequencing has been used in many areas, including forensic genetics. Due to the rapid development of sequencing technology, whole mtDNA sequencing is now possible and may be used in epidemiological and forensic studies. This study aimed to use whole mtDNA sequencing to investigate 47 Chongqing Han populations in southwest China and the diversity in the mtGenome reference data.

Material/Methods

The mtDNA of 47 Chongqing Han populations was generated using the Ion Torrent Personal Genome Machine (PGM) system. The extent of the effects of the mtDNA on the subpopulations was investigated and compared with six other populations from published studies. Pairwise fixation index (FST), a measure of population differentiation due to genetic structure, were calculated. Analysis of molecular variance (AMOVA) was performed, and 1257 hypervariable region data sets were added to the principal component analysis (PCA).

Results

The whole mtDNA sequencing data of 47 southwest Chinese Han populations were successfully recovered. Expanding the sequencing rage increased the discrimination power of mtDNA from three-times to 25-times based on different populations. The subpopulation effects showed 20 times the differences in match probability when compared with south China regions.

Conclusions

Whole mtDNA sequencing distinguished between individuals from 47 Chongqing Han populations in southwest China and has potential applications that include high-quality forensic identification.

Mitochondrial Haplogroups N9 and G Are Associated with Metabolic Syndrome Among Human Immunodeficiency Virus-Infected Patients in China

Increasing evidence shows that mitochondrial DNA (mtDNA) variations have an important effect on metabolic disorders, but such studies have not been conducted in HIV-infected patients in Asia. We investigated the distribution of mtDNA haplogroups and their correlation with metabolic disorders in HIV-infected patients. A cross-sectional survey was performed among 296 HIV patients older than the age of 40 years in a rural prefecture, Eastern China. The entire mtDNA sequence was amplified by polymerase chain reaction using four overlapping pairs of primers that have been standardly used. In this sample, mtDNA haplogroups B, D, M7, and F were the most dominant haplogroups. The overall prevalence of metabolic syndrome (MetS) was 36.1%, and was highest (77.8%) among those with haplogroup G and lowest (21.4%) among those with haplogroup M8. In multivariable analysis, haplogroups G and N9 were significantly associated with the presence of MetS [adjusted odds ratio (aOR) = 13.5, 95% confidence interval (CI): 1.9-94.7; aOR = 8.1, 95% CI: 1.8-36.1; respectively]. Moreover, patients with haplogroup G had increased odds of elevated glycated hemoglobin (HbA1c) (aOR = 10.1, 95% CI: 1.4-71.1), patients with haplogroup N9 had increased odds of elevated triglycerides (aOR = 13.5, 95% CI: 2.4-76.8). No significant association between mtDNA haplogroups and other MetS components was observed. Our data demonstrate the association between mtDNA haplogroups and MetS in HIV-infected patients. The Asian-specific mtDNA haplogroups G and N9 may confer higher risk for the development of MetS in HIV-infected patients, which requires further longitudinal investigation.

Assessment of associations between mitochondrial DNA haplogroups and attention deficit and hyperactivity disorder in Korean children

Attention deficit hyperactivity disorder (ADHD) is a multifactorial disorder with multiple environmental and biological etiologies, including genetic factors. Until now, several genetic variants have been reported to be significantly associated with ADHD. Recently, the relationship between mitochondrial DNA (mtDNA) haplogroups and psychiatric disorders such as schizophrenia has also been reported. However, currently there are no reports pertaining to the genetic association between mtDNA haplogroups and ADHD. Therefore, we performed an mtDNA haplogroup analysis of a total of 472 Korean children (150 Children with ADHD and 322 controls). The 20 East Asian specific mtDNA haplogroups were determined using the SNaPshot assay. We also sequenced the displacement loop (D-loop) region, position 15,971-613. Our results showed that haplogroup B4 was significantly associated with ADHD (OR, 1.90; 95% CI, 1.055-3.429; p = 0.031). A marginally significant association was found in subjects with ADHD and haplogroup B5 (OR, 0.26; 95% CI, 0.059-1.139; p = 0.041). When stratified based on gender, an association was also observed between haplogroup B5 and boys diagnosed with ADHD (OR, 0.17; 95% CI, 0.022-1.340; p = 0.048). Compared with boys, girls with ADHD carried an excess of the haplogroup D4b (OR, 4.83; 95% CI, 1.352-17.272; p = 0.014). Stratified analysis of subtypes also showed significant results (combined: haplogroup B4, p = 0.007; inattentive: haplogroup F, p = 0.022). Our results showed a possible role of mtDNA haplogroups in the genetic etiology of ADHD and ADHD symptoms in Korean children.

