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Inoue M, Sato Y. An update and frequency distribution of Y chromosome haplogroups in modern Japanese males. J Hum Genet 2024; 69:107-114. [PMID: 38123667 DOI: 10.1038/s10038-023-01214-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
Japanese males belong to the Y chromosome C1a1, C2, D1a2a, D1a2a-12f2b, O1b2, O1b2a1a1, O2a2b1, and O2a1b haplogroups. Notably, the regional frequency of each haplogroup is homogeneous. Owing to recent developments in genome sequencing technology, the phylogenetic tree of Y chromosome haplogroups is updated annually. Therefore, in this study, we aimed to provide an update on the Y chromosome haplogroups of modern Japanese males and examine their regional distributions. Using 1,640 samples of Japanese males from seven Japanese cities (Nagasaki, Fukuoka, Tokushima, Osaka, Kanazawa, Kawasaki, and Sapporo), haplogroups C1a1, C2, D1a2a, D1a2a-12f2b, O1b2, and O1b2a1a1 were updated based on the latest phylogenetic tree. Haplogroup C1a1 was mainly classified into C1a1a1a and C1a1a1b subgroups; C1a1a1b was more common in Tokushima and Osaka than in the other regions. Haplogroup C2 was mainly classified into C2a, C2b1a1a, C2b1a1b, C2b1a2, and C2b1b subgroups and exhibited frequency differences in Osaka. Haplogroup D1a2a was classified into D1a2a1c1 and D1a2a2 subgroups, and its frequency varied between Tokushima and Osaka. Haplogroup D1a2a-12f2b was classified into D1a2a1a2b1a1a and D1a2a1a3 subgroups; however, no significant frequency differences were observed. Haplogroup O1b2 was classified into O1b2a1a2a1a, O1b2a1a2a1b, and O1b2a1a3 subgroups, with frequency differences between Nagasaki and Kanazawa. Haplogroup O1b2a1a1 was mainly classified into O1b2a1a1a, O1b2a1a1b, and O1b2a1a1c subgroups; however, no significant frequency differences were observed. Our findings suggest that gene flow in the Kinki region is caused by human migration.
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Affiliation(s)
- Makoto Inoue
- Department of Pharmaceutical Information Science, Tokushima University Graduate School of Biomedical Sciences, Tokushima, 770-8505, Japan
| | - Youichi Sato
- Department of Pharmaceutical Information Science, Tokushima University Graduate School of Biomedical Sciences, Tokushima, 770-8505, Japan.
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2
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Srigyan M, Bolívar H, Ureña I, Santana J, Petersen A, Iriarte E, Kırdök E, Bergfeldt N, Mora A, Jakobsson M, Abdo K, Braemer F, Smith C, Ibañez JJ, Götherström A, Günther T, Valdiosera C. Bioarchaeological evidence of one of the earliest Islamic burials in the Levant. Commun Biol 2022; 5:554. [PMID: 35672445 PMCID: PMC9174286 DOI: 10.1038/s42003-022-03508-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/20/2022] [Indexed: 11/27/2022] Open
Abstract
The Middle East plays a central role in human history harbouring a vast diversity of ethnic, cultural and religious groups. However, much remains to be understood about past and present genomic diversity in this region. Here we present a multidisciplinary bioarchaeological analysis of two individuals dated to the late 7th and early 8th centuries, the Umayyad Era, from Tell Qarassa, an open-air site in modern-day Syria. Radiocarbon dates and burial type are consistent with one of the earliest Islamic Arab burials in the Levant. Interestingly, we found genomic similarity to a genotyped group of modern-day Bedouins and Saudi rather than to most neighbouring Levantine groups. This study represents the genomic analysis of a secondary use site with characteristics consistent with an early Islamic burial in the Levant. We discuss our findings and possible historic scenarios in the light of forces such as genetic drift and their possible interaction with religious and cultural processes (including diet and subsistence practices). Ancient genomic and archaeological data combine to identify a surprisingly early Islamic burial in modern day Syria.
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Affiliation(s)
- Megha Srigyan
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Héctor Bolívar
- Centre for Palaeogenetics, 10691, Stockholm, Sweden.,Instituto del Patrimonio Cultural de España, 28040, Madrid, Spain
| | - Irene Ureña
- Centre for Palaeogenetics, 10691, Stockholm, Sweden
| | - Jonathan Santana
- Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de G.C., E35001, Spain
| | | | - Eneko Iriarte
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001, Burgos, Spain
| | - Emrah Kırdök
- Department of Biotechnology, Mersin University, 33343, Mersin, Turkey
| | | | - Alice Mora
- Dept. Archaeology and History, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Khaled Abdo
- General Directorate of Antiquities and Museums, Damascus, Syrian Arab Republic
| | - Frank Braemer
- Université Côte d'Azur, CNRS, Culture et Environment, Préhistoire Antiquité Moyen Age, Nice, France
| | - Colin Smith
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001, Burgos, Spain.,Dept. Archaeology and History, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Juan José Ibañez
- Archaeology of Social Dynamics, Milà i Fontanals Institution, Spanish National Research Council (CSIC), Barcelona, Spain
| | | | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
| | - Cristina Valdiosera
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001, Burgos, Spain. .,Dept. Archaeology and History, La Trobe University, Melbourne, VIC, 3086, Australia.
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3
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The impact of prehistoric human dispersals on the presence of tobacco-related oral cancer in Northeast India. Gene 2021; 813:146098. [PMID: 34952175 DOI: 10.1016/j.gene.2021.146098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Northeast (NE) India is a subject of debate for predicting its involvement in prehistoric anatomically modern human (AMH) dispersal. The unique lifestyle and genetic characteristics of native ethnic groups in this region are believed to be responsible for their susceptibility to tobacco-related oral cancer (TrOC). The present study assessed mitochondrial macro-haplogroup (mHG) diversity and TrOC susceptibility autosomal loci to evaluate the impact of prehistoric AMH dispersal on the present day's high TrOC prevalence in major NE Indian ethnics. METHODS We considered 175 unrelated individuals from 35 ethnic groups and previously published 374 sequences for sequencing-based assessment of mtDNA-based marker by subsequent analyses like haplogroup diversity, phylogenetic, genetic structure by AMOVA, and MDS, descriptive statistics of demographic parameters, and migration analysis. Besides, we selected prolonged tobacco-chewing 124 case-control individuals from similar ethnic backgrounds for genotyping 115 autosomal loci in Sequenom iPLEX MassARRAY™ platform and mined 1000genome data (n = 398) for consequent global admixture and ancestry-specific allele frequencies-based analyses. RESULTS Our mtDNA-based findings suggested that NE populations were distinct from other Indian populations, owing to the first wave of migration from ancient southern China (∼54kya) and two successive spatial expansion events at ∼45kya and ∼43kya. Consequently, it probably acted as another source for prehistoric AMH dispersal in N/NE Asia. Besides, the second wave of back-migration from SE Asia (∼40kya) probably replaced the mitochondrial footprints of survivors from the first migrants and introduced the TrOC susceptibility traits in this region. Afterward, the autosomal marker-based observations on the transition of the disease-associated admixture component 'K6' from SE Asia reconfirmed these results. Moreover, we also observed that the mitochondrial mHG 'R' is significantly associated with the risk of TrOC (OR > 9.5) in NE India. Furthermore, the possible onset of the phenotypic expression of those traits was predicted at ∼4kya, thus, contributing to present-day's TrOC prevalence. CONCLUSIONS This study reflects its uniqueness by revealing an updated AMH dispersal route for the peopling in and out of NE India, which probably introduced the disease-causing traits in the ancestral NE Indian population. Those traits were then imprinted in their genome to get transferred through their respective generations, forming the present-day's TrOC-prevalent NE Indian population.
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Bose A, Platt DE, Parida L, Drineas P, Paschou P. Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India. Mol Biol Evol 2021; 38:1809-1819. [PMID: 33481022 PMCID: PMC8097304 DOI: 10.1093/molbev/msaa321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a data set of 891 individuals from 90 well-defined groups. Bringing together geography, genetics, and demographic factors, we developed Correlation Optimization of Genetics and Geodemographics to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure using a ridge leverage score statistic. Integrating data from India with a data set of additional 1,323 individuals from 50 Eurasian populations, we find that Indo-European and Dravidian speakers of India show shared genetic drift with Europeans, whereas the Tibeto-Burman speaking tribal groups have maximum shared genetic drift with East Asians.
