1
|
Parson W, Amory C, King T, Preick M, Berger C, König A, Huber G, Anslinger K, Bayer B, Weichhold G, Sänger T, Lutz-Bonengel S, Pfeiffer H, Hofreiter M, Pfründer D, Hohoff C, Brinkmann B. Kaspar Hauser's alleged noble origin - New molecular genetic analyses resolve the controversy. iScience 2024; 27:110539. [PMID: 39246441 PMCID: PMC11379569 DOI: 10.1016/j.isci.2024.110539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/21/2024] [Accepted: 07/16/2024] [Indexed: 09/10/2024] Open
Abstract
Kaspar Hauser's parentage has been the subject of research and debate for nearly 200 years. As for his possible aristocratic descent through the House of Baden, there is suspicion that he was swapped as a baby, kidnapped, and kept in isolation to bring a collateral lineage to the throne. In the last 28 years, various genetic analyses have been carried out to investigate this possible aristocratic origin. Previous results using less sensitive Sanger and electrophoresis-based methods were contradictory, and moreover, the authenticity of some samples was disputed, thus leaving the question open. Our analyses using modern capture- and whole genome-based massively parallel sequencing techniques reveal that the mitochondrial DNA haplotypes in different samples attributed to Kaspar Hauser were identical, demonstrating authenticity for the first time, and clearly different from the mitochondrial lineage of the House of Baden, which rules out a maternal relationship and thus the widely believed "Prince theory".
Collapse
Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Turi King
- Department of Life Sciences, Milner Centre for Evolution, University of Bath, Bath, UK
- Department of Genetics, University of Leicester, Leicester, UK
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Michaela Preick
- Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Anna König
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Katja Anslinger
- Institute of Legal Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Birgit Bayer
- Institute of Legal Medicine, Ludwig-Maximilians-University, Munich, Germany
| | | | - Timo Sänger
- Institute of Forensic Medicine, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sabine Lutz-Bonengel
- Institute of Forensic Medicine, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University Hospital Münster, Münster, Germany
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | | | - Carsten Hohoff
- Institute of Legal Medicine, University Hospital Münster, Münster, Germany
- Privatinstitut für Forensische Molekulargenetik GmbH, Emsdetten, Germany
- Institut für forensische Genetik, Münster, Germany
| | - Bernd Brinkmann
- Institute of Legal Medicine, University Hospital Münster, Münster, Germany
- Institut für forensische Genetik, Münster, Germany
| |
Collapse
|
2
|
Ahlawat B, Dewangan H, Pasupuleti N, Dwivedi A, Rajpal R, Pandey S, Kumar L, Thangaraj K, Rai N. Investigating linguistic and genetic shifts in East Indian tribal groups. Heliyon 2024; 10:e34354. [PMID: 39082022 PMCID: PMC11284423 DOI: 10.1016/j.heliyon.2024.e34354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
South Asia is home to almost a quarter of the world's total population and is home to significant ethnolinguistic diversity. Previous studies of linguistic and genetic affiliations of Indian populations suggest that the formation of these distinct groups was a protracted and complex phenomenon involving multiple waves of migration, cultural assimilation, and genetic admixture. The evolutionary processes of migration, mixing and merging of populations thus impact the culture and linguistic diversity of different groups, some of which may retain their linguistic affinities despite genetic admixture with other groups, or vice versa. Our study examines the relationship of genetic and linguistic affinities between Austroasiatic and Indo-European speakers in adjacent geographical regions of Eastern India. We analyzed 224 mitogenomes and 0.65 million SNP genotypes from 40 unrelated individuals belonging to the Bathudi, Bhumij, Ho, and Mahali ethnic groups from the Eastern Indian state of Odisha. These four groups are speakers of Austroasiatic languages who have adopted elements from Indo-European languages spoken in neighbouring regions. Our results suggest that these groups have the greatest maternal genetic affinity with other Austroasiatic-speaking groups in India. Allele frequency-based analyses, genome-wide SNPs, haplotype-based methods and IBD sharing further support the genetic similarity of these East Indian groups to Austroasiatic speakers of South Asia rather than regional populations speaking Indo-European and Dravidian languages. Our study shows that these populations experienced linguistic mixing, likely due to industrialization and modernization that brought them into close cultural contact with neighbouring Indo-European-speaking groups. However, linguistic change in these groups is not reflected in genetic mixing in these populations, as they appear to maintain strict genetic boundaries while simultaneously experiencing cultural mixing.
Collapse
Affiliation(s)
- Bhavna Ahlawat
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
- Department of Anthropology, Panjab University, Chandigarh, 160014, India
| | - Hemlata Dewangan
- Shreyanshi Health Care Private Limited, Raipur, Chattisgarh, 492001, India
| | - Nagarjuna Pasupuleti
- CSIR—Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Aparna Dwivedi
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Richa Rajpal
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Saurabh Pandey
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - Lomous Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - Kumarasamy Thangaraj
- CSIR—Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| |
Collapse
|
3
|
Borisova TV, Cherdonova AM, Pshennikova VG, Teryutin FM, Morozov IV, Bondar AA, Baturina OA, Kabilov MR, Romanov GP, Solovyev AV, Fedorova SA, Barashkov NA. High prevalence of m.1555A > G in patients with hearing loss in the Baikal Lake region of Russia as a result of founder effect. Sci Rep 2024; 14:15342. [PMID: 38961196 PMCID: PMC11222474 DOI: 10.1038/s41598-024-66254-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Tuyara V Borisova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Aleksandra M Cherdonova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Vera G Pshennikova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Fedor M Teryutin
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Igor V Morozov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
- Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Alexander A Bondar
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Olga A Baturina
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Marsel R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Georgii P Romanov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Aisen V Solovyev
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Sardana A Fedorova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Nikolay A Barashkov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia.
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia.
| |
Collapse
|
4
|
Sequeira JJ, Vinuthalakshmi K, Das R, van Driem G, Mustak MS. The maternal U1 haplogroup in the Koraga tribe as a correlate of their North Dravidian linguistic affinity. Front Genet 2024; 14:1303628. [PMID: 38384360 PMCID: PMC10880486 DOI: 10.3389/fgene.2023.1303628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/31/2023] [Indexed: 02/23/2024] Open
Abstract
Introduction: The Koraga tribe are an isolated endogamous tribal group found in the southwest coastal region of India. The Koraga language shares inherited grammatical features with North Dravidian languages. To seek a possible genetic basis for this exceptionality and understand the maternal lineage pattern, we have aimed to reconstruct the inter-population and intra-population relationships of the Koraga tribal population by using mtDNA markers for the hypervariable regions along with a partial coding region sequence analysis. Methods and Results: Amongst the 96 individuals studied, we observe 11 haplogroups, of which a few are shared and others are unique to the clans Soppu, Oṇṭi and Kuṇṭu. In addition to several deep rooted Indian-specific lineages of macrohaplogroups M and U, we observe a high frequency of the U1 lineage (∼38%), unique to the Koraga. A Bayesian analysis of the U1 clade shows that the Koraga tribe share their maternal lineage with ancestral populations of the Caucasus at the cusp of the Last Glacial Maximum. Discussion: Our study suggests that the U1 lineage found in the Indian subcontinent represents a remnant of a post-glacial dispersal. The presence of West Asian U1 when viewed along with historical linguistics leads us to hypothesise that Koraga represents a mother tongue retained by a vanquished population group that fled southward at the demise of the Indus civilisation as opposed to a father tongue, associated with a particular paternal lineage.
Collapse
Affiliation(s)
| | | | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
| | - Mohammed S. Mustak
- Department of Applied Zoology, Mangalore University, Mangalore, Karnataka, India
| |
Collapse
|
5
|
Kumar L, Chowdhari A, Sequeira JJ, Mustak MS, Banerjee M, Thangaraj K. Genetic Affinities and Adaptation of the South-West Coast Populations of India. Genome Biol Evol 2023; 15:evad225. [PMID: 38079532 PMCID: PMC10745260 DOI: 10.1093/gbe/evad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Evolutionary event has not only altered the genetic structure of human populations but also associated with social and cultural transformation. South Asian populations were the result of migration and admixture of genetically and culturally diverse groups. Most of the genetic studies pointed to large-scale admixture events between Ancestral North Indian (ANI) and Ancestral South Indian (ASI) groups, also additional layers of recent admixture. In the present study, we have analyzed 213 individuals inhabited in South-west coast India with traditional warriors and feudal lord status and historically associated with migratory events from North/North West India and possible admixture with West Eurasian populations, whose genetic links are still missing. Analysis of autosomal Single Nucleotide Polymorphism (SNP) markers suggests that these groups possibly derived their ancestry from some groups of North West India having additional Middle Eastern genetic components. Higher distribution of West Eurasian mitochondrial haplogroups also points to female-mediated admixture. Estimation of Effective Migration Surface (EEMS) analysis indicates Central India and Godavari basin as a crucial transition zone for population migration from North and North West India to South-west coastal India. Selection screen using 3 distinct outlier-based approaches revealed genetic signatures related to Immunity and protection from Viral infections. Thus, our study suggests that the South-west coastal groups with traditional warriors and feudal lords' status are of a distinct lineage compared to Dravidian and Gangetic plain Indo-Europeans and are remnants of very early migrations from North West India following the Godavari basin to Karnataka and Kerala.