Spectrum of mitochondrial genome instability and implication of mitochondrial haplogroups in Korean patients with acute myeloid leukemia

Background

Mitochondrial DNA (mtDNA) mutations may regulate the progression and chemosensitivity of leukemia. Few studies regarding mitochondrial aberrations and haplogroups in acute myeloid leukemia (AML) and their clinical impacts have been reported. Therefore, we focused on the mtDNA length heteroplasmies minisatellite instability (MSI), copy number alterations, and distribution of mitochondrial haplogroups in Korean patients with AML.

Methods

This study investigated 74 adult patients with AML and 70 controls to evaluate mtDNA sequence alterations, MSI, mtDNA copy number, haplogroups, and their clinical implications. The hypervariable (HV) control regions (HV1 and HV2), tRNA^leu1gene, and cytochrome b gene of mtDNA were analyzed. Two mtDNA minisatellite markers, 16189 poly-C (¹⁶¹⁸⁴CCCCCTCCCC¹⁶¹⁹³, 5CT4C) and 303 poly-C (³⁰³CCCCCCCTCCCCC³¹⁵, 7CT5C), were used to examine the mtDNA MSI.

Results

In AML, most mtDNA sequence variants were single nucleotide substitutions, but there were no significant differences compared to those in controls. The number of mtMSI patterns increased in AML. The mean mtDNA copy number of AML patients increased approximately 9-fold compared to that of controls (P<0.0001). Haplogroup D4 was found in AML with a higher frequency compared to that in controls (31.0% vs. 15.7%, P=0.046). None of the aforementioned factors showed significant impacts on the outcomes.

Conclusion

AML cells disclosed more heterogeneous patterns with the mtMSI markers and had increased mtDNA copy numbers. These findings implicate mitochondrial genome instability in primary AML cells. Therefore, mtDNA haplogroup D4 might be associated with AML risk among Koreans.

Human mitochondrial DNA haplogroup M8a influences the penetrance of m.8684C>T in Han Chinese men with non-obstructive azoospermia

RESEARCH QUESTION

What is the role of mitochondrial DNA (mtDNA) in the pathogenesis of non-obstructive azoospermia (NOA)?

DESIGN

mtDNA genome sequencing followed by an independent population validation were performed in 628 NOA cases and 584 healthy controls. Antioxidant capacity of serum was evaluated in 54 randomly selected cases out of 536 and 49 out of 489 controls.

RESULTS

In the screening stage, 13 mtDNA haplogroups (hg) were ascertained, and 10 susceptible variants were observed. In the validation stage, hg M8* in individuals was found to be associated with increased risk of NOA [odds ratio (OR) 2.61, 95% confidence interval (CI) 1.47-4.61] (P=0.001). Unexpectedly, the frequency of m.8684C>T, the defining marker for hg M8a, was also higher in NOA (OR 4.14, 95% CI 1.56-11.03) (P=0.002). Subsequently, the frequency distributions were compared among the sub-hg of hg M8* (including hg M8a, C and Z) and, intriguingly, no significance was found in hg C and Z. Additionally, the level of total antioxidant capacity was significantly decreased (P<0.05) compared with the control group.

CONCLUSIONS

hg M8a background in general played an active role in the penetrance of 8684C>T in NOA, and mtDNA genetic variants (causing low antioxidant levels) might increase mtDNA damage and impair normal spermatogenesis.

Hi-MC: a novel method for high-throughput mitochondrial haplogroup classification

Effective approaches for assessing mitochondrial DNA (mtDNA) variation are important to multiple scientific disciplines. Mitochondrial haplogroups characterize branch points in the phylogeny of mtDNA. Several tools exist for mitochondrial haplogroup classification. However, most require full or partial mtDNA sequence which is often cost prohibitive for studies with large sample sizes. The purpose of this study was to develop Hi-MC, a high-throughput method for mitochondrial haplogroup classification that is cost effective and applicable to large sample sizes making mitochondrial analysis more accessible in genetic studies. Using rigorous selection criteria, we defined and validated a custom panel of mtDNA single nucleotide polymorphisms that allows for accurate classification of European, African, and Native American mitochondrial haplogroups at broad resolution with minimal genotyping and cost. We demonstrate that Hi-MC performs well in samples of European, African, and Native American ancestries, and that Hi-MC performs comparably to a commonly used classifier. Implementation as a software package in R enables users to download and run the program locally, grants greater flexibility in the number of samples that can be run, and allows for easy expansion in future revisions. Hi-MC is available in the CRAN repository and the source code is freely available at https://github.com/vserch/himc.