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Affiliation(s)
- Aritra Bose
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Daniel E Platt
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Laxmi Parida
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Petros Drineas
- Computer Science Department, Purdue University, West Lafayette, IN, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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5
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Mehta P, Singh P, Gupta NJ, Sankhwar SN, Chakravarty B, Thangaraj K, Rajender S. Mutations in the desert hedgehog (DHH) gene in the disorders of sexual differentiation and male infertility. J Assist Reprod Genet 2021; 38:1871-1878. [PMID: 33712994 DOI: 10.1007/s10815-021-02140-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/02/2021] [Indexed: 11/25/2022] Open
Abstract
PURPOSE To identify the contribution of mutations in the Desert Hedgehog (DHH) gene to the disorders of sexual differentiation (DSD) and male infertility. METHODS The study included a total 430 subjects, including 47 gonadal dysgenesis cases, 6 patients with undescended testis and infertility characterized by azoospermia, 125 infertile male patients characterized by oligoasthenozoospermia, 24 patients with oligoasthenoteratozoospermia, and 200 ethnically matched normozoospermic fertile men who had fathered a child in the last two years. Sequencing of the complete coding region of the DHH gene was undertaken to find its contribution to the DSD and male infertility. RESULTS We observed four novel mutations in the DHH gene in the cases with different reproductive anomalies. A synonymous substitution, c. 543C>T (p.His181His) was observed in 6.6% oligoasthenozoospermic infertile males and 1.5% normozoospermic fertile control samples (RR = 4.4077, 95%CI 1.19-16.29). Another synonymous substitution, c.990G>A (p.Ala330Ala) was observed in an infertile patient with unilateral undescended testis (case #12). Insertion of G at c.1156insG (p.Arg385fs) was observed in a case with bilateral undescended testis and azoospermia (case #23). In gonadal dysgenesis category, two mutations, insertion of G at c.1156insG (p.Arg385fs) and c.997A>G (p.Thr333Ala) substitution were observed in one case (case #34). These mutations were completely absent in control samples. CONCLUSION Mutations in the DHH gene impact reproduction with mild mutations affecting fertility, and severe or multiple mutations resulting in gonadal dysgenesis.
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Affiliation(s)
- Poonam Mehta
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, India
| | | | | | | | | | - Kumarasamy Thangaraj
- Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, India
- Centre for Cellular and Molecular Biology, Hyderabad, India
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Singh Rajender
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India.
- Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, India.
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6
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Tripathi P, Singh R, Raghav A, Sankhwar SN, Bansal SK, Negi MPS, Gautam KA. TNF-α gene polymorphisms and risk of urinary bladder cancer – A case-control study and meta-analysis. Meta Gene 2021. [DOI: 10.1016/j.mgene.2020.100848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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7
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OSADA NAOKI, KAWAI YOSUKE. Exploring models of human migration to the Japanese archipelago using genome-wide genetic data. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.201215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- NAOKI OSADA
- Faculty of Information Science and Technology, Hokkaido University, Sapporo
| | - YOSUKE KAWAI
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo
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8
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Mohan AV, Orozco-terWengel P, Shanker K, Vences M. The Andaman day gecko paradox: an ancient endemic without pronounced phylogeographic structure. Sci Rep 2020; 10:11745. [PMID: 32678130 PMCID: PMC7367275 DOI: 10.1038/s41598-020-68402-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 06/15/2020] [Indexed: 11/20/2022] Open
Abstract
The Andaman day gecko (Phelsuma andamanensis) is endemic to the Andaman Archipelago, located ~ 6000 km away from Madagascar where the genus Phelsuma likely evolved. We complemented existing phylogenetic data with additional markers to show that this species consistently branches off early in the evolution of the genus Phelsuma, and this early origin led us to hypothesize that island populations within the Andaman Archipelago could have further diversified. We sampled the Andaman day gecko from all major islands in the Andamans, developed new microsatellite markers and amplified mitochondrial markers to study population diversification. We detected high allelic diversity in microsatellites, but surprisingly poor geographical structuring. This study demonstrates that the Andaman day gecko has a panmictic population (K = 1), but with weak signals for two clusters that we name ‘North’ (North Andaman, Middle Andaman, Interview, Baratang, Neil, and Long Islands) and ‘South’ (Havelock, South Andaman, Little Andaman Islands). The mitochondrial COI gene uncovered wide haplotype sharing across islands with the presence of several private haplotypes (except for the Little Andaman Island, which only had an exclusive private haplotype) signalling ongoing admixture. This species differs from two other Andaman endemic geckos for which we provide comparative mitochondrial data, where haplotypes show a distinct phylogeographic structure. Testing population history scenarios for the Andaman day gecko using Approximate Bayesian Computation (ABC) supports two possible scenarios but fails to tease apart whether admixture or divergence produced the two weak clusters. Both scenarios agree that admixture and/or divergence prior to the onset of the last glacial maximum shaped the genetic diversity and structure detected in this study. ABC supports population expansion, possibly explained by anthropogenic food subsidies via plantations of cash crops, potentially coupled with human mediated dispersal resulting in the observed panmictic population. The Andaman day gecko may thus be a rare example of an island endemic reptile benefiting from habitat modification and increased movement in its native range.
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Affiliation(s)
- Ashwini V Mohan
- Department of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, 38106, Braunschweig, Germany. .,Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India.
| | | | - Kartik Shanker
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, 38106, Braunschweig, Germany
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9
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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.
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10
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KANZAWA-KIRIYAMA HIDEAKI, JINAM TIMOTHYA, KAWAI YOSUKE, SATO TAKEHIRO, HOSOMICHI KAZUYOSHI, TAJIMA ATSUSHI, ADACHI NOBORU, MATSUMURA HIROFUMI, KRYUKOV KIRILL, SAITOU NARUYA, SHINODA KENICHI. Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan. ANTHROPOL SCI 2019. [DOI: 10.1537/ase.190415] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
| | - TIMOTHY A. JINAM
- Division of Population Genetics, National Institute of Genetics, Mishima
| | - YOSUKE KAWAI
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo
| | - TAKEHIRO SATO
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
| | - KAZUYOSHI HOSOMICHI
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
| | - ATSUSHI TAJIMA
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
| | - NOBORU ADACHI
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo
| | - HIROFUMI MATSUMURA
- Second Division of Physical Therapy, School of Health Sciences, Sapporo Medical University, Sapporo
| | - KIRILL KRYUKOV
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara
| | - NARUYA SAITOU
- Division of Population Genetics, National Institute of Genetics, Mishima
| | - KEN-ICHI SHINODA
- Department of Anthropology, National Museum of Nature and Science, Tsukuba
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11
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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.
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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
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12
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Gupta N, Sudhakar DVS, Gangwar PK, Sankhwar SN, Gupta NJ, Chakraborty B, Thangaraj K, Gupta G, Rajender S. Mutations in the prostate specific antigen (PSA/KLK3) correlate with male infertility. Sci Rep 2017; 7:11225. [PMID: 28894123 PMCID: PMC5593825 DOI: 10.1038/s41598-017-10866-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/12/2017] [Indexed: 12/20/2022] Open
Abstract
Prostate specific antigen (PSA/KLK3) is known to be the chief executor of the fragmentation of semenogelins, dissolution of semen coagulum, thereby releasing sperm for active motility. Recent research has found that semenogelins also play significant roles in sperm fertility by affecting hyaluronidase activity, capacitation and motility, thereby making PSA important for sperm fertility beyond simple semen liquefaction. PSA level in semen has been shown to correlate with sperm motility, suggesting that PSA level/activity can affect fertility. However, no study investigating the genetic variations in the KLK3/PSA gene in male fertility has been undertaken. We analyzed the complete coding region of the KLK3 gene in ethnically matched 875 infertile and 290 fertile men to find if genetic variations in KLK3 correlate with infertility. Interestingly, this study identified 28 substitutions, of which 8 were novel (not available in public databases). Statistical comparison of the genotype frequencies showed that five SNPs, rs266881 (OR = 2.92, P < 0.0001), rs174776 (OR = 1.91, P < 0.0001), rs266875 (OR = 1.44, P = 0.016), rs35192866 (OR = 4.48, P = 0.025) and rs1810020 (OR = 2.08, P = 0.034) correlated with an increased risk of infertility. On the other hand, c.206 + 235 T > C, was more freuqent in the control group, showing protective association. Our findings suggest that polymorphisms in the KLK3 gene correlate with infertility risk.
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Affiliation(s)
- Nishi Gupta
- Central Drug Research Institute, Lucknow, India
| | | | | | | | | | | | | | - Gopal Gupta
- Central Drug Research Institute, Lucknow, India
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13
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Mondal M, Bergström A, Xue Y, Calafell F, Laayouni H, Casals F, Majumder PP, Tyler-Smith C, Bertranpetit J. Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. Hum Genet 2017; 136:499-510. [PMID: 28444560 DOI: 10.1007/s00439-017-1800-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/10/2017] [Indexed: 01/25/2023]
Abstract
We present 42 new Y-chromosomal sequences from diverse Indian tribal and non-tribal populations, including the Jarawa and Onge from the Andaman Islands, which are analysed within a calibrated Y-chromosomal phylogeny incorporating South Asian (in total 305 individuals) and worldwide (in total 1286 individuals) data from the 1000 Genomes Project. In contrast to the more ancient ancestry in the South than in the North that has been claimed, we detected very similar coalescence times within Northern and Southern non-tribal Indian populations. A closest neighbour analysis in the phylogeny showed that Indian populations have an affinity towards Southern European populations and that the time of divergence from these populations substantially predated the Indo-European migration into India, probably reflecting ancient shared ancestry rather than the Indo-European migration, which had little effect on Indian male lineages. Among the tribal populations, the Birhor (Austro-Asiatic-speaking) and Irula (Dravidian-speaking) are the nearest neighbours of South Asian non-tribal populations, with a common origin in the last few millennia. In contrast, the Riang (Tibeto-Burman-speaking) and Andamanese have their nearest neighbour lineages in East Asia. The Jarawa and Onge shared haplogroup D lineages with each other within the last ~7000 years, but had diverged from Japanese haplogroup D Y-chromosomes ~53000 years ago, most likely by a split from a shared ancestral population. This analysis suggests that Indian populations have complex ancestry which cannot be explained by a single expansion model.