Collapse
Affiliation(s)
- Lomous Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Anuhya Chowdhari
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Jaison J Sequeira
- Department of Applied Zoology, Mangalore University, Mangalore 574199, India
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalore 574199, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India
| | | |
Collapse
|
6
|
Tayyeh AM, Sequeira JJ, Kumar L, Babu I, van Driem G, Mustak MS. The maternal ancestry of the Kavaratti islanders and the last glacial maximum aftermath. Mol Genet Genomics 2023; 298:1467-1477. [PMID: 37823939 DOI: 10.1007/s00438-023-02072-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/23/2023] [Indexed: 10/13/2023]
Abstract
The prehistoric human settlement of the Lakshadweep islands remains a mystery for various reasons. Uncertainty about the existence of indigenous tribes in these islands and the lack of folklore records present major obstacles to the reconstruction of Lakshadweep ancestry. However, with extant population data, we seek to understand the maternal ancestry of the Kavaratti islanders. Mitochondrial control region variation analysis of 80 individuals from this island shows maternal links with the populations in the northwestern region of the South Asian mainland. The founder clade R30b2, observed in the Kavaratti islanders, is so far present only in the Scheduled Castes from the Punjab region, Jat Sikhs and Nairs. All other mainland populations carry basal R30 or R30a subclades. The presence of a specific Uralic U4 lineage in our samples, in addition to the Indo-European affinity observed in the phylogeny tree, substantiates a northwestern maternal ancestry of the Kavaratti islanders and implies an ancestral admixture with early humans in the Near East at the time of the last glacial maximum (LGM). Based on our Bayesian analysis, we furthermore propose that a group bearing mostly R30b2 during the LGM recovery, moved eastward and southward, where they received Indian-specific M haplogroups. Hence, the maternal ancestry of the Kavaratti islanders is evidently a consequence of the demographic changes in the northwestern region of the Indian subcontinent caused by the Last Glacial Maximum. The haplogroup distribution pattern and nucleotide sequence data produced in this study will enrich the forensic database of the Lakshadweep islands.
Collapse
Affiliation(s)
- Alnoman Mundher Tayyeh
- Department of Applied Zoology, Mangalore University, Mangalagangothri, 574199, India
- Department of Biosciences, Biotechnology Unit, Mangalore University, Mangalagangothri, 574199, India
| | | | - Lomous Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Idrees Babu
- Department of Science and Technology, Lakshadweep Administration, Kavaratti, 682555, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Länggassstrasse 49, 3012, Bern, Switzerland
| | | |
Collapse
|
7
|
Kristjansson D, Schurr TG, Bohlin J, Jugessur A. Phylogeographic history of mitochondrial haplogroup J in Scandinavia. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:298-315. [PMID: 36790764 PMCID: PMC10100211 DOI: 10.1002/ajpa.24666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/10/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach. METHODS Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates. RESULTS Haplogroup J originated approximately 42.6 kya (95% CI: 30.0-64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers. CONCLUSIONS Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.
Collapse
Affiliation(s)
- Dana Kristjansson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jon Bohlin
- Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| |
Collapse
|
8
|
Sikdar M. Complete mitochondrial DNA sequence tries to settle hitherto putative history of Kayastha population of India. Am J Hum Biol 2022; 35:e23851. [PMID: 36571462 DOI: 10.1002/ajhb.23851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVES Indian caste system is unique as it has an inimitable type of class system where the social ordering is done based on birth. Within the caste system, there is a distinct endogamous population known as the Kayastha, who have had inconclusive stratification records due to unidentified historical records. METHODS To gain a more inclusive view on the history and genetic affinities of Kayastha people, complete mitochondrial genomes from 15 individuals of a Kayastha population from North-western India have been sequenced. RESULTS Interestingly, three novel sub-clades (U2b2a, M3d2, and M33a3b) have been identified that represent unique Kayastha motifs. CONCLUSION The haplotype-based analysis suggests that the Kayastha population shares genetic affinities with the Indo-European and Sino-Tibetan populations found in the trans-Himalayan region. The FST based population comparison and the MDS plot indicates that Kayastha people have close maternal genetic affinity with the available genetic database of Brahmins, Kashmiris, and Tharus. The maternal genetic lineages among Kayastha population shows deep in situ origin that emerged much before settled life developed on this sub-continent. Both mtDNA and Y-chromosome markers, trace the genetic lineages of Kayastha population with Tharus, who regard themselves Kshatriya, corroborated by the oral history of the Kayasthas for their Kshatriya affiliation. It also validates genetic heritage of earliest settlers of India in both indigenous tribal and caste populations.
Collapse
Affiliation(s)
- Mithun Sikdar
- DNA Laboratory Unit, Anthropological Survey of India, Southern Regional Center, Mysore, India
| |
Collapse
|
9
|
Zhang X, Sun A, Ge J. Origin and Spread of the ALDH2 Glu504Lys Allele. PHENOMICS (CHAM, SWITZERLAND) 2021; 1:222-228. [PMID: 36939783 PMCID: PMC9590465 DOI: 10.1007/s43657-021-00017-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 01/14/2023]
Abstract
Gene polymorphism of acetaldehyde dehydrogenase 2 (ALDH2), a key enzyme for alcohol metabolism in humans, can affect catalytic activity. The ALDH2 Glu504Lys mutant allele has a high-frequency distribution in East Asian populations and has been demonstrated to be associated with an increased risk of cardiovascular disease, stroke, and tumors. Available evidence suggests that the evolution of the ALDH2 gene has been influenced by multiple factors. Random mutations produce Glu504Lys, and genetic drift alters the frequency of this allele; additionally, environmental factors such as hepatitis B virus infection and high-elevation hypoxia affect its frequency through selective effects, ultimately resulting in a high frequency of this allele in East Asian populations. Here, the origin, selection, and spread of the ALDH2 Glu504Lys allele are discussed, and an outlook for further research is proposed to realize a precision medical strategy based on the genetic and environmental variations in ALDH2.
Collapse
Affiliation(s)
- Xiaokai Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Aijun Sun
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| |
Collapse
|
10
|
Yang XY, Rakha A, Chen W, Hou J, Qi XB, Shen QK, Dai SS, Sulaiman X, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Adnan A, Zhao RH, Yao YG, Su B, Peng MS, Zhang YP. Tracing the Genetic Legacy of the Tibetan Empire in the Balti. Mol Biol Evol 2021; 38:1529-1536. [PMID: 33283852 PMCID: PMC8042757 DOI: 10.1093/molbev/msaa313] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The rise and expansion of Tibetan Empire in the 7th to 9th centuries AD affected the course of history across East Eurasia, but the genetic impact of Tibetans on surrounding populations remains undefined. We sequenced 60 genomes for four populations from Pakistan and Tajikistan to explore their demographic history. We showed that the genomes of Balti people from Baltistan comprised 22.6–26% Tibetan ancestry. We inferred a single admixture event and dated it to about 39–21 generations ago, a period that postdated the conquest of Baltistan by the ancient Tibetan Empire. The analyses of mitochondrial DNA, Y, and X chromosome data indicated that both ancient Tibetan males and females were involved in the male-biased dispersal. Given the fact that the Balti people adopted Tibetan language and culture in history, our study suggested the impact of Tibetan Empire on Baltistan involved dominant cultural and minor demic diffusion.
Collapse
Affiliation(s)
- Xing-Yan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Juzhi Hou
- Key Laboratory of Alpine Ecology (LAE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Xue-Bin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xierzhatijiang Sulaiman
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan
| | | | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, China
| | - Ruo-Han Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
11
|
Padh H. Sequencing and comparative genome analysis of three Indians. Mamm Genome 2021; 32:401-412. [PMID: 34086082 DOI: 10.1007/s00335-021-09882-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/26/2021] [Indexed: 11/27/2022]
Abstract
Remarkable advancement in DNA sequencing (NGS) technology has made personal genome analysis feasible and affordable. Here we present the whole genome sequencing and analysis of three individuals, two males and one female, from different parts of India. Comparison with the Reference Human Genome and the variant database showed a total of 4.0-4.85 million variants, primarily single nucleotide variants (SNVs), 350-600 K small insertions and deletions (INDELs), and previously unreported novel variants. The analysis of Y-chromosome and mitochondrial haplogroups revealed that the ancestors of the individual arrived on the subcontinent at very different times using distinctly different migration routes. Approximately, 500,000 novel SNPs and about 89,000 novel INDELs have been submitted to the NCBI as novel variants. PCA and Admix analysis revealed that the IHGP03, a Mizoram male from the Northeast region, is strikingly different from the other two Indian genomes. Collectively, the data suggest the complexity of the Indian population admix developed from several distinct waves of human migration over tens of thousands of years.