Ancient DNA reveals genetic connections between early Di-Qiang and Han Chinese

Background

Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed, there is no evidence to support this view. Here we analyzed the human remains from an early Di-Qiang site (Mogou site dated ~4000 years old) and compared them to other ancient DNA across China, including an early Han-related site (Hengbei site dated ~3000 years old) to establish the underlying genetic relationship between the Di-Qiang and ancestors of Han Chinese.

Results

We found Mogou mtDNA haplogroups were highly diverse, comprising 14 haplogroups: A, B, C, D (D*, D4, D5), F, G, M7, M8, M10, M13, M25, N*, N9a, and Z. In contrast, Mogou males were all Y-DNA haplogroup O3a2/P201; specifically one male was further assigned to O3a2c1a/M117 using targeted unique regions on the non-recombining region of the Y-chromosome. We compared Mogou to 7 other ancient and 38 modern Chinese groups, in a total of 1793 individuals, and found that Mogou shared close genetic distances with Taojiazhai (a more recent Di-Qiang population), Hengbei, and Northern Han. We modeled their interactions using Approximate Bayesian Computation, and support was given to a potential admixture of ~13-18% between the Mogou and Northern Han around 3300–3800 years ago.

Conclusions

Mogou harbors the earliest genetically identifiable Di-Qiang, ancestral to the Taojiazhai, and up to ~33% paternal and ~70% of its maternal haplogroups could be found in present-day Northern Han Chinese.

Electronic supplementary material

The online version of this article (10.1186/s12862-017-1082-0) contains supplementary material, which is available to authorized users.

Phylogeographic and genome-wide investigations of Vietnam ethnic groups reveal signatures of complex historical demographic movements

The territory of present-day Vietnam was the cradle of one of the world’s earliest civilizations, and one of the first world regions to develop agriculture. We analyzed the mitochondrial DNA (mtDNA) complete control region of six ethnic groups and the mitogenomes from Vietnamese in The 1000 Genomes Project (1000G). Genome-wide data from 1000G (~55k SNPs) were also investigated to explore different demographic scenarios. All Vietnamese carry South East Asian (SEA) haplotypes, which show a moderate geographic and ethnic stratification, with the Mong constituting the most distinctive group. Two new mtDNA clades (M7b1a1f1 and F1f1) point to historical gene flow between the Vietnamese and other neighboring countries. Bayesian-based inferences indicate a time-deep and continuous population growth of Vietnamese, although with some exceptions. The dramatic population decrease experienced by the Cham 700 years ago (ya) fits well with the Nam tiến (“southern expansion”) southwards from their original heartland in the Red River Delta. Autosomal SNPs consistently point to important historical gene flow within mainland SEA, and add support to a main admixture event occurring between Chinese and a southern Asian ancestral composite (mainly represented by the Malay). This admixture event occurred ~800 ya, again coinciding with the Nam tiến.

Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population

Mitochondrial DNA (mtDNA) genome analysis has been a potent tool in forensic practice as well as in the understanding of human phylogeny in the maternal lineage. The traditional mtDNA analysis is focused on the control region, but the introduction of massive parallel sequencing (MPS) has made the typing of the entire mtDNA genome (mtGenome) more accessible for routine analysis. The complete mtDNA information can provide large amounts of novel genetic data for diverse populations as well as improved discrimination power for identification. The genetic diversity of the mtDNA sequence in different ethnic populations has been revealed through MPS analysis, but the Korean population not only has limited MPS data for the entire mtGenome, the existing data is mainly focused on the control region. In this study, the complete mtGenome data for 186 Koreans, obtained using Ion Torrent Personal Genome Machine (PGM) technology and retrieved from rather common mtDNA haplogroups based on the control region sequence, are described. The results showed that 24 haplogroups, determined with hypervariable regions only, branched into 47 subhaplogroups, and point heteroplasmy was more frequent in the coding regions. In addition, sequence variations in the coding regions observed in this study were compared with those presented in other reports on different populations, and there were similar features observed in the sequence variants for the predominant haplogroups among East Asian populations, such as Haplogroup D and macrohaplogroups M9, G, and D. This study is expected to be the trigger for the development of Korean specific mtGenome data followed by numerous future studies.