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Affiliation(s)
- Mayukh Mondal
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
| | - Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | | | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK.
| | - Jaume Bertranpetit
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain.
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Duda P, Jan Zrzavý. Human population history revealed by a supertree approach. Sci Rep 2016; 6:29890. [PMID: 27431856 PMCID: PMC4949479 DOI: 10.1038/srep29890] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/23/2016] [Indexed: 01/01/2023] Open
Abstract
Over the past two decades numerous new trees of modern human populations have been published extensively but little attention has been paid to formal phylogenetic synthesis. We utilized the "matrix representation with parsimony" (MRP) method to infer a composite phylogeny (supertree) of modern human populations, based on 257 genetic/genomic, as well as linguistic, phylogenetic trees and 44 admixture plots from 200 published studies (1990-2014). The resulting supertree topology includes the most basal position of S African Khoisan followed by C African Pygmies, and the paraphyletic section of all other sub-Saharan peoples. The sub-Saharan African section is basal to the monophyletic clade consisting of the N African-W Eurasian assemblage and the consistently monophyletic Eastern superclade (Sahul-Oceanian, E Asian, and Beringian-American peoples). This topology, dominated by genetic data, is well-resolved and robust to parameter set changes, with a few unstable areas (e.g., West Eurasia, Sahul-Melanesia) reflecting the existing phylogenetic controversies. A few populations were identified as highly unstable "wildcard taxa" (e.g. Andamanese, Malagasy). The linguistic classification fits rather poorly on the supertree topology, supporting a view that direct coevolution between genes and languages is far from universal.
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Affiliation(s)
- Pavel Duda
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Center for Theoretical Study, Charles University and Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Zrzavý
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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Anwesh M, Kumar KV, Nagarajan M, Chander MP, Kartick C, Paluru V. Elucidating the richness of bacterial groups in the gut of Nicobarese tribal community – Perspective on their lifestyle transition. Anaerobe 2016; 39:68-76. [DOI: 10.1016/j.anaerobe.2016.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 02/22/2016] [Accepted: 03/01/2016] [Indexed: 12/21/2022]
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16
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Carlus SJ, Sarkar S, Bansal SK, Singh V, Singh K, Jha RK, Sadasivam N, Sadasivam SR, Gireesha PS, Thangaraj K, Rajender S. Is MTHFR 677 C>T Polymorphism Clinically Important in Polycystic Ovarian Syndrome (PCOS)? A Case-Control Study, Meta-Analysis and Trial Sequential Analysis. PLoS One 2016; 11:e0151510. [PMID: 26983014 PMCID: PMC4794143 DOI: 10.1371/journal.pone.0151510] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 02/29/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Optimum efficiency of the folate pathway is considered essential for adequate ovarian function. 677 C>T substitution in the 5, 10-methylene tertrahydrofolatereductase (MTHFR) gene compromises activity of the MTHFR enzyme by about 50%. The significance of correlation between 677C>T substitution and PCOS remains dubious due to the low power of published studies. METHODS AND RESULTS We analyzed MTHFR 677 C>T site in ethnically two different PCOS case-control groups (total 261 cases and 256 controls) from India. The data analysis revealed a lack of association between this polymorphism and PCOS [OR = 1.11 (95%CI = 0.71-1.72), P = 0.66]. Group-wise analysis on the basis of ethnicity also revealed no association in any of the ethnic groups [Indo-Europeans, P = 1; Dravidians, P = 0.70]. Homocysteine levels did not differ significantly between cases (15.51 μmol/L, SD = 2.89) and controls (15.89 μmol/L, SD = 2.23). We also undertook a meta-analysis on 960 cases and 1028 controls, which suggested a significant association of the substitution with PCOS in the dominant model of analysis (OR = 1.47 (95%CI = 1.04-2.09), P = 0.032]. Trial sequential analysis corroborated findings of the traditional meta-analysis. However, we found that the conclusions of meta-analysis were strongly influenced by studies that deviated from the Hardy Weinberg equilibrium. A careful investigation of each study and a trial sequential analysis suggested that 677 C>T substitution holds no clinical significance in PCOS in most of the populations. CONCLUSION In conclusion, MTHFR 677 C>T polymorphism does not affect PCOS risk in India. The association seen in the meta-analysis is due to an outlier study and studies showing deviation from the Hardy Weinberg equilibrium.
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Affiliation(s)
- S. Justin Carlus
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Centre for Genetics and Inherited Diseases (CGID), Taibah University, Al- Madinah, Kingdom of Saudi Arabia
| | - Saumya Sarkar
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India
| | | | | | | | - Rajesh Kumar Jha
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India
| | | | | | | | | | - Singh Rajender
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India
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V G A, S R, K M M, K T, S A, S N, A MP, J M, D A. Clinical, cytogenetic and molecular analysis of androgen insensitivity syndromes from south Indian cohort and detection and in-silico characterization of androgen receptor gene mutations. Clin Chim Acta 2015; 453:123-30. [PMID: 26688387 DOI: 10.1016/j.cca.2015.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 12/07/2015] [Accepted: 12/10/2015] [Indexed: 01/07/2023]
Abstract
Rare cases of 9 complete androgen insensitivity syndromes, 9 cases of partial androgen insensitivity syndromes and equal number of male control samples were selected for this study. Few strong variations in clinical features were noticed; Giemsa banded metaphase revealed a 46,XY karyotype and the frequency of chromosome aberrations were significantly higher when compared with control samples. DNA sequence analysis of the androgen receptor gene of androgen insensitivity syndromes revealed three missense mutations - c.C1713>G resulting in the replacement of a highly conserved histidine residue with glutamine p.(His571Glu) in DNA-binding domain, c.A1715>G resulting in the replacement of a highly conserved tyrosine residue with cysteine p.(Tyr572Cys) in DNA-binding domain and c.G2599>A resulting in the replacement of a highly conserved valine residue with methionine p.(Val867Met) in ligand-binding domain of androgen receptor gene respectively. The heterozygous type of mutations c.C1713>G and c.G2599>A observed in mothers of the patients for familial cases concluding that the mutation was inherited from the mother. The novel mutation c.C1713>G is reported first time in androgen insensitivity syndrome. In-silico analysis of mutations observed in androgen receptor gene of androgen insensitivity syndrome predicted that the substitution at Y572C and V867M could probably disrupt the protein structure and function.
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Affiliation(s)
- Abilash V G
- Division of Biomolecules and Genetics, School of Biosciences and Technology, VIT University, Vellore 632 014, Tamilnadu, India.
| | - Radha S
- Division of Biomolecules and Genetics, School of Biosciences and Technology, VIT University, Vellore 632 014, Tamilnadu, India
| | - Marimuthu K M
- University of Madras, New No.55 (Old.No.26), Ist Main Road, Indira Nagar, Adyar, Chennai 600020, Tamilnadu, India
| | - Thangaraj K
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Arun S
- Human Molecular Genetics Laboratory, Department of Zoology, Bharathiar University, Coimbatore-641046, Tamil Nadu, India
| | - Nishu S
- Division of Biomolecules and Genetics, School of Biosciences and Technology, VIT University, Vellore 632 014, Tamilnadu, India
| | - Mohana Priya A
- Bioinformatics Division, School of Biosciences and Technology, VIT University, Vellore 632 014, Tamilnadu, India
| | - Meena J
- Institute of Obstetrics and Gynecology, Madras Medical College, Government Hospital for Women and Children, Egmore, Chennai 600 008, Tamil Nadu, India
| | - Anuradha D
- Institute of Obstetrics and Gynecology, Madras Medical College, Government Hospital for Women and Children, Egmore, Chennai 600 008, Tamil Nadu, India
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Choubey VK, Sankhwar SN, Carlus SJ, Singh AN, Dalela D, Thangaraj K, Rajender S. SRD5A2 gene polymorphisms and the risk of benign prostatic hyperplasia but not prostate cancer. Asian Pac J Cancer Prev 2015; 16:1033-6. [PMID: 25735326 DOI: 10.7314/apjcp.2015.16.3.1033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Testosterone, a primary androgen in males, is converted into its most active form, dihydrotestosterone (DHT), by 5α-reductase type 2 (encoded by the SRD5A2 gene) in the prostate. DHT is necessary for prostatic growth and has five times higher binding affinity than testosterone for androgen receptors. We hypothesized that polymorphic variations in the SRD5A2 gene may affect the risk of benign prostatic hyperplasia and prostate cancer. MATERIALS AND METHODS We analyzed SRD5A2 gene polymorphisms in 217 BPH patients, 192 PCa cases, and 171 controls. Genotyping was undertaken using direct DNA sequencing. Genotype data were compared between cases and controls using a Chi square statistical tool. RESULTS We found that the A49T locus was monomorphic with 'AA' genotype in all subjects. At V89L locus, the presence of 'VV' showed a marginally significant correlation with increased BPH risk (p=0.047). At the (TA)n locus, longer TA repeats were found to be protective against BPH (p=0.003). However, neither of these polymoprhisms correlated with the risk of PCa. CONCLUSIONS We conclude that A49T is monomorphic in the study population, VV marginally correlates with BPH risk, and longer (TA)n repeats are protective against BPH. None of these polymorphisms affect the risk of PCa.