Collapse
Affiliation(s)
- Harish Padh
- Former Vice-Chancellor, Sardar Patel University, Vallabh Vidyanagar, Gujarat, 388120, India.
| |
Collapse
|
12
|
Sharma S, Singh Y, Sandhir R, Singh S, Ganju L, Kumar B, Varshney R. Mitochondrial DNA mutations contribute to high altitude pulmonary edema via increased oxidative stress and metabolic reprogramming during hypobaric hypoxia. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148431. [PMID: 33862004 DOI: 10.1016/j.bbabio.2021.148431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/27/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
High altitude pulmonary edema (HAPE) is experienced by non-acclimatized sea level individuals on exposure to high altitude hypoxic conditions. Available evidence suggests that genetic factors and perturbed mitochondrial redox status may play an important role in HAPE pathophysiology. However, the precise mechanism has not been fully understood. In the present study, sequencing of mitochondrial DNA (mtDNA) from HAPE subjects and acclimatized controls was performed to identify pathogenic mutations and to determine their role in HAPE. Hypobaric hypoxia induced oxidative stress and metabolic alterations were also assessed in HAPE subjects. mtDNA copy number, mitochondrial oxidative phosphorylation (mtOXPHOS) activity, mitochondrial biogenesis were measured to determine mitochondrial functions. The data revealed that the mutations in Complex I genes affects the secondary structure of protein in HAPE subjects. Further, increased oxidative stress during hypobaric hypoxia, reduced mitochondrial biogenesis and mtOXPHOS activity induced metabolic reprogramming appears to contribute to mitochondrial dysfunctions in HAPE individuals. Haplogroup analysis suggests that mtDNA haplogroup H2a2a1 has potential contribution in the pathobiology of HAPE in lowlanders. This study also suggests contribution of altered mitochondrial functions in HAPE susceptibility.
Collapse
Affiliation(s)
- Swati Sharma
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India; Department of Biochemistry, Basic Medical Sciences Block II, Panjab University, Chandigarh 160014, India
| | - Yamini Singh
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India.
| | - Rajat Sandhir
- Department of Biochemistry, Basic Medical Sciences Block II, Panjab University, Chandigarh 160014, India
| | - Sayar Singh
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| | - Lilly Ganju
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| | - Bhuvnesh Kumar
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| | - Rajeev Varshney
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| |
Collapse
|
13
|
Chen C, Li Y, Tao R, Jin X, Guo Y, Cui W, Chen A, Yang Y, Zhang X, Zhang J, Li C, Zhu B. The Genetic Structure of Chinese Hui Ethnic Group Revealed by Complete Mitochondrial Genome Analyses Using Massively Parallel Sequencing. Genes (Basel) 2020; 11:E1352. [PMID: 33202591 PMCID: PMC7698084 DOI: 10.3390/genes11111352] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 01/10/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Yuchun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610017, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Wei Cui
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610017, China
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
| |
Collapse
|
14
|
Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data. Sci Rep 2020; 10:10075. [PMID: 32572090 PMCID: PMC7308293 DOI: 10.1038/s41598-020-66953-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/27/2020] [Indexed: 12/14/2022] Open
Abstract
The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.
Collapse
|
15
|
Singh M, Sarkar A, Kumar D, Nandineni MR. The genetic affinities of Gujjar and Ladakhi populations of India. Sci Rep 2020; 10:2055. [PMID: 32029844 PMCID: PMC7005309 DOI: 10.1038/s41598-020-59061-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 01/22/2020] [Indexed: 11/27/2022] Open
Abstract
The Union Territories of Jammu and Kashmir (J&K) and Ladakh in North India owing to their unique geographic location offer a wide variety of landscape from plains to high altitudes and is a congruence of many languages and cultural practices. Here, we present the genetic diversity studies of Gujjars from Jammu region of J&K and Ladakhi population based on a battery of autosomal single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), Y-chromosomal STRs and the control region of the mitochondrial genome. These two populations were observed to be genetically distant to each other as well as to other populations from India. Interestingly, Y-STR analyses showed a closer affinity of Gujjars to other nomadic populations of Pashtuns from Baghlans and Kunduz provinces of Afghanistan and Pashtuns and Sindhis of Pakistan. Gujjars exhibited lesser genetic diversity as compared to Ladakhi population. M30f and M9 were the most abundant mitochondrial haplogroups observed among Gujjars and Ladakhis, respectively. A lower matrilineal to patrilineal diversity was observed for both these populations. The current study presents the first comprehensive analysis of Gujjars and Ladakhis and reveals their unique genetic affiliations with other populations of the world.
Collapse
Affiliation(s)
- Mugdha Singh
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana State, India
- Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anujit Sarkar
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Devinder Kumar
- Central Forensic Science Laboratory, Kolkata, West Bengal, India
| | - Madhusudan R Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana State, India.
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana State, India.
| |
Collapse
|
16
|
Rare human mitochondrial HV lineages spread from the Near East and Caucasus during post-LGM and Neolithic expansions. Sci Rep 2019; 9:14751. [PMID: 31611588 PMCID: PMC6791841 DOI: 10.1038/s41598-019-48596-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/21/2019] [Indexed: 01/05/2023] Open
Abstract
Of particular significance to human population history in Eurasia are the migratory events that connected the Near East to Europe after the Last Glacial Maximum (LGM). Utilizing 315 HV*(xH,V) mitogenomes, including 27 contemporary lineages first reported here, we found the genetic signatures for distinctive movements out of the Near East and South Caucasus both westward into Europe and eastward into South Asia. The parallel phylogeographies of rare, yet widely distributed HV*(xH,V) subclades reveal a connection between the Italian Peninsula and South Caucasus, resulting from at least two (post-LGM, Neolithic) waves of migration. Many of these subclades originated in a population ancestral to contemporary Armenians and Assyrians. One such subclade, HV1b-152, supports a postexilic, northern Mesopotamian origin for the Ashkenazi HV1b2 lineages. In agreement with ancient DNA findings, our phylogenetic analysis of HV12 and HV14, the two exclusively Asian subclades of HV*(xH,V), point to the migration of lineages originating in Iran to South Asia before and during the Neolithic period. With HV12 being one of the oldest HV subclades, our results support an origin of HV haplogroup in the region defined by Western Iran, Mesopotamia, and the South Caucasus, where the highest prevalence of HV has been found.
Collapse
|
17
|
Silva M, Justeau P, Rodrigues S, Oteo-Garcia G, Dulias K, Foody G, Fichera A, Yau B, Rito T, Wilson JF, Gandini F, Edwards CJ, Pala M, Soares PA, Richards MB. Untangling Neolithic and Bronze Age mitochondrial lineages in South Asia. Ann Hum Biol 2019; 46:140-144. [PMID: 31267777 DOI: 10.1080/03014460.2019.1623319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Two key moments shaped the extant South Asian gene pool within the last 10 thousand years (ka): the Neolithic period, with the advent of agriculture and the rise of the Harappan/Indus Valley Civilisation; and Late Bronze Age events that witnessed the abrupt fall of the Harappan Civilisation and the arrival of Indo-European speakers. This study focuses on the phylogeographic patterns of mitochondrial haplogroups H2 and H13 in the Indian Subcontinent and incorporates evidence from recently released ancient genomes from Central and South Asia. It found signals of Neolithic arrivals from Iran and later movements in the Bronze Age from Central Asia that derived ultimately from the Steppe. This study shows how a detailed mtDNA phylogeographic approach, combining both modern and ancient variation, can provide evidence of population movements, even in a scenario of strong male bias such as in the case of the Bronze Age Steppe dispersals.
Collapse
Affiliation(s)
- M Silva
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - P Justeau
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - S Rodrigues
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - G Oteo-Garcia
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - K Dulias
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - G Foody
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - A Fichera
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - B Yau
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - T Rito
- b School of Medicine , Life and Health Sciences Research Institute (ICVS), University of Minho , Braga , Portugal.,c ICVS/3B's , PT Government Associate Laboratory , Guimarães , Portugal
| | - J F Wilson
- d Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Teviot Place , Edinburgh , UK.,e MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine , University of Edinburgh, Western General Hospital , Edinburgh , UK
| | - F Gandini
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - C J Edwards
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - M Pala
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - P A Soares
- f CBMA (Centre of Molecular and Environmental Biology), Department of Biology , University of Minho , Braga , Portugal.,g Institute of Science and Innovation for Bio-Sustainability (IB-S) , University of Minho , Braga , Portugal
| | - M B Richards
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| |
Collapse
|
18
|
Sylvester C, Krishna MS, Rao JS, Chandrasekar A. Maternal genetic link of a south Dravidian tribe with native Iranians indicating bidirectional migration. Ann Hum Biol 2019; 46:175-180. [PMID: 30909755 DOI: 10.1080/03014460.2019.1599067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Background: The phylogeny of major mitochondrial DNA haplogroups has played a key role in assessing the people of India through molecular genetics. Aim: To resolve the phylogeny and phylogeographic pattern of autochthonous haplogroup R with its descendant haplogroup U in the Urali Kuruman tribal population of Southern India. Subjects and methods: Complete mitogenome sequences of 40 individuals were amplified and sequenced using the Sanger sequencing method. Mutations were scored referring to the revised Cambridge reference sequence, and phylogenetic trees were constructed using previously described sequences. Results: Novel sub-lineages of haplogroup R30: R30a1c1, and U1: U1a1c1d2, U1a1c1d2a were identified. Urali Kurumans pooled ancestry with the native Iranians sharing the sub-haplogroups R30a1c and U1a1c1d. The coalescence ages estimated for the sub-haplogroup R30a1c dates ∼ 9.4 ± 3.5 Kya and for subclade U1a1c1d dates ∼ 9.1 ± 2.7 Kya. Conclusion: The study revealed a genetic link between Iran and South Asia in the Neolithic time, indicating bidirectional migration and admixture.
