1
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Genome Analysis Using Whole-Exome Sequencing of Non-Syndromic Cleft Lip and/or Palate from Malagasy Trios Identifies Variants Associated with Cilium-Related Pathways and Asian Genetic Ancestry. Genes (Basel) 2023; 14:genes14030665. [PMID: 36980938 PMCID: PMC10048728 DOI: 10.3390/genes14030665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 03/10/2023] Open
Abstract
Background: Orofacial clefts (OFCs) are common congenital disabilities that can occur as isolated non-syndromic events or as part of Mendelian syndromes. OFC risk factors vary due to differences in regional environmental exposures, genetic variants, and ethnicities. In recent years, significant progress has been made in understanding OFCs, due to advances in sequencing and genotyping technologies. Despite these advances, very little is known about the genetic interplay in the Malagasy population. Methods: Here, we performed high-resolution whole-exome sequencing (WES) on non-syndromic cleft lip with or without palate (nCL/P) trios in the Malagasy population (78 individuals from 26 families (trios)). To integrate the impact of genetic ancestry admixture, we computed both global and local ancestries. Results: Participants demonstrated a high percentage of both African and Asian admixture. We identified damaging variants in primary cilium-mediated pathway genes WNT5B (one family), GPC4 (one family), co-occurrence in MSX1 (five families), WDR11 (one family), and tubulin stabilizer SEPTIN9 (one family). Furthermore, we identified an autosomal homozygous damaging variant in PHGDH (one family) gene that may impact metabiotic activity. Lastly, all variants were predicted to reside on local Asian genetic ancestry admixed alleles. Conclusion: Our results from examining the Malagasy genome provide limited support for the hypothesis that germline variants in primary cilia may be risk factors for nCL/P, and outline the importance of integrating local ancestry components better to understand the multi-ethnic impact on nCL/P.
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The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar. Nat Commun 2023; 14:14. [PMID: 36627274 PMCID: PMC9832013 DOI: 10.1038/s41467-022-35215-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/22/2022] [Indexed: 01/12/2023] Open
Abstract
Many of Madagascar's unique species are threatened with extinction. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. Here, we compile a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimate natural rates of extinction, colonization, and speciation. We measure how long it would take to restore Madagascar's mammalian biodiversity under these rates, the "evolutionary return time" (ERT). At the time of human arrival there were approximately 250 species of mammals on Madagascar, resulting from 33 colonisation events (28 by bats), but at least 30 of these species have gone extinct since then. We show that the loss of currently threatened species would have a much deeper long-term impact than all the extinctions since human arrival. A return from current to pre-human diversity would take 1.6 million years (Myr) for bats, and 2.9 Myr for non-volant mammals. However, if species currently classified as threatened go extinct, the ERT rises to 2.9 Myr for bats and 23 Myr for non-volant mammals. Our results suggest that an extinction wave with deep evolutionary impact is imminent on Madagascar unless immediate conservation actions are taken.
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3
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Zhang R, Ni X, Yuan K, Pan Y, Xu S. MultiWaverX: modeling latent sex-biased admixture history. Brief Bioinform 2022; 23:6590437. [PMID: 35598333 DOI: 10.1093/bib/bbac179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Sex-biased gene flow has been common in the demographic history of modern humans. However, the lack of sophisticated methods for delineating the detailed sex-biased admixture process prevents insights into complex admixture history and thus our understanding of the evolutionary mechanisms of genetic diversity. Here, we present a novel algorithm, MultiWaverX, for modeling complex admixture history with sex-biased gene flow. Systematic simulations showed that MultiWaverX is a powerful tool for modeling complex admixture history and inferring sex-biased gene flow. Application of MultiWaverX to empirical data of 17 typical admixed populations in America, Central Asia, and the Middle East revealed sex-biased admixture histories that were largely consistent with the historical records. Notably, fine-scale admixture process reconstruction enabled us to recognize latent sex-biased gene flow in certain populations that would likely be overlooked by much of the routine analysis with commonly used methods. An outstanding example in the real world is the Kazakh population that experienced complex admixture with sex-biased gene flow but in which the overall signature has been canceled due to biased gene flow from an opposite direction.