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Affiliation(s)
- Vimal Kumar Choubey
- Department of Urology, King George Medical University, Lucknow, India E-mail :
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Y-chromosome diversity suggests southern origin and Paleolithic backwave migration of Austro-Asiatic speakers from eastern Asia to the Indian subcontinent. Sci Rep 2015; 5:15486. [PMID: 26482917 PMCID: PMC4611482 DOI: 10.1038/srep15486] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/28/2015] [Indexed: 01/01/2023] Open
Abstract
Analyses of an Asian-specific Y-chromosome lineage (O2a1-M95)—the dominant paternal lineage in Austro-Asiatic (AA) speaking populations, who are found on both sides of the Bay of Bengal—led to two competing hypothesis of this group’s geographic origin and migratory routes. One hypothesis posits the origin of the AA speakers in India and an eastward dispersal to Southeast Asia, while the other places an origin in Southeast Asia with westward dispersal to India. Here, we collected samples of AA-speaking populations from mainland Southeast Asia (MSEA) and southern China, and genotyped 16 Y-STRs of 343 males who belong to the O2a1-M95 lineage. Combining our samples with previous data, we analyzed both the Y-chromosome and mtDNA diversities. We generated a comprehensive picture of the O2a1-M95 lineage in Asia. We demonstrated that the O2a1-M95 lineage originated in the southern East Asia among the Daic-speaking populations ~20–40 thousand years ago and then dispersed southward to Southeast Asia after the Last Glacial Maximum before moving westward to the Indian subcontinent. This migration resulted in the current distribution of this Y-chromosome lineage in the AA-speaking populations. Further analysis of mtDNA diversity showed a different pattern, supporting a previously proposed sex-biased admixture of the AA-speaking populations in India.
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20
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Détroit F, Corny J, Dizon EZ, Mijares AS. "Small size" in the Philippine human fossil record: is it meaningful for a better understanding of the evolutionary history of the negritos? Hum Biol 2015; 85:45-65. [PMID: 24297220 DOI: 10.3378/027.085.0303] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
"Pygmy populations" are recognized in several places over the world, especially in Western Africa and in Southeast Asia (Philippine "negritos," for instance). Broadly defined as "small-bodied Homo sapiens" (compared with neighboring populations), their origins and the nature of the processes involved in the maintenance of their phenotype over time are highly debated. Major results have been recently obtained from population genetics on present-day negrito populations, but their evolutionary history remains largely unresolved. We present and discuss the Upper Pleistocene human remains recovered from Tabon Cave and Callao Cave in the Philippines, which are potentially highly relevant to these research questions. Human fossils have been recovered in large numbers from Tabon Cave (Palawan Island) but mainly from reworked and mixed sediments from several archaeological layers. We review and synthesize the long and meticulous collaborative work done on the archives left from the 1960s excavations and on the field. The results demonstrate the long history of human occupations in the cave, since at least ~30,000 BP. The examination of the Tabon human remains shows a large variability: large and robust for one part of the sample, and small and gracile for the other part. The latter would fit quite comfortably within the range of variation of Philippine negritos. Farther north, on Luzon Island, the human third metatarsal recently recovered from Callao Cave and dated to ~66,000 BP is now the oldest direct evidence of human presence in the Philippines. Previous data show that, compared with H. sapiens (including Philippine negritos), this bone presents a very small size and several unusual morphological characteristics. We present a new analytical approach using three-dimensional geometric morphometrics for comparing the Callao fossil to a wide array of extant Asian mammals, including nonhuman primates and H. sapiens. The results demonstrate that the shape of the Callao metatarsal is definitely closer to humans than to any other groups. The fossil clearly belongs to the genus Homo; however, it remains at the margin of the variation range of H. sapiens. Because of its great antiquity and the presence of another diminutive species of the genus Homo in the Wallace area during this time period (H. floresiensis), we discuss here in detail the affinities and potential relatedness of the Callao fossil with negritos that are found today on Luzon Island.
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Affiliation(s)
- Florent Détroit
- UMR7194-Département de Préhistoire, Muséum national d'Histoire naturelle, Paris, France
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Stock JT. The skeletal phenotype of "negritos" from the Andaman Islands and Philippines relative to global variation among hunter-gatherers. Hum Biol 2015; 85:67-94. [PMID: 24297221 DOI: 10.3378/027.085.0304] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
The "negrito hypothesis" suggests that populations of small-bodied foragers in South and Southeast Asia who share common phenotypic characteristics may also share a common, ancient origin. The key defining characteristics of the "negrito" phenotype, small body size, dark skin, and tightly curled hair, have been interpreted as linking these populations to sub-Saharan Africans. The underlying assumption of this interpretation is that the observed phenotypic similarities likely reflect shared ancestry rather than phenotypic convergence. Current genetic evidence is inconclusive, as it both demonstrates that negrito populations have genetic affinities with neighboring populations but also rare and ancient variation that suggests considerable isolation. This study investigates the skeletal phenotype of Andaman Islanders and Aeta foragers from the Philippines in the context of the phenotypic variation among other hunter-gatherers globally, to test whether they show a common, unique physique apart from small body size. Particular emphasis is placed on the comparison of negrito phenotypes to African, Asian, and Australian hunter-gatherer diversity to investigate phenotypic similarities to other populations globally. The results demonstrate that despite sharing small adult stature, the Andaman Islanders and Aeta show variation in body dimensions. In particular, the Andaman Islanders share a pattern of narrow bi-iliac breadth and short upper limbs with the Khoisan (Later Stone Age Southern Africans), whereas the Aeta and Efé show broader bi-iliac breadths relative to lower limb lengths. Although general similarities in size and proportions remain between the Andamanese and Aeta, differences in humero-femoral indices and arm length between these groups and the Efé demonstrate that there is not a generic "pygmy" phenotype. Our interpretations of negrito origins and adaptation must account for this phenotypic variation.
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Affiliation(s)
- Jay T Stock
- Phenotypic Adaptability, Variation and Evolution Research Group, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 3DF, UK
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Chaubey G, Endicott P. The Andaman Islanders in a regional genetic context: reexamining the evidence for an early peopling of the archipelago from South Asia. Hum Biol 2015; 85:153-72. [PMID: 24297224 DOI: 10.3378/027.085.0307] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
The indigenous inhabitants of the Andaman Islands were considered by many early anthropologists to be pristine examples of a "negrito" substrate of humanity that existed throughout Southeast Asia. Despite over 150 years of research and study, questions over the extent of shared ancestry between Andaman Islanders and other small-bodied, gracile, dark-skinned populations throughout the region are still unresolved. This shared phenotype could be a product of shared history, evolutionary convergence, or a mixture of both. Recent population genetic studies have tended to emphasize long-term physical isolation of the Andaman Islanders and an affinity to ancestral populations of South Asia. We reexamine the genetic evidence from genome-wide autosomal single-nucleotide polymorphism (SNP) data for a shared history between the tribes of Little Andaman (Onge) and Great Andaman, and between these two groups and the rest of South and Southeast Asia (both negrito and non-negrito groups).
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Mattapally S, Nizamuddin S, Murthy KS, Thangaraj K, Banerjee SK. c.620C>T mutation in GATA4 is associated with congenital heart disease in South India. BMC MEDICAL GENETICS 2015; 16:7. [PMID: 25928801 PMCID: PMC4422155 DOI: 10.1186/s12881-015-0152-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/30/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND Congenital heart diseases (CHDs) usually refer to abnormalities in the structure and/or function of the heart that arise before birth. GATA4 plays an important role in embryonic heart development, hence the aim of this study was to find the association of GATA4 mutations with CHD among the south Indian CHD patients. METHOD GATA4 gene was sequenced in 100 CHD patients (ASD, VSD, TOF and SV) and 200 controls. Functional significance of the observed GATA4 mutations was analyzed using PolyPhen, SIFT, PMut, Plink, Haploview, ESE finder 3.0 and CONSITE. RESULTS We observed a total of 19 mutations, of which, one was in 5' UTR, 10 in intronic regions, 3 in coding regions and 5 in 3' UTR. Of the above mutations, one was associated with Atrial Septal Defect (ASD), two were found to be associated with Tetralogy of Fallot (TOF) and three (rs804280, rs4841587 and rs4841588) were strongly associated with Ventricular Septal Defect (VSD). Interestingly, one promoter mutation (-490 to 100 bp) i.e., 620 C>T (rs61277615, p-value = 0.008514), one splice junction mutation (G>A rs73203482; p-value = 9.6e-3, OR = 6.508) and one intronic mutation rs4841587 (p-value = 4.6e-3, OR = 4.758) were the most significant findings of this study. In silico analysis also proves that some of the mutations reported above are pathogenic. CONCLUSION The present study found that GATA4 genetic variations are associated with ASD, TOF and VSD in South Indian patients. In silico analysis provides further evidence that some of the observed mutations are pathogenic.
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Affiliation(s)
- Saidulu Mattapally
- Division of Pharmacology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500 007, India.
| | - Sheikh Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
| | - Kona Samba Murthy
- Innova Children's Heart Hospital, Tarnaka, Hyderabad, 500017, India.
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
| | - Sanjay K Banerjee
- Division of Pharmacology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500 007, India. .,Current Address: Drug Discovery Research Center, Translational Health Science and Technology Institute (THSTI), Gurgaon, HR-122016, Haryana, India.