Collapse
Affiliation(s)
- Charles Sylvester
- a Department of Studies in Zoology , University of Mysore , Mysore , India.,b Southern Regional Center , Anthropological Survey of India , Mysore , India
| | | | - Jaya Sankar Rao
- b Southern Regional Center , Anthropological Survey of India , Mysore , India
| | | |
Collapse
|
19
|
Tyagi A, Pramanik R, Vishnubhatla S, Bakhshi R, Bakhshi S. Prognostic impact of mitochondrial DNA D-loop variations in pediatric acute myeloid leukemia. Oncotarget 2019; 10:1334-1343. [PMID: 30863493 PMCID: PMC6407682 DOI: 10.18632/oncotarget.26665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/31/2019] [Indexed: 12/21/2022] Open
Abstract
The role of mitochondrial DNA (mt-DNA) changes, especially those in the regulatory D-loop region in Acute Myeloid Leukemia (AML) remains investigational. Consecutive 151 de novo pediatric AML patients, (≤18 yr) were prospectively enrolled from June 2013-August 2016, to assess the prognostic impact of mt-DNA D-loop variations (somatic/germline) on survival. For each patient, D-loop region was sequenced on baseline bone marrow and buccal swab, and mother’s blood sample. In 151 AML subjects, 1490 variations were found at 237 positions; 80.9% were germline and 19.1% somatic. The mean number of variations per position was 6.3. Variations with frequency ≥6 were analyzed for their impact on survival and 4 categories were created, namely “somatic-protective”, “somatic-hazardous”, “germline-protective” and “germline- hazardous”. Although, somatic-protective could not predict event free survival (EFS) or overall survival (OS), somatic-hazardous [(OS) HR = 2.33, p = 0.06] and germline-hazardous [(OS) HR = 2.85, p < 0.01] significantly predicted OS and EFS. Notably, the germline-protective, could significantly predict EFS (HR = 0.31, p = 0.03) and OS (HR = 0.19, p < 0.01), only when variations at ≥2 positions were present. On multivariate analysis, three positions namely 16111, 16126, 16362 and karyotype were found to be predictive of EFS. A prognostic index (PI) was developed using nomogram PI = (0.8*karyotype) + (1.0*c16111) + (0.7*t16362) + (1.2*t16126). Hazard ratio for EFS increased significantly with increasing PI reaching to a maximum of 3.3 (p < 0.01). In conclusion, the impact of mt-DNA D-loop variations on outcomes in pediatric AML depends on their nature (germline/somatic), position and mutational burden, highlighting their potential role as evolving prognostic biomarkers.
Collapse
Affiliation(s)
- Anudishi Tyagi
- Department of Medical Oncology, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Raja Pramanik
- Department of Medical Oncology, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | | | - Radhika Bakhshi
- Department of Biomedical Sciences, Shaheed Rajguru College of Applied Sciences, University of Delhi, New Delhi, India
| | - Sameer Bakhshi
- Department of Medical Oncology, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
20
|
Ji J, Xu M, Wang R, Wang Y, Qin Y, Li L, Zheng H, Yang S, Li S, Miao D, Jin L, Zhou L, Ling X, Xia Y, Lu C, Wang X. Human mitochondrial DNA haplogroup M8a influences the penetrance of m.8684C>T in Han Chinese men with non-obstructive azoospermia. Reprod Biomed Online 2018; 37:480-488. [PMID: 30236824 DOI: 10.1016/j.rbmo.2018.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 11/29/2022]
Abstract
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.
Collapse
Affiliation(s)
- Juan Ji
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Miaofei Xu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Rong Wang
- Research Centre for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Ying Wang
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Yufeng Qin
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle ParkNC27709, USA
| | - Lei Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Hongxiang Zheng
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Shuping Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Shilin Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Dengshun Miao
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Research Centre for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Lin Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Xiufeng Ling
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China.
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China.
| |
Collapse
|
21
|
Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science 2018; 361:511-516. [PMID: 30072539 PMCID: PMC6709593 DOI: 10.1126/science.aar8486] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/22/2018] [Indexed: 12/21/2022]
Abstract
Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores.
Collapse
Affiliation(s)
- Serena Tucci
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Rajiv C McCoy
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthew R Robinson
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Génopode, Quatier Sorge, Lausanne, Switzerland
| | - Chiara Barbieri
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | - Brad J Nelson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Wenqing Fu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Gludhug A Purnomo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Guido Barbujani
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Joshua M Akey
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA.
| |
Collapse
|
22
|
Sylvester C, Krishna MS, Rao JS, Chandrasekar A. Neolithic phylogenetic continuity inferred from complete mitochondrial DNA sequences in a tribal population of Southern India. Genetica 2018; 146:383-389. [PMID: 30032461 DOI: 10.1007/s10709-018-0030-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 07/15/2018] [Indexed: 11/28/2022]
Abstract
The subsequent human migrations that dispersed out of Africa, both prehistoric and historic and colonization of India by modern humans is unanimous, and phylogeny of major mitochondrial DNA haplogroups have played a key role in assessing the genetic origin of people of India. To address more such events, complete mitogenomes of 113 Melakudiya tribe of Southern India were sequenced and 46 individuals showed the presence of west Eurasian autochthonous haplogroups HV14 and U7. Phylogenetic analysis revealed two novel subclades HV14a1b and HV14a1b1 and sequences representing haplogroup U7 were included under previously described subclade U7a3a1a2* specific to India. Moreover, the present analysis on complete mtDNA reveals addition information of the spread and distribution of west Eurasian haplogroups in southern India, in tracing an unexplored genetic link between Melakudiya tribe with the people of Iranian Plateau, South Caucasus, and Central Asia. Coalescence ages of HV14 and U7a3a1a2* trees in the present study dates ~ 16.1 ± 4.3 and ~ 13.4 ± 5.6 kya respectively.
Collapse
Affiliation(s)
- Charles Sylvester
- Department of Studies in Zoology, University of Mysore, Mysore, India.,Anthropological Survey of India, Southern Regional Center, Mysore, India
| | | | - Jaya Sankar Rao
- Anthropological Survey of India, Southern Regional Center, Mysore, India
| | | |
Collapse
|
23
|
Tyagi A, Pramanik R, Vishnubhatla S, Ali S, Bakhshi R, Chopra A, Singh A, Bakhshi S. Pattern of mitochondrial D-loop variations and their relation with mitochondrial encoded genes in pediatric acute myeloid leukemia. Mutat Res 2018; 810:13-18. [PMID: 29883862 DOI: 10.1016/j.mrfmmm.2018.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/08/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Role of mitochondrial DNA variations, particularly in D loop region, remains investigational in acute myeloid leukaemia (AML). Consecutive 151 pediatric AML patients were prospectively enrolled from June 2013 to August 2016, for evaluating pattern of variations in mitochondrial D-loop region and to determine their association, if any, with expression of mitochondrial-encoded genes. For each patient, D-loop region was sequenced on baseline bone marrow, buccal swab and mother's blood sample. Real time PCR was used for relative gene expression of four mitochondrial DNA encoded genes viz. Nicotinamide-adenine-dineucleotide-dehydrogenase subunit 3 (ND3), Cytochrome-B (Cyt-B), Cytochrome c oxidase-I (COX1) and ATP-synthetase F0 subunit-6 (ATP6). Total 1490 variations were found at 237 positions in D-Loop; 1206 (80.9%) were germline and 284 (19.1%) were somatic. Positions 73-263 were identified as a probable hotspot region. G bases appeared to be most stable nucleotide (least number of single base substitutions) whereas T appeared to be most susceptible to variations with germline T-C being the commonest. Gene expression of Cyt-B was found to be significantly higher for any variation (somatic or germline) at positions 16,192 and 16,327 while it was significantly lower for variations at positions 16,051 and 207. Any variation at positions 152, 207 and 513 significantly decreased COX1 expression while those at positions 16,051 and 152 attenuated ATP6 expression. This first study evaluated type and overall pattern of D-loop variations in AML, and also showed that some of these variations in D loop region might have an effect on the mitochondrial-encoded genes which is new and valuable information in AML genomics.
Collapse
Affiliation(s)
- Anudishi Tyagi
- Department of Medical Oncology; Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India
| | - Raja Pramanik
- Department of Medical Oncology; Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India
| | | | - Safdar Ali
- Shaheed Rajguru College of Applied Sciences, India; University of Delhi , New Delhi
| | - Radhika Bakhshi
- Shaheed Rajguru College of Applied Sciences, India; University of Delhi , New Delhi
| | - Anita Chopra
- Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India; Department of Lab oncology
| | - Archna Singh
- All India Institute of Medical Sciences, New Delhi, India; Department of Biochemistry
| | - Sameer Bakhshi
- Department of Medical Oncology; Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India.
| |
Collapse
|
24
|
Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| |
Collapse
|
25
|
Kılınç GM, Kashuba N, Yaka R, Sümer AP, Yüncü E, Shergin D, Ivanov GL, Kichigin D, Pestereva K, Volkov D, Mandryka P, Kharinskii A, Tishkin A, Ineshin E, Kovychev E, Stepanov A, Alekseev A, Fedoseeva SA, Somel M, Jakobsson M, Krzewińska M, Storå J, Götherström A. Investigating Holocene human population history in North Asia using ancient mitogenomes. Sci Rep 2018; 8:8969. [PMID: 29895902 PMCID: PMC5997703 DOI: 10.1038/s41598-018-27325-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/25/2018] [Indexed: 12/21/2022] Open
Abstract
Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.