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Affiliation(s)
- Rui Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xumin Ni
- School of Mathematics and Statistics, Beijing Jiaotong University, Beijing, 100044, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuhua Xu
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.,Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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4
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Tofanelli S, Bertoncini S, Donati G. Early Human Colonization, Climate Change and Megafaunal Extinction in Madagascar: The Contribution of Genetics in a Framework of Reciprocal Causations. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.708345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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5
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Liu Y, Wang T, Wu X, Fan X, Wang W, Xie G, Li Z, Yang Q, Cao P, Yang R, Liu F, Dai Q, Feng X, Ping W, Miao B, Wu Y, Liu Y, Fu Q. Maternal genetic history of southern East Asians over the past 12,000 years. J Genet Genomics 2021; 48:899-907. [PMID: 34419425 DOI: 10.1016/j.jgg.2021.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/13/2022]
Abstract
Southern East Asia, including Guangxi and Fujian provinces in China, is home to diverse ethnic groups, languages, and cultures. Previous studies suggest a high complexity regarding population dynamics and the history of southern East Asians. However, large-scale genetic studies on ancient populations in this region are hindered by limited sample preservation. Here, using highly efficient DNA capture techniques, we obtain 48 complete mitochondrial genomes of individuals from Guangxi and Fujian in China and reconstruct their maternal genetic history over the past 12,000 years. We find a strong connection between southern East Asians dating to ~12,000-6000 years ago and present-day Southeast Asians. In addition, stronger genetic affinities to northern East Asians are observed in historical southern East Asians than Neolithic southern East Asians, suggesting increased interactions between northern and southern East Asians over time. Overall, we reveal dynamic connections between ancient southern East Asians and populations located in surrounding regions, as well as a shift in maternal genetic structure within the populations over time.
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Affiliation(s)
- Yalin Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Sino-Danish Center, University of the Chinese Academy of Sciences, Beijing 100049, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Northwest University, Xi'an 710069, China
| | - Xichao Wu
- Fujian Longyan Museum, Longyan 364000, China
| | - Xuechun Fan
- International Research Center for Austronesian Archaeology, Pingtan 350000, China; Fujian Museum, Fuzhou 350001, China
| | - Wei Wang
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China
| | - Guangmao Xie
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China; College of History, Culture and Tourism, Guangxi Normal University, Guilin 541001, China
| | - Zhen Li
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China
| | - Qingping Yang
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Bo Miao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Northwest University, Xi'an 710069, China
| | - Yun Wu
- Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; Archaeological Institute for Yangtze Civilization, Wuhan University, Wuhan 430072, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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6
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Ahmadi N, Ramanantsoanirina A, Santos JD, Frouin J, Radanielina T. Evolutionary Processes Involved in the Emergence and Expansion of an Atypical O. sativa Group in Madagascar. RICE (NEW YORK, N.Y.) 2021; 14:44. [PMID: 34014423 PMCID: PMC8137759 DOI: 10.1186/s12284-021-00479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Understanding crops genetic diversity and the evolutionary processes that accompanied their worldwide spread is useful for designing effective breeding strategies. Madagascar Island was one of the last major Old World areas where human settlement brought the introduction of Oryza sativa. Early studies in the island had reported the presence of a rice group specific to Madagascar. Using 24 K SNP, we compared diversity patterns at the whole genome and at haplotype (30 SNP-long segments along the genome) levels, between 620 Malagasy and 1929 Asian rice accessions. The haplotype level analysis aimed at identifying local genotypic variations, relative to the whole genome level, using a group assignment method that relies on kernel density estimation in a Principal Component Analysis feature space. Migration bottleneck had resulted in 10-25% reduction of diversity among the Malagasy representatives of indica and japonica populations. Compared to their Asian counterpart, they showed slightly lower indica and japonica introgressions, suggesting the two populations had undergone less recombination when migration to the island occurred. The origins of the Malagasy indica and japonica groups were delineated to indica subpopulation from the Indian subcontinent and to tropical japonica from the Malay Archipelago, respectively. The Malagasy-specific group (Gm) had a rather high gene diversity and an original haplotype pattern: much lower share of indica haplotypes, and much higher share of Aus and japonica haplotypes than indica. Its emergence and expansion are most probably due to inter-group recombination facilitated by sympatry between indica-Aus admixes and "Bulu" type landraces of japonica in the central high plateaux of Madagascar, and to human selection for adaptation to the lowland rice cultivation. Pattern of rice genetic diversity was also tightly associated with the history of human settlement in the island. Emergence of the Gm group is associated with the latest arrivals of Austronesians, who founded the Merina kingdom in the high plateaux and developed lowland rice cultivation. As an intermediary form between Aus, indica and japonica, the three pillars of O. sativa domestication, Gm represents a very valuable genetic resource in breeding for adaptation to cold tolerance in tropical highlands. We proposed the name Rojo for this new rice group.
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Affiliation(s)
- Nourollah Ahmadi
- CIRAD, UMR AGAP, TA-A 108/03, Avenue Agropolis, F-34398, Montpellier Cedex 5, France.