Genetic polymorphisms of 54 mitochondrial DNA SNP loci in Chinese Xibe ethnic minority group

We analyzed the genetic polymorphisms of 54 mitochondrial DNA (mtDNA) variants in Chinese Xibe ethnic minority group. A total of 137 unrelated healthy volunteers from Chinese Xibe group were the objects of our study. Among the selected loci, there were 51 variable positions including transitions and transversions, and single nucleotide transitions were common (83.93%) versus transversions. These variations defined 64 different mtDNA haplotypes exclusive of (CA)n and 9 bp deletion variation. The haplotype diversity and discrimination power in Xibe population were 0.9800 ± 0.004 and 0.9699, respectively. Besides, we compared Xibe group with 18 other populations and reconstructed a phylogenetic tree using Neighbor-Joining method. The result revealed that Xibe group was a close to Xinjiang Han and Yanbian Korean groups. Our data also indicated that Xibe group has a close relationship with Daur and Ewenki groups, which is reflected by the history that Xibe was influenced by Daur and Ewenki groups during the development of these groups. In conclusion, the variants we studied are polymorphic and could be used as informative genetic markers for forensic and population genetic application.

Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe

During the 1st millennium before the Common Era (BCE), nomadic tribes associated with the Iron Age Scythian culture spread over the Eurasian Steppe, covering a territory of more than 3,500 km in breadth. To understand the demographic processes behind the spread of the Scythian culture, we analysed genomic data from eight individuals and a mitochondrial dataset of 96 individuals originating in eastern and western parts of the Eurasian Steppe. Genomic inference reveals that Scythians in the east and the west of the steppe zone can best be described as a mixture of Yamnaya-related ancestry and an East Asian component. Demographic modelling suggests independent origins for eastern and western groups with ongoing gene-flow between them, plausibly explaining the striking uniformity of their material culture. We also find evidence that significant gene-flow from east to west Eurasia must have occurred early during the Iron Age.

Molecular Genealogy of a Mongol Queen's Family and Her Possible Kinship with Genghis Khan

Members of the Mongol imperial family (designated the Golden family) are buried in a secret necropolis; therefore, none of their burial grounds have been found. In 2004, we first discovered 5 graves belonging to the Golden family in Tavan Tolgoi, Eastern Mongolia. To define the genealogy of the 5 bodies and the kinship among them, SNP and/or STR profiles of mitochondria, autosomes, and Y chromosomes were analyzed. Four of the 5 bodies were determined to carry the mitochondrial DNA haplogroup D4, while the fifth carried haplogroup CZ, indicating that this individual had no kinship with the others. Meanwhile, Y-SNP and Y-STR profiles indicate that the males examined belonged to the R1b-M343 haplogroup. Thus, their East Asian D4 or CZ matrilineal and West Eurasian R1b-M343 patrilineal origins reveal genealogical admixture between Caucasoid and Mongoloid ethnic groups, despite a Mongoloid physical appearance. In addition, Y chromosomal and autosomal STR profiles revealed that the four D4-carrying bodies bore the relationship of either mother and three sons or four full siblings with almost the same probability. Moreover, the geographical distribution of R1b-M343-carrying modern-day individuals demonstrates that descendants of Tavan Tolgoi bodies today live mainly in Western Eurasia, with a high frequency in the territories of the past Mongol khanates. Here, we propose that Genghis Khan and his family carried Y-haplogroup R1b-M343, which is prevalent in West Eurasia, rather than the Y-haplogroup C3c-M48, which is prevalent in Asia and which is widely accepted to be present in the family members of Genghis Khan. Additionally, Tavan Tolgoi bodies may have been the product of marriages between the lineage of Genghis Khan’s Borjigin clan and the lineage of either the Ongud or Hongirad clans, indicating that these individuals were members of Genghis Khan’s immediate family or his close relatives.