Collapse
Affiliation(s)
- Gülşah Merve Kılınç
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden.
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden.,University of Oslo, Museum of Cultural History, 0164, Oslo, Norway
| | - Reyhan Yaka
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Arev Pelin Sümer
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Eren Yüncü
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Dmitrij Shergin
- Laboratory of Archaeology and Ethnography, Faculty of History and Methods, Department of Humanitarian and Aesthetic Education, Pedagogical Institute, Irkutsk State University, Irkutsk, 664011, Irkutsk, Oblast, Russia
| | | | - Dmitrii Kichigin
- Irkutsk National Research Technical University, Laboratory of Archaeology, Paleoecology and the Subsistence Strategies of the Peoples of Northern Asia, Irkutsk State Technical University, Irkutsk, 664074, Irkutsk Oblast, Russia
| | - Kjunnej Pestereva
- M. K. Ammosov North-Eastern Federal University (NEFU), Federal State Autonomous Educational Institution of Higher Education, Yakutsk, 677000, Sakha Republic, Russia
| | - Denis Volkov
- The Center for Preservation of Historical and Cultural Heritage of the Amur Region, Blagoveshchensk, 675000, Amur Oblast, Russia
| | - Pavel Mandryka
- Siberian Federal University, Krasnoyarsk, 660041, Krasnoyarskiy Kray, Russia
| | - Artur Kharinskii
- Irkutsk National Research Technical University, Laboratory of Archaeology, Paleoecology and the Subsistence Strategies of the Peoples of Northern Asia, Irkutsk State Technical University, Irkutsk, 664074, Irkutsk Oblast, Russia
| | - Alexey Tishkin
- The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Altaiskiy Kray, Russia
| | - Evgenij Ineshin
- Laboratory of Archaeology and Ethnography, Faculty of History and Methods, Department of Humanitarian and Aesthetic Education, Pedagogical Institute, Irkutsk State University, Irkutsk, 664011, Irkutsk, Oblast, Russia
| | - Evgeniy Kovychev
- Faculty of History, Transbaikal State University, Chita, 672039, Zabaykalsky Kray, Russia
| | - Aleksandr Stepanov
- M. K. Ammosov North-Eastern Federal University (NEFU), Federal State Autonomous Educational Institution of Higher Education, Yakutsk, 677000, Sakha Republic, Russia
| | - Aanatolij Alekseev
- The Institute for Humanities Research and Indigenous Studies (IHRISN), Academy of Sciences of the Sakha Republic, Yakutsk, 677000, Sakha Republic, Russia
| | | | - Mehmet Somel
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Mattias Jakobsson
- Department of Organismal Biology and SciLife Lab, Evolutionary Biology Centre, 75236, Uppsala, Sweden
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden.
| |
Collapse
|
26
|
Caporali L, Iommarini L, La Morgia C, Olivieri A, Achilli A, Maresca A, Valentino ML, Capristo M, Tagliavini F, Del Dotto V, Zanna C, Liguori R, Barboni P, Carbonelli M, Cocetta V, Montopoli M, Martinuzzi A, Cenacchi G, De Michele G, Testa F, Nesti A, Simonelli F, Porcelli AM, Torroni A, Carelli V. Peculiar combinations of individually non-pathogenic missense mitochondrial DNA variants cause low penetrance Leber's hereditary optic neuropathy. PLoS Genet 2018; 14:e1007210. [PMID: 29444077 PMCID: PMC5828459 DOI: 10.1371/journal.pgen.1007210] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 02/27/2018] [Accepted: 01/21/2018] [Indexed: 12/23/2022] Open
Abstract
We here report on the existence of Leber’s hereditary optic neuropathy (LHON) associated with peculiar combinations of individually non-pathogenic missense mitochondrial DNA (mtDNA) variants, affecting the MT-ND4, MT-ND4L and MT-ND6 subunit genes of Complex I. The pathogenic potential of these mtDNA haplotypes is supported by multiple evidences: first, the LHON phenotype is strictly inherited along the maternal line in one very large family; second, the combinations of mtDNA variants are unique to the two maternal lineages that are characterized by recurrence of LHON; third, the Complex I-dependent respiratory and oxidative phosphorylation defect is co-transferred from the proband’s fibroblasts into the cybrid cell model. Finally, all but one of these missense mtDNA variants cluster along the same predicted fourth E-channel deputed to proton translocation within the transmembrane domain of Complex I, involving the ND1, ND4L and ND6 subunits. Hence, the definition of the pathogenic role of a specific mtDNA mutation becomes blurrier than ever and only an accurate evaluation of mitogenome sequence variation data from the general population, combined with functional analyses using the cybrid cell model, may lead to final validation. Our study conclusively shows that even in the absence of a clearly established LHON primary mutation, unprecedented combinations of missense mtDNA variants, individually known as polymorphisms, may lead to reduced OXPHOS efficiency sufficient to trigger LHON. In this context, we introduce a new diagnostic perspective that implies the complete sequence analysis of mitogenomes in LHON as mandatory gold standard diagnostic approach. Leber’s hereditary optic neuropathy (LHON) is a common cause of maternally inherited vision loss. In the large majority of cases LHON is due to mitochondrial DNA (mtDNA) point mutations, clearly distinct from common polymorphisms normally found in the general population, affecting the mitochondrial function, thus defined as pathogenic. For the first time, we here demonstrate, on the genetic and functional ground, that unusual combinations of otherwise polymorphic and non-pathogenic mtDNA variants are sufficient for causing low-penetrance maternally inherited optic neuropathy in pedigrees fitting the LHON clinical diagnosis. Our findings bridge the blurry border between “pathogenic” and “neutral” mutations in an overall continuum that truly depends on the specific and sometime unique combination of variants characterizing each mitogenome. As a result, we conclude that, for an accurate diagnosis of LHON and possibly of other mitochondrial diseases, the only approach that can disclose all possible causative sources is complete mitogenome sequencing.
Collapse
Affiliation(s)
- Leonardo Caporali
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Chiara La Morgia
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandra Maresca
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Maria Lucia Valentino
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Francesca Tagliavini
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Valentina Del Dotto
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Claudia Zanna
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Rocco Liguori
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Michele Carbonelli
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Studio Oculistico D’Azeglio, Bologna, Italy
| | - Veronica Cocetta
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Monica Montopoli
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Andrea Martinuzzi
- IRCCS "E. Medea" Scientific Institute Conegliano-Pieve di Soligo Research Center, Pieve di Soligo, Italy
| | - Giovanna Cenacchi
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Giuseppe De Michele
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Anna Nesti
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Anna Maria Porcelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
- Health Sciences & Technologies (HST) CIRI, University of Bologna, Bologna, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Valerio Carelli
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
- * E-mail:
| |
Collapse
|
27
|
Almal S, Jeon S, Agarwal M, Patel S, Patel S, Bhak Y, Jun J, Bhak J, Padh H. Sequencing and analysis of the whole genome of Indian Gujarati male. Genomics 2018; 111:196-204. [PMID: 29432975 DOI: 10.1016/j.ygeno.2018.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/29/2018] [Accepted: 02/08/2018] [Indexed: 11/17/2022]
Abstract
The article presents the analysis of whole genome sequence of a Gujarati Indian individual (IHGP01) that was sequenced at 23.05× coverage with a total of 74.93 Gb of sequence data generated using Illumina HiSeq 2000 platform. Variant analysis revealed over 3.9 million single nucleotide variants (SNVs) and about 393,000 small insertions and deletions (InDels) including novel variants. The known variants were analyzed for their health and disease relevance and pharmacogenomic profile. Mitochondrial and Y-chromosome haplogroup analysis clearly indicated arrival on the continent not more than 20,000-25,000 years ago, following the route out of Africa to central Europe, then into Asian continent and subsequent migration to West part of the Indian subcontinent. The current research has added 141,000 novel genetic variations to the human DNA database. Functional analysis and validation of these novel variations and revelation of their role in health and disease will add a newer dimension to understand people of this subcontinent.
Collapse
Affiliation(s)
- Suhani Almal
- B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Thaltej, Ahmedabad, Gujarat, India
| | - Sungwon Jeon
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Milee Agarwal
- B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Thaltej, Ahmedabad, Gujarat, India
| | - Sweta Patel
- B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Thaltej, Ahmedabad, Gujarat, India
| | - Shivangi Patel
- B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Thaltej, Ahmedabad, Gujarat, India
| | - Youngjune Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - JeHoon Jun
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160, Republic of Korea
| | - Jong Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Personal Genomics Institute, Genome Research Foundation, Cheongju 28160, Republic of Korea; Geromics, Ulsan 44919, Republic of Korea
| | - Harish Padh
- Sardar Patel University, Vallabh Vidyanagar, Gujarat, India.
| |
Collapse
|
28
|
Sharma I, Sharma V, Khan A, Kumar P, Rai E, Bamezai RNK, Vilar M, Sharma S. Ancient Human Migrations to and through Jammu Kashmir- India were not of Males Exclusively. Sci Rep 2018; 8:851. [PMID: 29339819 PMCID: PMC5770440 DOI: 10.1038/s41598-017-18893-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/19/2017] [Indexed: 11/09/2022] Open
Abstract
Jammu and Kashmir (J&K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late-Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.