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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.
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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.
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25
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The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia. Hum Genet 2014; 133:1169-85. [DOI: 10.1007/s00439-014-1459-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/29/2014] [Indexed: 12/12/2022]
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Khurana P, Aggarwal A, Mitra S, Italia YM, Saraswathy KN, Chandrasekar A, Kshatriya GK. Y chromosome haplogroup distribution in Indo-European speaking tribes of Gujarat, western India. PLoS One 2014; 9:e90414. [PMID: 24614885 PMCID: PMC3948632 DOI: 10.1371/journal.pone.0090414] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/01/2014] [Indexed: 11/20/2022] Open
Abstract
The present study was carried out in the Indo-European speaking tribal population groups of Southern Gujarat, India to investigate and reconstruct their paternal population structure and population histories. The role of language, ethnicity and geography in determining the observed pattern of Y haplogroup clustering in the study populations was also examined. A set of 48 bi-allelic markers on the non-recombining region of Y chromosome (NRY) were analysed in 284 males; representing nine Indo-European speaking tribal populations. The genetic structure of the populations revealed that none of these groups was overtly admixed or completely isolated. However, elevated haplogroup diversity and FST value point towards greater diversity and differentiation which suggests the possibility of early demographic expansion of the study groups. The phylogenetic analysis revealed 13 paternal lineages, of which six haplogroups: C5, H1a*, H2, J2, R1a1* and R2 accounted for a major portion of the Y chromosome diversity. The higher frequency of the six haplogroups and the pattern of clustering in the populations indicated overlapping of haplogroups with West and Central Asian populations. Other analyses undertaken on the population affiliations revealed that the Indo-European speaking populations along with the Dravidian speaking groups of southern India have an influence on the tribal groups of Gujarat. The vital role of geography in determining the distribution of Y lineages was also noticed. This implies that although language plays a vital role in determining the distribution of Y lineages, the present day linguistic affiliation of any population in India for reconstructing the demographic history of the country should be considered with caution.
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Affiliation(s)
- Priyanka Khurana
- Department of Anthropology, School of Applied Sciences, Dr. Harisingh Gour University, Sagar, Madhya Pradesh, India
| | - Aastha Aggarwal
- South Asia Network for Chronic Disease, Public Health Foundation of India, Delhi, India
| | - Siuli Mitra
- Department of Anthropology, University of Delhi, Delhi, India
| | - Yazdi M. Italia
- Valsad Raktdan Kendra, R.N.C. Free Eye Hospital Complex, Valsad, Gujarat, India
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Rajender S, Gupta NJ, Chakrabarty B, Singh L, Thangaraj K. L712V mutation in the androgen receptor gene causes complete androgen insensitivity syndrome due to severe loss of androgen function. Steroids 2013; 78:1288-92. [PMID: 24055831 DOI: 10.1016/j.steroids.2013.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/02/2013] [Accepted: 09/06/2013] [Indexed: 10/26/2022]
Abstract
Inability to respond to the circulating androgens is named as androgen insensitivity syndrome (AIS). Mutations in the androgen receptor (AR) gene are the most common cause of AIS. A cause and effect relationship between some of these mutations and the AIS phenotype has been proven by in vitro studies. Several other mutations have been identified, but need to be functionally validated for pathogenicity. Screening of the AR mutations upon presumptive diagnosis of AIS is recommended. We analyzed a case of complete androgen insensitivity syndrome (CAIS) for mutations in the AR gene. Sequencing of the entire coding region revealed C>G mutation (CTT-GTT) at codon 712 (position according to the NCBI database) in exon 4 of the gene, resulting in replacement of leucine with valine in the ligand-binding domain of the AR protein. No incidence of this mutation was observed in 230 normal male individuals analyzed for comparison. In vitro androgen binding and transactivation assays using mutant clone showed approximately 71% loss of ligand binding and about 76% loss of transactivation function. We conclude that CAIS in this individual was due to L712V substitution in the androgen receptor protein.
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Affiliation(s)
- Singh Rajender
- Endocrinology Division, Central Drug Research Institute (Council of Scientific and Industrial Research), India.
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Heyer E, Georges M, Pachner M, Endicott P. Genetic diversity of four Filipino negrito populations from Luzon: comparison of male and female effective population sizes and differential integration of immigrants into Aeta and Agta communities. Hum Biol 2013; 85:189-208. [PMID: 24297226 DOI: 10.3378/027.085.0310] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
Genetic data corresponding to four negrito populations (two Aeta and two Agta; n = 120) from the Luzon region of the Philippines have been analyzed. These data comprise mitochondrial DNA (mtDNA) hypervariable segment 1 haplotypes and haplogroups, Y-chromosome haplogroups and short tandem repeats (STRs), autosomal STRs, and X-chromosome STRs. The genetic diversity and structure of the populations were investigated at a local, regional, and interregional level. We found a high level of autosomal differentiation, combined with no significant reduction in diversity, consistent with long-term settlement of the Luzon region by the ancestors of the Agta and Aeta followed by reduced gene flow between these two ethnolinguistic groups. Collectively, the Aeta have a much higher ratio of female:male effective population size than do the Agta, a finding that supports phylogenetic analysis of their mtDNA and Y-chromosome haplogroups, which suggests different genetic sex-biased contributions from putative Austronesian source populations. We propose that factors of social organization that led to the reduction in Agta female effective population size may also be linked to the limited incorporation of female lineages associated with the settlement of the Philippines by Austronesian speakers; conversely, the reduction in Aeta male effective population size, relative to females, could be indicative of a limited incorporation of male lineages associated with this demographic process.
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Affiliation(s)
- E Heyer
- UMR7206, EcoAnthropologie et Ethnobiologie, MNHN, CNRS, Université Paris Diderot, Paris, France
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Govindaraj P, Khan NA, Rani B, Rani DS, Selvaraj P, Jyothi V, Bahl A, Narasimhan C, Rakshak D, Premkumar K, Khullar M, Thangaraj K. Mitochondrial DNA variations associated with hypertrophic cardiomyopathy. Mitochondrion 2013; 16:65-72. [PMID: 24215792 DOI: 10.1016/j.mito.2013.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 10/17/2013] [Accepted: 10/29/2013] [Indexed: 01/11/2023]
Abstract
Hypertrophic cardiomyopathy (HCM) is a primary disorder, characterized by unexplained hypertrophy of the left ventricle that frequently involved in the inter-ventricular septum. Mitochondrial DNA (mtDNA) mutations and haplogroups have been found to be associated with several diseases. Therefore, in the present study, we have sequenced the complete mtDNA of 114 clinically well-characterized HCM patients to look for the role of mtDNA variations and haplogroups in HCM phenotype among Indian patients. Complete mtDNA analysis revealed 28 novel variations, 25 disease-associated and 50 private mutations. We found 13 (11.40%) HCM patients having novel non-synonymous and/or MT-tRNA variations, of which two (m.4797C>M and m.8728T>Y) were in heteroplasmic condition. In silico prediction showed that a few mutations are pathogenic, which may affect the energy production in the heart. Unlike some of the other studies, we did not find association of mitochondrial haplogroup with HCM.
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Affiliation(s)
- Periyasamy Govindaraj
- Department of Biomedical Science, School of Basic Medical Sciences, Bharathidasan University, Tiruchirappalli, India
| | | | - Bindu Rani
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Deepa Selvi Rani
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Ajay Bahl
- Department of Cardiology, PGIMER, Chandigarh, India
| | | | | | - Kumpati Premkumar
- Department of Biomedical Science, School of Basic Medical Sciences, Bharathidasan University, Tiruchirappalli, India
| | - Madhu Khullar
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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Ranaweera L, Kaewsutthi S, Win Tun A, Boonyarit H, Poolsuwan S, Lertrit P. Mitochondrial DNA history of Sri Lankan ethnic people: their relations within the island and with the Indian subcontinental populations. J Hum Genet 2013; 59:28-36. [PMID: 24196378 DOI: 10.1038/jhg.2013.112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 10/04/2013] [Accepted: 10/09/2013] [Indexed: 11/10/2022]
Abstract
Located only a short distance off the southernmost shore of the Greater Indian subcontinent, the island of Sri Lanka has long been inhabited by various ethnic populations. Mainly comprising the Vedda, Sinhalese (Up- and Low-country) and Tamil (Sri Lankan and Indian); their history of settlements on the island and the biological relationships among them have remained obscure. It has been hypothesized that the Vedda was probably the earliest inhabitants of the area, followed by Sinhalese and Tamil from the Indian mainland. This study, in which 271 individuals, representing the Sri Lankan ethnic populations mentioned, were typed for their mitochondrial DNA (mtDNA) hypervariable segment 1 (HVS-1) and part of hypervariable segment 2 (HVS-2), provides implications for their settlement history on the island. From the phylogenetic, principal coordinate and analysis of molecular variance results, the Vedda occupied a position separated from all other ethnic people of the island, who formed relatively close affiliations among themselves, suggesting a separate origin of the former. The haplotypes and analysis of molecular variance revealed that Vedda people's mitochondrial sequences are more related to the Sinhalese and Sri Lankan Tamils' than the Indian Tamils' sequences. MtDNA haplogroup analysis revealed that several West Eurasian haplogroups as well as Indian-specific mtDNA clades were found amongst the Sri Lankan populations. Through a comparison with the mtDNA HVS-1 and part of HVS-2 of Indian database, both Tamils and Sinhalese clusters were affiliated with Indian subcontinent populations than Vedda people who are believed to be the native population of the island of Sri Lanka.