Investigation on maternal lineage of a Neolithic group from northern Shaanxi based on ancient DNA

A magnetic bead purification method was successfully used to extract ancient DNA from the skeletal remains of 10 specimens excavated from Wuzhuangguoliang (Wzhgl) site, which was located in northern Shaanxi. The multidimensional scaling (MDS) and analysis of molecular variance approach (AMOVA) revealed that ancient Wzhgl people bored a very high similarity to southern Han Chinese. By constructing the MJ-network of various modern people including Han Chinese and Japanese, the phylogenetic analysis indicated that the Wzhgl population had close maternal distance with ancient Shandong and Xinjiang people. These findings indicated that Wzhgl contributed to the gene pool of Han Chinese and modern Japanese. In addition, population migration and interflow between Wzhgl people and ancient Shandong or Xinjiang probably occurred in Neolithic period.

Genetic analysis of mitochondrial DNA control region variations in four tribes of Khyber Pakhtunkhwa, Pakistan

Due to its geo strategic position at the crossroad of Asia, Pakistan has gained crucial importance of playing its pivotal role in subsequent human migratory events, both prehistoric and historic. This human movement became possible through an ancient overland network of trails called "The Silk Route" linking Asia Minor, Middle East China, Central Asia and Southeast Asia. This study was conducted to analyze complete mitochondrial control region samples of 100 individuals of four major Pashtun tribes namely, Bangash, Khattak, Mahsuds and Orakzai in the province of Khyber Pakhtunkhwa, Pakistan. All Pashtun tribes revealed high genetic diversity which is comparable to the other Central Asian, Southeast Asian and European populations. The configuration of genetic variation and heterogeneity further unveiled through Multidimensional Scaling, Principal Component Analysis and phylogenetic analysis. The results revealed that Pashtun are the composite mosaic of West Eurasian ancestry of numerous geographic origin. They received substantial gene flow during different invasive movements and have a high element of the Western provenance. The most common haplogroups reported in this study are: South Asian haplogroups M (28%) and R (8%); whereas, West Asians haplogroups are present, albeit in high frequencies (67%) and widespread over all; HV (15%), U (17%), H (9%), J (8%), K (8%), W (4%), N (3%) and T (3%). Moreover, we linked the unexplored genetic connection between Ashkenazi Jews and Pashtun. The presence of specific haplotypes J1b (4%) and K1a1b1a (5%) pointed to a genetic connection of Jewish conglomeration in Khattak tribe. This was a result of an ancient genetic influx in the early Neolithic period that led to the formation of a diverse genetic substratum in present day Pashtun.

Mitochondrial DNA Haplogroups and the Risk of Sporadic Parkinson's Disease in Han Chinese

Background:

Mitochondrial dysfunction is linked to the pathogenesis of Parkinson's disease (PD). However, the precise role of mitochondrial DNA (mtDNA) variations is obscure. On the other hand, mtDNA haplogroups have been inconsistently reported to modify the risk of PD among different population. Here, we try to explore the relationship between mtDNA haplogroups and sporadic PD in a Han Chinese population.

Methods:

Nine single-nucleotide polymorphisms, which define the major Asian mtDNA haplogroups (A, B, C, D, F, G), were detected via polymerase chain reaction-restriction fragment length polymorphism or denaturing polyacrylamide gel electrophoresis in 279 sporadic PD patients and 510 matched controls of Han population.

Results:

Overall, the distribution of mtDNA haplogroups did not show any significant differences between patients and controls. However, after stratification by age at onset, the frequency of haplogroup B was significantly lower in patients with early-onset PD (EOPD) compared to the controls (odds ratio [OR] =0.225, 95% confidence interval [CI]: 0.082–0.619, P = 0.004), while other haplogroups did not show significant differences. After stratification by age at examination, among subjects younger than 50 years of age: Haplogroup B also showed a lower frequency in PD cases (OR = 0.146, 95% CI: 0.030–0.715, P = 0.018) while haplogroup D presented a higher risk of PD (OR = 3.579, 95% CI: 1.112–11.523, P = 0.033), other haplogroups also did not show significant differences in the group.

Conclusions:

Our study indicates that haplogroup B might confer a lower risk for EOPD and people younger than 50 years in Han Chinese, while haplogroup D probably lead a higher risk of PD in people younger than 50 years of age. In brief, particular Asian mtDNA haplogroups likely play a role in the pathogenesis of PD among Han Chinese.