Collapse
Affiliation(s)
- Indu Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India
| | - Varun Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India
| | - Akbar Khan
- Department of Zoology, University of Jammu, Jammu and Kashmir, 180006, India
| | - Parvinder Kumar
- Department of Zoology, University of Jammu, Jammu and Kashmir, 180006, India
- Institute of Human Genetics, University of Jammu, Jammu and Kashmir, 180006, India
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India
| | | | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, 20036, USA
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India.
| |
Collapse
|
29
|
Comparative analysis of lactic acidosis induced by linezolid and vancomycin therapy using cohort and case-control studies of incidence and associated risk factors. Eur J Clin Pharmacol 2017; 74:405-411. [PMID: 29222713 DOI: 10.1007/s00228-017-2377-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/12/2017] [Indexed: 10/18/2022]
Abstract
PURPOSE Lactic acidosis is a rare complication of linezolid (LZD) therapy, and its incidence and risk factors remain unknown. This study aimed to compare the incidence of LZD-associated lactic acidosis (LALA) and vancomycin (VAN)-associated lactic acidosis (VALA) and investigate the risk factors for LALA. METHODS We performed a retrospective cohort study using propensity score-matched analyses comparing the incidence of lactic acidosis between LZD and VAN therapy. We included adult patients administered LZD or VAN between April 2014 and March 2016 and extracted patient baseline data. In a case-control study, we identified the risk factors of lactic acidosis in patients treated with LZD. RESULTS We identified 94 and 313 patients who were administered LZD and VAN, respectively. The incidence of lactic acidosis after LZD and VAN therapy was 10.6 and 0.3%, respectively. After propensity score-matched analyses, the incidence of lactic acidosis with LZD therapy was significantly higher than that with VAN therapy [10.0% (8/80) vs. 0% (0/80), respectively; risk difference, 0.1; 95% confidence interval (CI), 0.03-0.17; p = 0.004]. In a case-control study, 10 patients with LALA were matched to 20 non-lactic acidosis patients by age and sex. Patients with LALA were more likely to have renal insufficiency than non-lactic acidosis patients that were in the univariate analysis (odds ratio, 7.4; 95% CI, 1.0-84.4; p = 0.02). CONCLUSIONS This study indicates that LALA occurs more frequently than VALA does and is associated with renal insufficiency. Therefore, close monitoring of kidney function and serum lactate is recommended during LZD therapy.
Collapse
|
30
|
Affiliation(s)
- M.K. Bhasin
- Department of Anthropology, University of Delhi, Delhi 110 007, India
| |
Collapse
|
31
|
Affiliation(s)
- M.K. Bhasin
- Department of Anthroplogy, University of Delhi, Delhi 110 007, India
| |
Collapse
|
32
|
Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
Collapse
Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| |
Collapse
|
33
|
Vahia MN, Yadav N, Ladiwala U, Mathur D. A diffusion based study of population dynamics: Prehistoric migrations into South Asia. PLoS One 2017; 12:e0176985. [PMID: 28493906 PMCID: PMC5426639 DOI: 10.1371/journal.pone.0176985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 04/20/2017] [Indexed: 01/04/2023] Open
Abstract
A diffusion equation has been used to study migration of early humans into the South Asian subcontinent. The diffusion equation is tempered by a set of parameters that account for geographical features like proximity to water resources, altitude, and flatness of land. The ensuing diffusion of populations is followed in time-dependent computer simulations carried out over a period of 10,000 YBP. The geographical parameters are determined from readily-available satellite data. The results of our computer simulations are compared to recent genetic data so as to better correlate the migratory patterns of various populations; they suggest that the initial populations started to coalesce around 4,000 YBP before the commencement of a period of relative geographical isolation of each population group. The period during which coalescence of populations occurred appears consistent with the established timeline associated with the Harappan civilization and also, with genetic admixing that recent genetic mapping data reveal. Our results may contribute to providing a timeline for the movement of prehistoric people. Most significantly, our results appear to suggest that the Ancestral Austro-Asiatic population entered the subcontinent through an easterly direction, potentially resolving a hitherto-contentious issue.
Collapse
Affiliation(s)
- Mayank N. Vahia
- Tata Institute of Fundamental Research, Mumbai, India
- * E-mail:
| | - Nisha Yadav
- Tata Institute of Fundamental Research, Mumbai, India
| | - Uma Ladiwala
- Tata Institute of Fundamental Research, Mumbai, India
| | - Deepak Mathur
- Tata Institute of Fundamental Research, Mumbai, India
| |
Collapse
|
34
|
Silva M, Oliveira M, Vieira D, Brandão A, Rito T, Pereira JB, Fraser RM, Hudson B, Gandini F, Edwards C, Pala M, Koch J, Wilson JF, Pereira L, Richards MB, Soares P. A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. BMC Evol Biol 2017; 17:88. [PMID: 28335724 PMCID: PMC5364613 DOI: 10.1186/s12862-017-0936-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND India is a patchwork of tribal and non-tribal populations that speak many different languages from various language families. Indo-European, spoken across northern and central India, and also in Pakistan and Bangladesh, has been frequently connected to the so-called "Indo-Aryan invasions" from Central Asia ~3.5 ka and the establishment of the caste system, but the extent of immigration at this time remains extremely controversial. South India, on the other hand, is dominated by Dravidian languages. India displays a high level of endogamy due to its strict social boundaries, and high genetic drift as a result of long-term isolation which, together with a very complex history, makes the genetic study of Indian populations challenging. RESULTS We have combined a detailed, high-resolution mitogenome analysis with summaries of autosomal data and Y-chromosome lineages to establish a settlement chronology for the Indian Subcontinent. Maternal lineages document the earliest settlement ~55-65 ka (thousand years ago), and major population shifts in the later Pleistocene that explain previous dating discrepancies and neutrality violation. Whilst current genome-wide analyses conflate all dispersals from Southwest and Central Asia, we were able to tease out from the mitogenome data distinct dispersal episodes dating from between the Last Glacial Maximum to the Bronze Age. Moreover, we found an extremely marked sex bias by comparing the different genetic systems. CONCLUSIONS Maternal lineages primarily reflect earlier, pre-Holocene processes, and paternal lineages predominantly episodes within the last 10 ka. In particular, genetic influx from Central Asia in the Bronze Age was strongly male-driven, consistent with the patriarchal, patrilocal and patrilineal social structure attributed to the inferred pastoralist early Indo-European society. This was part of a much wider process of Indo-European expansion, with an ultimate source in the Pontic-Caspian region, which carried closely related Y-chromosome lineages, a smaller fraction of autosomal genome-wide variation and an even smaller fraction of mitogenomes across a vast swathe of Eurasia between 5 and 3.5 ka.
Collapse
Affiliation(s)
- Marina Silva
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Marisa Oliveira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Daniel Vieira
- Department of Informatics, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreia Brandão
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Teresa Rito
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana B Pereira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Ross M Fraser
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, UK.,Synpromics Ltd, Nine Edinburgh Bioquarter, Edinburgh, EH16 4UX, UK
| | - Bob Hudson
- Archaeology Department, University of Sydney, Sydney, NSW, 2006, Australia
| | - Francesca Gandini
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Ceiridwen Edwards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - John Koch
- University of Wales Centre for Advanced Welsh and Celtic Studies, National Library of Wales, Aberystwyth, SY23 3HH, Wales, UK
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, Scotland, UK
| | - Luísa Pereira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
| | - Pedro Soares
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal. .,CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| |
Collapse
|
35
|
Phylogenetic and population-based approaches to mitogenome variation do not support association with male infertility. J Hum Genet 2016; 62:361-371. [PMID: 27904151 DOI: 10.1038/jhg.2016.130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 11/08/2022]
Abstract
Infertility has a complex multifactorial etiology and a high prevalence worldwide. Several studies have pointed to variation in the mitochondrial DNA (mtDNA) molecule as a factor responsible for the different disease phenotypes related to infertility. We analyzed 53 mitogenomes of infertile males from Galicia (northwest Spain), and these haplotypes were meta-analyzed phylogenetically with 43 previously reported from Portugal. Taking advantage of the large amount of information available, we additionally carried out association tests between patient mtDNA single-nucleotide polymorphisms (mtSNPs) and haplogroups against Iberian matched controls retrieved from The 1000 Genomes Project and the literature. Phylogenetic and association analyses did not reveal evidence of association between mtSNPs/haplogroups and infertility. Ratios and patterns in patients of nonsynonymous/synonymous changes, and variation at homoplasmic, heteroplasmic and private variants, fall within expected values for healthy individuals. Moreover, the haplogroup background of patients was variable and fits well with patterns typically observed in healthy western Europeans. We did not find evidence of association of mtSNPs or haplogroups pointing to a role for mtDNA in male infertility. A thorough review of the literature on mtDNA variation and infertility revealed contradictory findings and methodological and theoretical problems that overall undermine previous positive findings.