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Affiliation(s)
- Lanka Ranaweera
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supannee Kaewsutthi
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Aung Win Tun
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Hathaichanoke Boonyarit
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Samerchai Poolsuwan
- Faculty of Sociology and Anthropology, Thammasat University, PraChan, Bangkok, Thailand
| | - Patcharee Lertrit
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Gupta N, Sarkar S, David A, Gangwar PK, Gupta R, Khanna G, Sankhwar SN, Khanna A, Rajender S. Significant impact of the MTHFR polymorphisms and haplotypes on male infertility risk. PLoS One 2013; 8:e69180. [PMID: 23874907 PMCID: PMC3715460 DOI: 10.1371/journal.pone.0069180] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/05/2013] [Indexed: 11/19/2022] Open
Abstract
Background Methylenetetrahydrofolate reductase (MTHFR) converts 5,10-methylene tetrahydrofolate to 5-methyl tetrahydrofolate and affects the activity of cellular cycles participating in nucleotide synthesis, DNA repair, genome stability, maintenance of methyl pool, and gene regulation. Genetically compromised MTHFR activity has been suggested to affect male fertility. The objective of the present study was to find the impact on infertility risk of c.203G>A, c.1298A>C, and c.1793G>A polymorphisms in the MTHFR gene. Methods PCR-RFLP and DNA sequencing were used to genotype the common SNPs in the MTHFR gene in 630 infertile and 250 fertile males. Chi-square test was applied for statistical comparison of genotype data. Linkage disequilibrium between the SNPs and the frequency of common haplotypes were assessed using Haploview software. Biochemical levels of total homocysteine (tHcy) and folic acid were measured. Meta-analysis on c.1298A>C polymorphism was performed using data from ten studies, comprising 2734 cases and 2737 controls. Results c.203G>A and c.1298A>C were found to be unrelated to infertility risk. c.1793G>A was protective against infertility (P = 0.0008). c.677C>T and c.1793G>A were in significant LD (D’ = 0.9). Folic acid and tHcy level did not correlate with male infertility. Pooled estimate on c.1298A>C data from all published studies including our data showed no association of this polymorphism with male infertility (Odds ratio = 1.035, P = 0.56), azoospermia (Odds ratio = 0.97, P = 0.74), or oligoasthenoteratozoospermia (Odds ratio = 0.92, p = 0.29). Eight haplotypes with more than 1% frequency were detected, of which CCGA was protective against infertility (p = 0.02), but the significance of the latter was not seen after applying Bonferroni correction. Conclusion Among MTHFR polymorphisms, c.203G>A and c.1298A>C do not affect infertility risk and c.1793G>A is protective against infertility. Haplotype analysis suggested that risk factors on the MTHFR locus do not extend too long on the DNA string.
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Affiliation(s)
- Nishi Gupta
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
| | - Saumya Sarkar
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
| | - Archana David
- Ajanta Hospitals and IVF Centre Pvt. Ltd., Lucknow, India
| | | | - Richa Gupta
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
| | - Gita Khanna
- Ajanta Hospitals and IVF Centre Pvt. Ltd., Lucknow, India
| | | | - Anil Khanna
- Ajanta Hospitals and IVF Centre Pvt. Ltd., Lucknow, India
| | - Singh Rajender
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
- * E-mail:
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Wang CC, Li H. Inferring human history in East Asia from Y chromosomes. INVESTIGATIVE GENETICS 2013; 4:11. [PMID: 23731529 PMCID: PMC3687582 DOI: 10.1186/2041-2223-4-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 04/19/2013] [Indexed: 02/06/2023]
Abstract
East Asia harbors substantial genetic, physical, cultural and linguistic diversity, but the detailed structures and interrelationships of those aspects remain enigmatic. This question has begun to be addressed by a rapid accumulation of molecular anthropological studies of the populations in and around East Asia, especially by Y chromosome studies. The current Y chromosome evidence suggests multiple early migrations of modern humans from Africa via Southeast Asia to East Asia. After the initial settlements, the northward migrations during the Paleolithic Age shaped the genetic structure in East Asia. Subsequently, recent admixtures between Central Asian immigrants and northern East Asians enlarged the genetic divergence between southern and northern East Asia populations. Cultural practices, such as languages, agriculture, military affairs and social prestige, also have impacts on the genetic patterns in East Asia. Furthermore, application of Y chromosome analyses in the family genealogy studies offers successful showcases of the utility of genetics in studying the ancient history.
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Affiliation(s)
- Chuan-Chao Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, China
| | - Hui Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, China
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Venkataraman VV, Kraft TS, Desilva JM, Dominy NJ. Phenotypic Plasticity of Climbing-Related Traits in the Ankle Joint of Great Apes and Rainforest Hunter-Gatherers. Hum Biol 2013; 85:309-28. [DOI: 10.3378/027.085.0315] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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Benjamin G. Why Have the Peninsular “Negritos” Remained Distinct? Hum Biol 2013; 85:445-84. [DOI: 10.3378/027.085.0321] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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Tamang R, Singh L, Thangaraj K. Complex genetic origin of Indian populations and its implications. J Biosci 2013; 37:911-9. [PMID: 23107926 DOI: 10.1007/s12038-012-9256-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000 years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.
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Affiliation(s)
- Rakesh Tamang
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007
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36
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Mitochondrial DNA variations in ova and blastocyst: implications in assisted reproduction. Mitochondrion 2013; 13:96-105. [PMID: 23333796 DOI: 10.1016/j.mito.2013.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/30/2012] [Accepted: 01/07/2013] [Indexed: 11/20/2022]
Abstract
Mitochondrial DNA (mtDNA) of oocyte is critical for its function, embryo quality and development. Analysis of complete mtDNA of 49 oocytes and 18 blastocysts from 67 females opting for IVF revealed 437 nucleotide variations. 40.29% samples had either disease associated or non-synonymous novel or pathogenic mutation in evolutionarily conserved regions. Samples with disease associated mtDNA mutations had low fertilization rate and poor embryo quality, however no difference in implantation or clinical pregnancy rate was observed. Screening mtDNA from oocyte/blastocyst is a simple, clinically reliable method for diagnostic evaluation of female infertility and may reduce risk of mtDNA disease transmission.
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Jobling MA. Significant others. INVESTIGATIVE GENETICS 2012; 3:21. [PMID: 23078838 PMCID: PMC3487975 DOI: 10.1186/2041-2223-3-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 10/09/2012] [Indexed: 12/05/2022]
Affiliation(s)
- Mark A Jobling
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Tamang R, Thangaraj K. Genomic view on the peopling of India. INVESTIGATIVE GENETICS 2012; 3:20. [PMID: 23020857 PMCID: PMC3514343 DOI: 10.1186/2041-2223-3-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 08/07/2012] [Indexed: 01/11/2023]
Abstract
India is known for its vast human diversity, consisting of more than four and a half thousand anthropologically well-defined populations. Each population differs in terms of language, culture, physical features and, most importantly, genetic architecture. The size of populations varies from a few hundred to millions. Based on the social structure, Indians are classified into various caste, tribe and religious groups. These social classifications are very rigid and have remained undisturbed by emerging urbanisation and cultural changes. The variable social customs, strict endogamy marriage practices, long-term isolation and evolutionary forces have added immensely to the diversification of the Indian populations. These factors have also led to these populations acquiring a set of Indian-specific genetic variations responsible for various diseases in India. Interestingly, most of these variations are absent outside the Indian subcontinent. Thus, this review is focused on the peopling of India, the caste system, marriage practice and the resulting health and forensic implications.
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Affiliation(s)
- Rakesh Tamang
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
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Telles S, Naveen KV, Dash M. Yoga reduces symptoms of distress in tsunami survivors in the andaman islands. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012; 4:503-9. [PMID: 18227918 PMCID: PMC2176139 DOI: 10.1093/ecam/nem069] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2007] [Accepted: 05/08/2007] [Indexed: 11/16/2022]
Abstract
A month after the December 2004 tsunami the effect of a 1 week yoga program was evaluated on self rated fear, anxiety, sadness and disturbed sleep in 47 survivors in the Andaman Islands. Polygraph recordings of the heart rate, breath rate and skin resistance were also made. Among the 47 people, 31 were settlers from the mainland (i.e. India, ML group) and 16 were endogenous people (EP group). There was a significant decrease in self rated fear, anxiety, sadness and disturbed sleep in both groups, and in the heart and breath rate in the ML group, and in the breath rate alone in the EP group, following yoga (P < 0.05, t-test). This suggests that yoga practice may be useful in the management of stress following a natural disaster in people with widely differing social, cultural and spiritual beliefs.