Endothelial Cell Bioenergetics and Mitochondrial DNA Damage Differ in Humans Having African or West Eurasian Maternal Ancestry

BACKGROUND

We hypothesized that endothelial cells having distinct mitochondrial genetic backgrounds would show variation in mitochondrial function and oxidative stress markers concordant with known differential cardiovascular disease susceptibilities. To test this hypothesis, mitochondrial bioenergetics were determined in endothelial cells from healthy individuals with African versus European maternal ancestries.

METHODS AND RESULTS

Bioenergetics and mitochondrial DNA (mtDNA) damage were assessed in single-donor human umbilical vein endothelial cells belonging to mtDNA haplogroups H and L, representing West Eurasian and African maternal ancestries, respectively. Human umbilical vein endothelial cells from haplogroup L used less oxygen for ATP production and had increased levels of mtDNA damage compared with those in haplogroup H. Differences in bioenergetic capacity were also observed in that human umbilical vein endothelial cells belonging to haplogroup L had decreased maximal bioenergetic capacities compared with haplogroup H. Analysis of peripheral blood mononuclear cells from age-matched healthy controls with West Eurasian or African maternal ancestries showed that haplogroups sharing an A to G mtDNA mutation at nucleotide pair 10398 had increased mtDNA damage compared with those lacking this mutation. Further study of angiographically proven patients with coronary artery disease and age-matched healthy controls revealed that mtDNA damage was associated with vascular function and remodeling and that age of disease onset was later in individuals from haplogroups lacking the A to G mutation at nucleotide pair 10398.

CONCLUSIONS

Differences in mitochondrial bioenergetics and mtDNA damage associated with maternal ancestry may contribute to endothelial dysfunction and vascular disease.

The Use and Effectiveness of Triple Multiplex System for Coding Region Single Nucleotide Polymorphism in Mitochondrial DNA Typing of Archaeologically Obtained Human Skeletons from Premodern Joseon Tombs of Korea

Previous study showed that East Asian mtDNA haplogroups, especially those of Koreans, could be successfully assigned by the coupled use of analyses on coding region SNP markers and control region mutation motifs. In this study, we tried to see if the same triple multiplex analysis for coding regions SNPs could be also applicable to ancient samples from East Asia as the complementation for sequence analysis of mtDNA control region. By the study on Joseon skeleton samples, we know that mtDNA haplogroup determined by coding region SNP markers successfully falls within the same haplogroup that sequence analysis on control region can assign. Considering that ancient samples in previous studies make no small number of errors in control region mtDNA sequencing, coding region SNP analysis can be used as good complimentary to the conventional haplogroup determination, especially of archaeological human bone samples buried underground over long periods.

A genome-wide association study of mitochondrial DNA in Chinese men identifies two risk single nucleotide substitutions for idiopathic oligoasthenospermia

Mitochondrial DNA (mtDNA) is believed to be both the source and target of reactive oxygen species (ROS), and mtDNA genetic alterations have been reported to be associated with molecular defects in the oxidative phosphorylation (OXPHOS) system. In order to investigate the potentially susceptible mtDNA genetic variants to oligoasthenospermia, we conducted a two-stage study in 921 idiopathic infertile men with oligoasthenospermia and 766 healthy controls using comprehensive molecular analysis. In the screen stage, we used next generation sequencing (NGS) in 233 cases and 233 controls to screen oligoasthenospermia susceptible mitochondrial genetic variants. In total, seven variants (C5601T, T12338C, A12361G, G13928C, A15235G, C16179T and G16291A) were screened to be potentially associated with idiopathic oligoasthenospermia. In the validation stage, we replicated these variants in 688 cases and 533 healthy controls using SNPscan. Our results demonstrated that the genetic alteration of C16179T was associated with idiopathic male infertility (odds ratio (OR) 3.10, 95% CI 1.41-6.79) (p=3.10×10(-3)). To elucidate the exact role of the genetic variants in spermatogenesis, two main sperm parameters (sperm count and motility) were taken into account. We found that C16179T was associated with both low sperm count and motility, with ORs of 4.18 (95% CI 1.86-9.40) (p=1.90×10(-4)) and 3.17 (95% CI 1.40-7.16) (p=3.50×10(-3)), respectively. Additionally, A12361G was found to be associated with low sperm count, with an OR of 3.30 (95% CI 1.36-8.04) (p=5.50×10(-3)). These results indicated that C16179T influenced both the process of spermatogenesis and sperm motility, while A12361G may just only participate in the process of spermatogenesis. Further investigation in larger populations and functional characterizations are needed to validate our findings.

Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: insights into prehistoric population movements in the Tarim Basin, China

Background

The Tarim Basin in western China, known for its amazingly well-preserved mummies, has been for thousands of years an important crossroad between the eastern and western parts of Eurasia. Despite its key position in communications and migration, and highly diverse peoples, languages and cultures, its prehistory is poorly understood. To shed light on the origin of the populations of the Tarim Basin, we analysed mitochondrial DNA polymorphisms in human skeletal remains excavated from the Xiaohe cemetery, used by the local community between 4000 and 3500 years before present, and possibly representing some of the earliest settlers.

Results

Xiaohe people carried a wide variety of maternal lineages, including West Eurasian lineages H, K, U5, U7, U2e, T, R*, East Eurasian lineages B, C4, C5, D, G2a and Indian lineage M5.

Conclusion

Our results indicate that the people of the Tarim Basin had a diverse maternal ancestry, with origins in Europe, central/eastern Siberia and southern/western Asia. These findings, together with information on the cultural context of the Xiaohe cemetery, can be used to test contrasting hypotheses of route of settlement into the Tarim Basin.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0237-5) contains supplementary material, which is available to authorized users.

A study of genetic polymorphisms in mitochondrial DNA hypervariable regions I and II of the five major ethnic groups and Vedda population in Sri Lanka

Diversity of the hypervariable regions (HV) I and II of the mitochondrial genome was studied in maternally unrelated Sri Lankans (N=202) from six ethnic groups (i.e.: Sinhalese, Sri Lankan Tamil, Muslim, Malay, Indian Tamil and Vedda). DNA was extracted from blood and buccal swabs and HVI and HVII regions were PCR amplified and sequenced. Resulting sequences were aligned and edited between 16024-16365 and 73-340 regions and compared with revised Cambridge reference sequences (rCRS). One hundred and thirty-five unique haplotypes and 22 shared haplotypes were observed. A total of 145 polymorphic sites and 158 polymorphisms were observed. Hypervariable region I showed a higher polymorphic variation than hypervariable region II. Nucleotide diversities were quite low and similar for all ethnicities apart from a slightly higher value for Indian Tamils and a much lower value for the Vedda population compared to the other groups. When the total population was considered South Asian (Indian) haplogroups were predominant, but there were differences in the distribution of phylo-geographical haplogroups between ethnic groups. Sinhalese, Sri Lankan Tamil and Vedda populations had a considerable presence of West Eurasian haplogroups. About 2/3rd of the Vedda population comprised of macro-haplogroup N or its subclades R and U, whereas macro-haplogroup M was predominant in all other populations. The Vedda population clustered separately from other groups and Sri Lankan Tamils showed a closer genetic affiliation to Sinhalese than to Indian Tamils. Thus this study provides useful information for forensic analysis and anthropological studies of Sri Lankans.

Ancient DNA reveals that the genetic structure of the northern Han Chinese was shaped prior to 3,000 years ago

The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area.

Identification of kinship and occupant status in Mongolian noble burials of the Yuan Dynasty through a multidisciplinary approach

The Yuan Dynasty (AD 1271-1368) was the first dynasty in Chinese history where a minority ethnic group (Mongols) ruled. Few cemeteries containing Mongolian nobles have been found owing to their tradition of keeping burial grounds secret and their lack of historical records. Archaeological excavations at the Shuzhuanglou site in the Hebei province of China led to the discovery of 13 skeletons in six separate tombs. The style of the artefacts and burials indicate the cemetery occupants were Mongol nobles. However, the origin, relationships and status of the chief occupant (M1m) are unclear. To shed light on the identity of the principal occupant and resolve the kin relationships between individuals, a multidisciplinary approach was adopted, combining archaeological information, stable isotope data and molecular genetic data. Analysis of autosomal, mitochondrial and Y-chromosomal DNA show that some of the occupants were related. The available evidence strongly suggests that the principal occupant may have been the Mongol noble Korguz. Our study demonstrates the power of a multidisciplinary approach in elucidating information about the inhabitants of ancient historical sites.