Collapse
|
36
|
Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM. Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. BMC Evol Biol 2016; 16:246. [PMID: 27832758 PMCID: PMC5105315 DOI: 10.1186/s12862-016-0816-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022] Open
Abstract
Background From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia. Results The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side. Conclusions The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Patricia Marrero
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain.
| |
Collapse
|
37
|
Waldman YY, Biddanda A, Dubrovsky M, Campbell CL, Oddoux C, Friedman E, Atzmon G, Halperin E, Ostrer H, Keinan A. The genetic history of Cochin Jews from India. Hum Genet 2016; 135:1127-43. [PMID: 27377974 PMCID: PMC5020127 DOI: 10.1007/s00439-016-1698-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/12/2016] [Indexed: 12/03/2022]
Abstract
Cochin Jews form a small and unique community on the Malabar coast in southwest India. While the arrival time of any putative Jewish ancestors of the community has been speculated to have taken place as far back as biblical times (King Solomon’s era), a Jewish community in the Malabar coast has been documented only since the 9th century CE. Here, we explore the genetic history of Cochin Jews by collecting and genotyping 21 community members and combining the data with that of 707 individuals from 72 other Indian, Jewish, and Pakistani populations, together with additional individuals from worldwide populations. We applied comprehensive genome-wide analyses based on principal component analysis, FST, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing, allele sharing autocorrelation decay and contrasting the X chromosome with the autosomes. We find that, as reported by several previous studies, the genetics of Cochin Jews resembles that of local Indian populations. However, we also identify considerable Jewish genetic ancestry that is not present in any other Indian or Pakistani populations (with the exception of the Jewish Bene Israel, which we characterized previously). Combined, Cochin Jews have both Jewish and Indian ancestry. Specifically, we detect a significant recent Jewish gene flow into this community 13–22 generations (~470–730 years) ago, with contributions from Yemenite, Sephardi, and Middle-Eastern Jews, in accordance with historical records. Genetic analyses also point to high endogamy and a recent population bottleneck in this population, which might explain the increased prevalence of some recessive diseases in Cochin Jews.
Collapse
Affiliation(s)
- Yedael Y Waldman
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | - Arjun Biddanda
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Maya Dubrovsky
- Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel Hashomer, 52621, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | | | - Carole Oddoux
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Eitan Friedman
- Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel Hashomer, 52621, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Eran Halperin
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
- The Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
- International Computer Science Institute, Berkeley, CA, 94704, USA
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
| |
Collapse
|
38
|
Krzywanski DM, Moellering DR, Westbrook DG, Dunham-Snary KJ, Brown J, Bray AW, Feeley KP, Sammy MJ, Smith MR, Schurr TG, Vita JA, Ambalavanan N, Calhoun D, Dell'Italia L, Ballinger SW. Endothelial Cell Bioenergetics and Mitochondrial DNA Damage Differ in Humans Having African or West Eurasian Maternal Ancestry. ACTA ACUST UNITED AC 2016; 9:26-36. [PMID: 26787433 DOI: 10.1161/circgenetics.115.001308] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 01/13/2016] [Indexed: 01/09/2023]
Abstract
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.
Collapse
Affiliation(s)
- David M Krzywanski
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Douglas R Moellering
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - David G Westbrook
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Kimberly J Dunham-Snary
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Jamelle Brown
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Alexander W Bray
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Kyle P Feeley
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Melissa J Sammy
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Matthew R Smith
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Theodore G Schurr
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Joseph A Vita
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Namasivayam Ambalavanan
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - David Calhoun
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Louis Dell'Italia
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Scott W Ballinger
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.).
| |
Collapse
|
39
|
Chaitanya L, Ralf A, van Oven M, Kupiec T, Chang J, Lagacé R, Kayser M. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine. Hum Mutat 2015; 36:1236-47. [PMID: 26387877 PMCID: PMC5057296 DOI: 10.1002/humu.22905] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/01/2015] [Indexed: 11/13/2022]
Abstract
Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications.
Collapse
Affiliation(s)
- Lakshmi Chaitanya
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Arwin Ralf
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Mannis van Oven
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Tomasz Kupiec
- Institute of Forensic ResearchSection of Forensic GeneticsKrakówPoland
| | - Joseph Chang
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Robert Lagacé
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| |
Collapse
|
40
|
Negi N, Tamang R, Pande V, Sharma A, Shah A, Reddy AG, Vishnupriya S, Singh L, Chaubey G, Thangaraj K. The paternal ancestry of Uttarakhand does not imitate the classical caste system of India. J Hum Genet 2015; 61:167-72. [PMID: 26511066 DOI: 10.1038/jhg.2015.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/03/2015] [Accepted: 09/11/2015] [Indexed: 01/17/2023]
Abstract
Although, there have been rigorous research on the Indian caste system by several disciplines, it is still one of the most controversial socioscientific topic. Previous genetic studies on the subcontinent have supported a classical hierarchal sharing of genetic component by various castes of India. In the present study, we have used high-resolution mtDNA and Y chromosomal markers to characterize the genetic structuring of the Uttarakhand populations in the context of neighboring regions. Furthermore, we have tested whether the genetic structuring of caste populations at different social levels of this region, follow the classical chaturvarna system. Interestingly, we found that this region showed a high level of variation for East Eurasian ancestry in both maternal and paternal lines of descent. Moreover, the intrapopulation comparison showed a high level of heterogeneity, likely because of different caste hierarchy, interpolated on asymmetric admixture of populations inhabiting on both sides of the Himalayas.
Collapse
Affiliation(s)
- Neetu Negi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Rakesh Tamang
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Biocentre, Tartu, Estonia.,Department of Zoology, University of Calcutta, Kolkata, India.,Department of Genetics, Osmania University, Hyderabad, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Amrita Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Anish Shah
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alla G Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Genome Foundation, Hyderabad, India
| | | | | |
Collapse
|
41
|
Abstract
CONTEXT India is considered a treasure for geneticists and evolutionary biologists due to its vast human diversity, consisting of more than 4500 anthropologically well-defined populations (castes, tribes and religious groups). Each population differs in terms of endogamy, language, culture, physical features, geographic and climatic position and genetic architecture. These factors contributed to India-specific genetic variations which may be responsible for various common diseases in India and its migratory populations. As a result, interpretations of the origins and affinities of Indian populations as well as health and disease conditions require complex and sophisticated genetic analysis. Evidence of ancient human dispersals and settlements is preserved in the genome of Indian inhabitants and this has been extensively analysed in conventional and genomic analyses. OBJECTIVE AND METHODS Using genomic analyses of STRs and Alu on a set of populations, this study estimates the level and extent of genetic variation and its implications. RESULTS The results show that Indian populations have a higher level of unique genetic diversity which is structured by many social processes and geographical attributes of the country. CONCLUSION This overview highlights the need to study the anthropological structure and evolutionary history of Indian populations while designing genomic and epigenomic investigations.
Collapse
Affiliation(s)
- Sarabjit S Mastana
- Human Genomics Lab, Centre for Global Health and Human Development, School of Sport, Exercise and Health Sciences, Loughborough University , Loughborough , UK
| |
Collapse
|
42
|
Wu Z, Zhang H, Jin W, Liu Y, Lu L, Chen Q, Zhang R. The Effect of Renin-Angiotensin-Aldosterone System Blockade Medications on Contrast-Induced Nephropathy in Patients Undergoing Coronary Angiography: A Meta-Analysis. PLoS One 2015; 10:e0129747. [PMID: 26083525 PMCID: PMC4470628 DOI: 10.1371/journal.pone.0129747] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 05/12/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Contrast-induced nephropathy (CIN) is the main complication of contrast media administration (CM) in patients undergoing coronary angiography (CAG) and percutaneous coronary intervention (PCI). There are inconsistent results in the literature regarding the effect of renin-angiotensin-aldosterone system (RAAS) blockers (angiotensin-converting enzyme inhibitors [ACEIs] and angiotensin receptor blockers [ARBs]) on CIN. We evaluated the association between the administration of ACEI/ARBs and CIN, as well as the effect of ACEI/ARBs on post-procedural changes in renal function index, in patients undergoing CAG. METHODS We searched Pubmed, EMBASE, Cochrane Central Register of Controlled Trials and ClinicalTrials.gov for relevant studies. The primary search generated 893 potentially relevant articles. A total of 879 studies were excluded because they did not meet the selection criteria. Finally, 14 studies were eligible for inclusion. There were 7,288 patients that received ACEI/ARBs and 8,159 patients that received placebo or naive to ACEI/ARBs in the study. A random or a fixed effect model was used to calculate the pooled odd ratios (ORs). RESULTS The risk of CIN was significantly increased in the ACEI/ARBs group compared to the control group (OR= 1.50, 95%CI: 1.03-2.18, P =0.03). The magnitude of association was significantly reinforced in the observational studies (OR=1.84, 95%CI 1.19-2.85, P=0.006) but not in the randomized controlled trials (OR=0.88, 95%CI 0.41-1.90 P=0.74). The summary adjusted OR of 4 observational studies was 1.56 (95%CI 1.25-1.94, P<0.0001) and was weaker than the unadjusted OR. CONCLUSIONS Although there is some evidence to suggest that the administration of RAAS blockers was associated with the increased risk of CIN in patients undergoing CAG, the robustness of our study remains weak. The results are based on small observational studies and need further validation.