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Affiliation(s)
- Shirley Telles
- Swami Vivekananda Yoga Research Foundation (A Yoga University), Bangalore, India
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Trejaut J, Lee CL, Yen JC, Loo JH, Lin M. Ancient migration routes of Austronesian-speaking populations in oceanic Southeast Asia and Melanesia might mimic the spread of nasopharyngeal carcinoma. CHINESE JOURNAL OF CANCER 2012; 30:96-105. [PMID: 21272441 PMCID: PMC4013338 DOI: 10.5732/cjc.010.10589] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mitochondrial DNA (mtDNA) and non-recombining Y chromosome (NRY) are inherited uni-parentally from mother to daughter or from father to son respectively. Their polymorphism has initially been studied throughout populations of the world to demonstrate the "Out of Africa" hypothesis. Here, to correlate the distribution of nasopharyngeal carcinoma (NPC) in different populations of insular Asia, we analyze the mtDNA information (lineages) obtained from genotyping of the hyper variable region (HVS I & II) among 1400 individuals from island Southeast Asia (ISEA), Taiwan and Fujian and supplemented with the analysis of relevant coding region polymorphisms. Lineages that best represented a clade (a branch of the genetic tree) in the phylogeny were further analyzed using complete genomic mtDNA sequencing. Finally, these complete mtDNA sequences were used to construct a most parsimonious tree which now constitutes the most up-to-date mtDNA dataset available on ISEA and Taiwan. This analysis has exposed new insights of the evolutionary history of insular Asia and has strong implications in assessing possible correlations with linguistic, archaeology, demography and the NPC distribution in populations within these regions. To obtain a more objective and balanced genetic point of view, slowly evolving biallelic Y single nucleotide polymorphism (Y-SNP) was also analyzed. As in the first step above, the technique was first applied to determine affinities (macro analysis) between populations of insular Asia. Secondly, sixteen Y short tandem repeats (Y-STR) were used as they allow deeper insight (micro analysis) into the relationship between individuals of a same region. Together, mtDNA and NRY allowed a better definition of the relational, demographic, cultural and genetic components that constitute the make up of the present day peoples of ISEA. Outstanding findings were obtained on the routes of migration that occurred along with the spread of NPC during the settlement of insular Asia. The results of this analysis will be discussed using a conceptual approach.
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Affiliation(s)
- Jean Trejaut
- Mackay Memorial Hospital, #45 Min-Sheng Road, Tamsui 25115, Taiwan
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Jinam TA, Hong LC, Phipps ME, Stoneking M, Ameen M, Edo J, Saitou N. Evolutionary History of Continental Southeast Asians: “Early Train” Hypothesis Based on Genetic Analysis of Mitochondrial and Autosomal DNA Data. Mol Biol Evol 2012; 29:3513-27. [DOI: 10.1093/molbev/mss169] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Timothy A. Jinam
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Lih-Chun Hong
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University (Sunway Campus), Selangor, Malaysia
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mahmood Ameen
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Juli Edo
- Department of Anthropology, Faculty of Arts and Social Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Naruya Saitou
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
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Perreault C, Mathew S. Dating the origin of language using phonemic diversity. PLoS One 2012; 7:e35289. [PMID: 22558135 PMCID: PMC3338724 DOI: 10.1371/journal.pone.0035289] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 03/14/2012] [Indexed: 12/21/2022] Open
Abstract
Language is a key adaptation of our species, yet we do not know when it evolved. Here, we use data on language phonemic diversity to estimate a minimum date for the origin of language. We take advantage of the fact that phonemic diversity evolves slowly and use it as a clock to calculate how long the oldest African languages would have to have been around in order to accumulate the number of phonemes they possess today. We use a natural experiment, the colonization of Southeast Asia and Andaman Islands, to estimate the rate at which phonemic diversity increases through time. Using this rate, we estimate that present-day languages date back to the Middle Stone Age in Africa. Our analysis is consistent with the archaeological evidence suggesting that complex human behavior evolved during the Middle Stone Age in Africa, and does not support the view that language is a recent adaptation that has sparked the dispersal of humans out of Africa. While some of our assumptions require testing and our results rely at present on a single case-study, our analysis constitutes the first estimate of when language evolved that is directly based on linguistic data.
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Affiliation(s)
| | - Sarah Mathew
- Centre for the Study of Cultural Evolution, Stockholm University, Stockholm, Sweden
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Suhasini G, Sonaa E, Shila S, Srikumari CR, Jayaraman G, Ramesh A. Genetic admixture studies on four in situ evolved, two migrant and twenty-one ethnic populations of Tamil Nadu, south India. J Genet 2012; 90:191-202. [PMID: 21869467 DOI: 10.1007/s12041-011-0067-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We analysed the genetic structure of ≈ 1000 samples representing 27 ethnic groups settled in Tamil Nadu, south India, derived from two linguistic families (Dravidians and Indo-Europeans) representing four religious groups (Hinduism, Islam, Christianity and Jainism) using 11 mtDNA markers. Out of 27 ethnic groups, four are in situ populations (Anglo-Indian, Labbai Muslim, Nadar Christian and south Indian Jain) and two are migrants (Gypsy and north Indian Jain) from north India to Tamil Nadu, and 21 are native ethnic groups. Six of the markers we used were monomorphic (HaeIII663, HpaI3592, AluI5176, AluI7025, AluI13262, 9-bp deletion) and five markers were polymorphic (DdeI10394, AluI10397, HinfI12308, HincII13259 and HaeIII16517). Haplogroup frequencies, genetic affinities and admixture analysis are based on the genotype data of polymorphic markers observed in these populations. Haplogroup frequencies indicate that various ethnic groups entered Tamil Nadu during different time periods. Genetic affinities and admixture estimates revealed that the ethnic groups possessing advanced knowledge of farming cluster in a branch (C), and could be the late arrived settlers as agriculture, was introduced to this region at about 5 to 3 thousand years ago. In situ ethnic groups appear to have arisen at various times as a result of the prevailing dominant socio-cultural forces. Hierarchical Hindu caste system created many ethnic groups in the history of its existence; some of them became isolated for considerable period of time. Over all, among Tamil ethnic groups, in spite of caste systems' rigidity, built in flexibility in the system in the form of hypergamy and hypogamy had allowed maternal gene flow between them.
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Affiliation(s)
- G Suhasini
- Department of Genetics, Dr ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai 600 113, India.
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Riccio ME, Nunes JM, Rahal M, Kervaire B, Tiercy JM, Sanchez-Mazas A. The Austroasiatic Munda population from India and Its enigmatic origin: a HLA diversity study. Hum Biol 2011; 83:405-35. [PMID: 21740156 DOI: 10.3378/027.083.0306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Austroasiatic linguistic family disputes its origin between two geographically distant regions of Asia, India, and Southeast Asia, respectively. As genetic studies based on classical and gender-specific genetic markers provided contradictory results to this debate thus far, we investigated the HLA diversity (HLA-A, -B, and -DRB1 loci) of an Austroasiatic Munda population from Northeast India and its relationships with other populations from India and Southeast Asia. Because molecular methods currently used to test HLA markers often provide ambiguous results due to the high complexity of this polymorphism, we applied two different techniques (reverse PCR-SSO typing on microbeads arrays based on Luminex technology, and PCR-SSP typing) to type the samples. After validating the resulting frequency distributions through the original statistical method described in our companion article ( Nunes et al. 2011 ), we compared the HLA genetic profile of the sampled Munda to those of other Asiatic populations, among which Dravidian and Indo-European-speakers from India and populations from East and Southeast Asia speaking languages belonging to different linguistic families. We showed that the Munda from Northeast India exhibit a peculiar genetic profile with a reduced level of HLA diversity compared to surrounding Indian populations. They also exhibit less diversity than Southeast Asian populations except at locus DRB1. Several analyses using genetic distances indicate that the Munda are much more closely related to populations from the Indian subcontinent than to Southeast Asian populations speaking languages of the same Austroasiatic linguistic family. On the other hand, they do not share a closer relationship with Dravidians compared with Indo-Europeans, thus arguing against the idea that the Munda share a common and ancient Indian origin with Dravidians. Our results do not favor either a scenario where the Munda would be representative of an ancestral Austroasiatic population giving rise to an eastward Austroasiatic expansion to Southeast Asia. Rather, their peculiar genetic profile is better explained by a decrease in genetic diversity through genetic drift from an ancestral population having a genetic profile similar to present-day Austroasiatic populations from Southeast Asia (thus suggesting a possible southeastern origin), followed by intensive gene flow with neighboring Indian populations. This conclusion is in agreement with archaeological and linguistic information. The history of the Austroasiatic family represents a fascinating example where complex interactions among culturally distinct human populations occurred in the past.
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Affiliation(s)
- Maria Eugenia Riccio
- Laboratory of Anthropology, Genetics, and Peopling History (AGP), Laboratory of Anthropology, Genetics, and Peopling History (AGP), Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Switzerland.