Ancient DNA reveals a migration of the ancient Di-qiang populations into Xinjiang as early as the early Bronze Age

Xinjiang is at the crossroads between East and West Eurasia, and it harbors a relatively complex genetic history. In order to better understand the population movements and interactions in this region, mitochondrial and Y chromosome analyses on 40 ancient human remains from the Tianshanbeilu site in eastern Xinjiang were performed. Twenty-nine samples were successfully assigned to specific mtDNA haplogroups, including the west Eurasian maternal lineages of U and W and the east Eurasian maternal lineages of A, C, D, F, G, Z, M7, and M10. In the male samples, two Y chromosome haplogroups, C* and N1 (xN1a, N1c), were successfully assigned. Our mitochondrial and Y-chromosomal DNA analyses combined with the archaeological studies revealed that the Di-qiang populations from the Hexi Corridor had migrated to eastern Xinjiang and admixed with the Eurasian steppe populations in the early Bronze Age.

Mitochondrial DNA Haplogroup A may confer a genetic susceptibility to AIDS group from Southwest China

The acquired immunodeficiency syndrome (AIDS) in humans was one of the chronic infections caused by human immunodeficiency virus (HIV), and the interactions between viral infection and mitochondrial energetic implicated that mitochondrial DNA (mtDNA) variation(s) may effect genetic susceptibility to AIDS. Thus, to illustrate the maternal genetic structure and further identify whether mtDNA variation(s) can effect HIV infection among southwest Chinese AIDS group, the whole mtDNA control region sequences of 70 AIDS patients and 480 health individuals from southwest China were analyzed here. Our results indicated the plausible recent genetic admixture results of AIDS group; comparison of matrilineal components between AIDS and matched Han groups showed that mtDNA haplogroup A (p = 0.048, OR = 3.006, 95% CI = 1.109-8.145) has a significant higher difference between the two groups; further comparison illustrated that mtDNA mutations 16,209 (p = 0.046, OR = 2.607, 95% CI = 0.988-6.876) and 16,319 (p = 0.009, OR = 2.965, 95% CI = 1.278-6.876) have significant differences between AIDS and matched control groups, and both of which were the defining variations of mtDNA haplogroup A, they further confirmed that mtDNA haplogroup A may confer genetic susceptibility to AIDS. Our results suggested that haplogroup A may confer a genetic susceptibility to AIDS group from Southwest China.

Mitochondrial DNA haplogroup D4b is a protective factor for ischemic stroke in Chinese Han population

Mitochondrial DNA (mtDNA) haplogroups affect the assembly and stability of the mitochondrial respiratory chain, which is potentially related to susceptibility to ischemic stroke (IS). However, the role of mtDNA in IS has not been comprehensively studied. The purpose of this study was to explore whether mtDNA polymorphisms and haplogroups are involved in the etiology of IS in the Chinese Han population. We recruited 200 patients with IS and 200 matched controls and genotyped them for 18 mtDNA single nucleotide polymorphisms defining the major Eastern Asian haplogroups by SNaPshot minisequencing. We also sequenced the hypervariable segment I (HVS-I), position 16051-16400. The prevalence of haplogroup D4b was significantly lower in IS patients than in healthy controls (0 and 8 %, respectively, corrected P = 2 × 10(-5), odds ratio = 0.028, 95 % confidence interval = 0.002-0.468).The positive association between haplogroup D4b and IS may be related to the protective effect of haplogroup D4b against oxidative damage, which decreases the risk of IS. Our study provides the first evidence that haplogroup D4b is a potential genetic protective factor for IS in the Chinese Han population.

Paternal and maternal genetic analysis of a desert Keriyan population: Keriyans are not the descendants of Guge Tibetans

The Keriyan people live in an isolated village in the Taklimakan Desert in Xinjiang, Western China. The origin and migration of the Keriyans remains unclear. We studied paternal and maternal genetic variance through typing Y-STR loci and sequencing the complete control region of the mtDNA and compared them with other adjacent populations. Data show that the Keriyan have relatively low genetic diversity on both the paternal and maternal lineages and possess both European and Asian specific haplogroups, indicating Keriyan is an admixture population of West and East. There is a gender-bias in the extent of contribution from Europe vs. Asia to the Keriyan gene pool. Keriyans have more genetic affinity to Uyghurs than to Tibetans. The Keriyan are not the descendants of the Guge Tibetans.