Collapse
Affiliation(s)
- Zhijun Wu
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Huan Zhang
- Division of Nephrology, Changhai Hospital, Second Military Medical University, Shanghai, People’s Republic of China
| | - Wei Jin
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Yan Liu
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Lin Lu
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Qiujing Chen
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Ruiyan Zhang
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| |
Collapse
|
43
|
Fregel R, Cabrera V, Larruga JM, Abu-Amero KK, González AM. Carriers of Mitochondrial DNA Macrohaplogroup N Lineages Reached Australia around 50,000 Years Ago following a Northern Asian Route. PLoS One 2015; 10:e0129839. [PMID: 26053380 PMCID: PMC4460043 DOI: 10.1371/journal.pone.0129839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 05/13/2015] [Indexed: 01/17/2023] Open
Abstract
Background The modern human colonization of Eurasia and Australia is mostly explained by a single-out-of-Africa exit following a southern coastal route throughout Arabia and India. However, dispersal across the Levant would better explain the introgression with Neanderthals, and more than one exit would fit better with the different ancient genomic components discovered in indigenous Australians and in ancient Europeans. The existence of an additional Northern route used by modern humans to reach Australia was previously deduced from the phylogeography of mtDNA macrohaplogroup N. Here, we present new mtDNA data and new multidisciplinary information that add more support to this northern route. Methods MtDNA hypervariable segments and haplogroup diagnostic coding positions were analyzed in 2,278 Saudi Arabs, from which 1,725 are new samples. Besides, we used 623 published mtDNA genomes belonging to macrohaplogroup N, but not R, to build updated phylogenetic trees to calculate their coalescence ages, and more than 70,000 partial mtDNA sequences were screened to establish their respective geographic ranges. Results The Saudi mtDNA profile confirms the absence of autochthonous mtDNA lineages in Arabia with coalescence ages deep enough to support population continuity in the region since the out-of-Africa episode. In contrast to Australia, where N(xR) haplogroups are found in high frequency and with deep coalescence ages, there are not autochthonous N(xR) lineages in India nor N(xR) branches with coalescence ages as deep as those found in Australia. These patterns are at odds with the supposition that Australian colonizers harboring N(xR) lineages used a route involving India as a stage. The most ancient N(xR) lineages in Eurasia are found in China, and inconsistently with the coastal route, N(xR) haplogroups with the southernmost geographical range have all more recent radiations than the Australians. Conclusions Apart from a single migration event via a southern route, phylogeny and phylogeography of N(xR) lineages support that people carrying mtDNA N lineages could have reach Australia following a northern route through Asia. Data from other disciplines also support this scenario.
Collapse
Affiliation(s)
- Rosa Fregel
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
- * E-mail:
| | - Vicente Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Jose M. Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Khaled K. Abu-Amero
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ana M. González
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| |
Collapse
|
44
|
Aggarwal S, Phadke SR. Medical genetics and genomic medicine in India: current status and opportunities ahead. Mol Genet Genomic Med 2015; 3:160-71. [PMID: 26029702 PMCID: PMC4444157 DOI: 10.1002/mgg3.150] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences Hyderabad, India ; Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics Hyderabad, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India
| |
Collapse
|
45
|
ArunKumar G, Tatarinova TV, Duty J, Rollo D, Syama A, Arun VS, Kavitha VJ, Triska P, Greenspan B, Wells RS, Pitchappan R. Genome-wide signatures of male-mediated migration shaping the Indian gene pool. J Hum Genet 2015; 60:493-9. [DOI: 10.1038/jhg.2015.51] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 04/13/2015] [Accepted: 04/17/2015] [Indexed: 02/02/2023]
|
46
|
Palanichamy MG, Mitra B, Zhang CL, Debnath M, Li GM, Wang HW, Agrawal S, Chaudhuri TK, Zhang YP. West Eurasian mtDNA lineages in India: an insight into the spread of the Dravidian language and the origins of the caste system. Hum Genet 2015; 134:637-47. [PMID: 25832481 DOI: 10.1007/s00439-015-1547-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/25/2015] [Indexed: 11/28/2022]
Abstract
There is no indication from the previous mtDNA studies that west Eurasian-specific subclades have evolved within India and played a role in the spread of languages and the origins of the caste system. To address these issues, we have screened 14,198 individuals (4208 from this study) and analyzed 112 mitogenomes (41 new sequences) to trace west Eurasian maternal ancestry. This has led to the identification of two autochthonous subhaplogroups--HV14a1 and U1a1a4, which are likely to have originated in the Dravidian-speaking populations approximately 10.5-17.9 thousand years ago (kya). The carriers of these maternal lineages might have settled in South India during the time of the spread of the Dravidian language. In addition to this, we have identified several subsets of autochthonous U7 lineages, including U7a1, U7a2b, U7a3, U7a6, U7a7, and U7c, which seem to have originated particularly in the higher-ranked caste populations in relatively recent times (2.6-8.0 kya with an average of 5.7 kya). These lineages have provided crucial clues to the differentiation of the caste system that has occurred during the recent past and possibly, this might have been influenced by the Indo-Aryan migration. The remaining west Eurasian lineages observed in the higher-ranked caste groups, like the Brahmins, were found to cluster with populations who possibly arrived from west Asia during more recent times.
Collapse
Affiliation(s)
- Malliya Gounder Palanichamy
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, 650 091, Yunnan, China,
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Li YC, Wang HW, Tian JY, Liu LN, Yang LQ, Zhu CL, Wu SF, Kong QP, Zhang YP. Ancient inland human dispersals from Myanmar into interior East Asia since the Late Pleistocene. Sci Rep 2015; 5:9473. [PMID: 25826227 PMCID: PMC4379912 DOI: 10.1038/srep09473] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/27/2015] [Indexed: 01/08/2023] Open
Abstract
Given the existence of plenty of river valleys connecting Southeast and East Asia, it is possible that some inland route(s) might have been adopted by the initial settlers to migrate into the interior of East Asia. Here we analyzed mitochondrial DNA (mtDNA) HVS variants of 845 newly collected individuals from 14 Myanmar populations and 5,907 published individuals from 115 populations from Myanmar and its surroundings. Enrichment of basal lineages with the highest genetic diversity in Myanmar suggests that Myanmar was likely one of the differentiation centers of the early modern humans. Intriguingly, some haplogroups were shared merely between Myanmar and southwestern China, hinting certain genetic connection between both regions. Further analyses revealed that such connection was in fact attributed to both recent gene flow and certain ancient dispersals from Myanmar to southwestern China during 25-10 kya, suggesting that, besides the coastal route, the early modern humans also adopted an inland dispersal route to populate the interior of East Asia.
Collapse
Affiliation(s)
- Yu-Chun Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua-Wei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Jiao-Yang Tian
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Na Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Chun-Ling Zhu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| |
Collapse
|
48
|
Kundu S, Ghosh SK. Trend of different molecular markers in the last decades for studying human migrations. Gene 2014; 556:81-90. [PMID: 25510397 DOI: 10.1016/j.gene.2014.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 12/07/2014] [Accepted: 12/11/2014] [Indexed: 12/15/2022]
Abstract
Anatomically modern humans are known to have widely migrated throughout history. Different scientific evidences suggest that the entire human population descended from just several thousand African migrants. About 85,000 years ago, the first wave of human migration was out of Africa, that followed the coasts through the Middle East, into Southern Asia via Sri Lanka, and in due course around Indonesia and into Australia. Another wave of migration between 40,000 and 12,000 years ago brought humans northward into Europe. However, the frozen north limited human expansion in Europe, and created a land bridge, "Bering land bridge", connecting Asia with North America about 25,000 years ago. Although fossil data give the most direct information about our past, it has certain anomalies. So, molecular archeologists are now using different molecular markers to trace the "most recent common ancestor" and also the migration pattern of modern humans. In this study, we have studied the trend of molecular markers and also the methodologies implemented in the last decades (2003-2014). From our observation, we can say that D-loop region of mtDNA and Y chromosome based markers are predominant. Nevertheless, mtDNA, especially the D-loop region, has some unique features, which makes it a more effective marker for tracing prehistoric footprints of modern human populations. Although, natural selection should also be taken into account in studying mtDNA based human migration. As per technology is concerned, Sanger sequencing is the major technique that is being used in almost all studies. But, the emergence of different cost-effective-and-easy-to-handle NGS platforms has increased its popularity over Sanger sequencing in studying human migration.
Collapse
Affiliation(s)
- Sharbadeb Kundu
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Pin-788011 Assam, India
| | - Sankar Kumar Ghosh
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Pin-788011 Assam, India.
| |
Collapse
|
49
|
Wang HW, Xu Y, Miao YL, Luo HY, Wang KH. Mitochondrial DNA Haplogroup A may confer a genetic susceptibility to AIDS group from Southwest China. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2221-4. [PMID: 25431816 DOI: 10.3109/19401736.2014.982630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
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.
Collapse
Affiliation(s)
- Hua-Wei Wang
- a Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University , Yunnan Province , China
| | - Yu Xu
- a Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University , Yunnan Province , China
| | - Ying-Lei Miao
- a Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University , Yunnan Province , China
| | - Hua-You Luo
- a Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University , Yunnan Province , China
| | - Kun-Hua Wang
- a Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University , Yunnan Province , China
| |
Collapse
|
50
|
Ovchinnikov IV, Malek MJ, Drees K, Kholina OI. Mitochondrial DNA variation in Tajiks living in Tajikistan. Leg Med (Tokyo) 2014; 16:390-5. [DOI: 10.1016/j.legalmed.2014.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 07/31/2014] [Accepted: 07/31/2014] [Indexed: 11/27/2022]
|