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Scholes C, Siddle K, Ducourneau A, Crivellaro F, Järve M, Rootsi S, Bellatti M, Tabbada K, Mormina M, Reidla M, Villems R, Kivisild T, Lahr MM, Migliano AB. Genetic diversity and evidence for population admixture in Batak Negritos from Palawan. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:62-72. [DOI: 10.1002/ajpa.21544] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Gallego Romero I, Basu Mallick C, Liebert A, Crivellaro F, Chaubey G, Itan Y, Metspalu M, Eaaswarkhanth M, Pitchappan R, Villems R, Reich D, Singh L, Thangaraj K, Thomas MG, Swallow DM, Mirazón Lahr M, Kivisild T. Herders of Indian and European cattle share their predominant allele for lactase persistence. Mol Biol Evol 2011; 29:249-60. [PMID: 21836184 DOI: 10.1093/molbev/msr190] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Milk consumption and lactose digestion after weaning are exclusively human traits made possible by the continued production of the enzyme lactase in adulthood. Multiple independent mutations in a 100-bp region--part of an enhancer--approximately 14-kb upstream of the LCT gene are associated with this trait in Europeans and pastoralists from Saudi Arabia and Africa. However, a single mutation of purported western Eurasian origin accounts for much of observed lactase persistence outside Africa. Given the high levels of present-day milk consumption in India, together with archaeological and genetic evidence for the independent domestication of cattle in the Indus valley roughly 7,000 years ago, we sought to determine whether lactase persistence has evolved independently in the subcontinent. Here, we present the results of the first comprehensive survey of the LCT enhancer region in south Asia. Having genotyped 2,284 DNA samples from across the Indian subcontinent, we find that the previously described west Eurasian -13910 C>T mutation accounts for nearly all the genetic variation we observed in the 400- to 700-bp LCT regulatory region that we sequenced. Geography is a significant predictor of -13910*T allele frequency, and consistent with other genomic loci, its distribution in India follows a general northwest to southeast declining pattern, although frequencies among certain neighboring populations vary substantially. We confirm that the mutation is identical by descent to the European allele and is associated with the same>1 Mb extended haplotype in both populations.
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Affiliation(s)
- Irene Gallego Romero
- Department of Biological Anthropology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom.
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Gupta N, Gupta S, Dama M, David A, Khanna G, Khanna A, Rajender S. Strong association of 677 C>T substitution in the MTHFR gene with male infertility--a study on an indian population and a meta-analysis. PLoS One 2011; 6:e22277. [PMID: 21799811 PMCID: PMC3140509 DOI: 10.1371/journal.pone.0022277] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Accepted: 06/17/2011] [Indexed: 02/02/2023] Open
Abstract
Background Methylenetetrahydrofolate reductase (MTHFR) is an important enzyme of folate and methionine metabolism, making it crucial for DNA synthesis and methylation. The objective of this study was to analyze MTHFR gene 677C>T polymorphism in infertile male individuals from North India, followed by a meta-analysis on our data and published studies. Methodology/Principal Findings We undertook genotyping on a total of 837 individuals including well characterized infertile (N = 522) and confirmed fertile (N = 315) individuals. The SNP was typed by direct DNA sequencing. Chi square test was done for statistical analysis. Published studies were searched using appropriate keywords. Source of data collection for meta-analysis included ‘Pubmed’, ‘Ovid’ and ‘Google Scholar’. Those studies analyzing 677C>T polymorphism in male infertility and presenting all relevant data were included in meta-analysis. The genotype data for infertile subjects and fertile controls was extracted from each study. Chi square test was done to obtain odds ratio (OR) and p-value. Meta-analysis was performed using Comprehensive Meta-analysis software (Version 2). The frequency of mutant (T) allele (p = 0.0025) and genotypes (CT+TT) (p = 0.0187) was significantly higher in infertile individuals in comparison to fertile controls in our case-control study. The overall summary estimate (OR) for allele and genotype meta-analysis were 1.304 (p = 0.000), 1.310 (p = 0.000), respectively, establishing significant association of 677C>T polymorphism with male infertility. Conclusions/Significance 677C>T substitution associated strongly with male infertility in Indian population. Allele and genotype meta-analysis also supported its strong correlation with male infertility, thus establishing it as a risk factor.
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Affiliation(s)
- Nishi Gupta
- Division of Endocrinology, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Saraswati Gupta
- IVF Department, Ajanta Hospitals and IVF Centre Pvt. Ltd., Lucknow, Uttar Pradesh, India
| | - Madhukar Dama
- Division of Endocrinology, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Archana David
- IVF Department, Ajanta Hospitals and IVF Centre Pvt. Ltd., Lucknow, Uttar Pradesh, India
| | - Geeta Khanna
- IVF Department, Ajanta Hospitals and IVF Centre Pvt. Ltd., Lucknow, Uttar Pradesh, India
| | - Anil Khanna
- IVF Department, Ajanta Hospitals and IVF Centre Pvt. Ltd., Lucknow, Uttar Pradesh, India
| | - Singh Rajender
- Division of Endocrinology, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
- * E-mail:
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Bengtsson CF, Olsen ME, Brandt LØ, Bertelsen MF, Willerslev E, Tobin DJ, Wilson AS, Gilbert MTP. DNA from keratinous tissue. Part I: hair and nail. Ann Anat 2011; 194:17-25. [PMID: 21530205 DOI: 10.1016/j.aanat.2011.03.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 03/05/2011] [Accepted: 03/22/2011] [Indexed: 11/26/2022]
Abstract
Keratinous tissues such as nail, hair, horn, scales and feather have been used as a source of DNA for over 20 years. Particular benefits of such tissues include the ease with which they can be sampled, the relative stability of DNA in such tissues once sampled, and, in the context of ancient genetic analyses, the fact that sampling generally causes minimal visual damage to valuable specimens. Even when freshly sampled, however, the DNA quantity and quality in the fully keratinized parts of such tissues is extremely poor in comparison to other tissues such as blood and muscle - although little systematic research has been undertaken to characterize how such degradation may relate to sample source. In this review paper we present the current understanding of the quality and limitations of DNA in two key keratinous tissues, nail and hair. The findings indicate that although some fragments of nuclear and mitochondrial DNA appear to be present in almost all hair and nail samples, the quality of DNA, both in quantity and length of amplifiable DNA fragments, vary considerably not just by species, but by individual, and even within individual between hair types.
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Affiliation(s)
- Camilla Friis Bengtsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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Wang HW, Mitra B, Chaudhuri TK, Palanichamy MG, Kong QP, Zhang YP. Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic. J Genet Genomics 2011; 38:117-22. [PMID: 21477783 DOI: 10.1016/j.jgg.2011.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 11/07/2010] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
Abstract
In view of the geographically closest location to Andaman archipelago, Myanmar was suggested to be the origin place of aboriginal Andamanese. However, for lacking any genetic information from this region, which has prevented to resolve the dispute on whether the aboriginal Andamanese were originated from mainland India or Myanmar. To solve this question and better understand the origin of the aboriginal Andamanese, we screened for haplogroups M31 (from which Andaman-specific lineage M31a1 branched off) and M32 among 846 mitochondrial DNAs (mtDNAs) sampled across Myanmar. As a result, two Myanmar individuals belonging to haplogroup M31 were identified, and completely sequencing the entire mtDNA genomes of both samples testified that the two M31 individuals observed in Myanmar were probably attributed to the recent gene flow from northeast India populations. Since no root lineages of haplogroup M31 or M32 were observed in Myanmar, it is unlikely that Myanmar may serve as the source place of the aboriginal Andamanese. To get further insight into the origin of this unique population, the detailed phylogenetic and phylogeographic analyses were performed by including additional 7 new entire mtDNA genomes and 113 M31 mtDNAs pinpointed from South Asian populations, and the results suggested that Andaman-specific M31a1 could in fact trace its origin to northeast India. Time estimation results further indicated that the Andaman archipelago was likely settled by modern humans from northeast India via the land-bridge which connected the Andaman archipelago and Myanmar around the Last Glacial Maximum (LGM), a scenario in well agreement with the evidence from linguistic and palaeoclimate studies.
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Affiliation(s)
- Hua-Wei Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, Yunnan Province, China
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Aruna M, Nagaraja T, Andal Bhaskar S, Tarakeswari S, Reddy AG, Thangaraj K, Singh L, Reddy BM. Novel alleles of HLA-DQ and -DR loci show association with recurrent miscarriages among South Indian women. Hum Reprod 2011; 26:765-74. [PMID: 21325036 DOI: 10.1093/humrep/der024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND In this study, recurrent miscarriages (RMs) are defined as loss of two or more clinically detectable pregnancies before 20 weeks of gestation. HLA has been thought to play a role in RM. However, the results of earlier studies on the role of different human leucocyte antigen (HLA) genes were conflicting and inconclusive. In the present study, we investigate HLA genes (HLA-DRA, HLA-DRB1, HLA-DQA1 and HLA-DQB1) in RM couples with unknown etiology and normal couples. METHODS Blood samples from 143 RM couples and 150 control couples were analyzed, firstly to validate previously reported association studies and secondly to explore whether any novel alleles or haplotypes specific to Indian populations can be observed to be associated with RM. HLA typing was carried out by DNA sequencing. RESULTS Results suggest an association of the DQB1*03:03:02 allele with RM (odd ratio = 2.66; p(c) = 0.02; confidence interval = 1.47-4.84). Haplotypes of the DQA1 and DQB1 risk alleles also showed a significant association with RM, albeit not after Bonferroni correction for multiple comparisons. CONCLUSIONS HLA-DQB1 appears to have a strong involvement in the manifestation of RM in this population from South India. The current genetic analysis of RM and control couples not only highlights the genes exhibiting a strong etiological role but also reflects the protective nature of some HLA genes against RM. Nevertheless, most of these alleles/haplotypes were not those that are implicated in RM in other ethnic backgrounds, and hence require further validation in other populations of India, from different ethnic and/or geographic backgrounds.
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Affiliation(s)
- Meka Aruna
- Molecular Anthropology Group, Biological Anthropology Unit, Indian Statistical Institute, Street No. 8, Habsiguda, Hyderabad 500007, India
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