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | | | - João D Santos
- CIRAD, UMR AGAP, TA-A 108/03, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Julien Frouin
- CIRAD, UMR AGAP, TA-A 108/03, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Tendro Radanielina
- Université de Antananarivo, département de biologie et écologie végétale, Antananarivo, Madagascar
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7
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Heiske M, Alva O, Pereda-Loth V, Van Schalkwyk M, Radimilahy C, Letellier T, Rakotarisoa JA, Pierron D. Genetic evidence and historical theories of the Asian and African origins of the present Malagasy population. Hum Mol Genet 2021; 30:R72-R78. [PMID: 33481023 DOI: 10.1093/hmg/ddab018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/23/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
The origin of the Malagasy population has been a subject of speculation since the 16th century. Contributions of African, Asian, Indian, Melanesian, Arabic and Persian populations have been suggested based on physical and cultural anthropology, oral tradition, linguistics and later also by archaeology. In the mid-20th century, increased knowledge of heredity rules and technical progress enabled the identification of African and Asian populations as main contributors. Recent access to the genomic landscape of Madagascar demonstrated pronounced regional variability in the relative contributions of these two ancestries, yet with significant presence of both African and Asian components throughout Madagascar. This article reviews the extent to which genetic results have settled historical questions concerning the origin of the Malagasy population. After an overview of the early literature, the genetic results of the 20th and 21th centuries are discussed and then complemented by the latest results in genome-wide analyses. While there is still much uncertainty regarding when, how and the circumstances under which the ancestors of the modern Malagasy population arrived on the island, we propose a scenario based on historical texts and genomic results.
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Affiliation(s)
- Margit Heiske
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | - Omar Alva
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | - Veronica Pereda-Loth
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | - Matthew Van Schalkwyk
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Chantal Radimilahy
- Musée d'Art et d'Archéologie, University of Antananarivo, Antananarivo, Madagascar
| | - Thierry Letellier
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | | | - Denis Pierron
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
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8
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Abstract
All results in this paper are based upon a new dataset consisting in 60 Swadesh lists of 207 items, overall 12,420 terms collected during 2018-2019. Each list corresponds to a different variety of Malagasy, which is not simply identified by the name of the ethnicity but also by the precise location where the variety was collected. This is very important since some traditional ethnic groups are a heritage of historical events rather than representing communities with similar habits and dialects. This new dataset is by far the best available, both for dimension and completeness. The varieties are classified both by standard tools, as the trees generated by UPGMA and NJ which privilege genealogy by detecting vertical transmissions, and by a new method which privileges horizontal exchanges. The new method results in a two-dimensional chart of Madagascar which realistically reproduces geography despite being generated only by comparison of words. The landing date of the ancestors of Malagasy is determined about 650 CE. This result is obtained by a straightforward approach based on the comparison of the UPGMA Malagasy family tree with the analogous tree of Romance family of languages for which all dates are well historically attested. We also propose an improved definition of Diversity computed for every locus in Madagascar and not only in places where the dialects were collected. Moreover, Diversity becomes a locally determined quantity as it is usually in biology. Diversity differences point to the South-East coast as the location where the first colonizers landed or, at least, where Malagasy variants started their dispersion. Finally, we find that the dialect spoken by the Mikea, a hunter-gatherer people in the South-West of Madagascar, is not very different from the variants of their neighbours Vezo and Masikoro. Therefore, Mikea unlikely can be linked to eventual aboriginal populations living in Madagascar prior to the main colonization event in 650 CE.
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Affiliation(s)
- Maurizio Serva
- Dipartimento di Ingegneria e Scienze dell’Informazione e Matematica, Università dell’Aquila, L’Aquila, Italy
| | - Michele Pasquini
- Dipartimento di Ingegneria e Scienze dell’Informazione e Matematica, Università dell’Aquila, L’Aquila, Italy
- * E-mail:
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9
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Impact of Ethnicity on the Prevalence of Early Repolarization Pattern in Children: Comparison Between Caucasian and African Populations. Pediatr Cardiol 2019; 40:1553-1558. [PMID: 31446474 DOI: 10.1007/s00246-019-02185-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/13/2019] [Indexed: 10/26/2022]
Abstract
The patterns and prevalence of early repolarization pattern (ER) in pediatric populations from ethnic backgrounds other than Caucasian have not been determined. Black African children (ages 4-12) from north-west Madagascar were prospectively recruited and their ECGs compared with those of age- and sex-matched Caucasian ethnicity individuals. ER was defined by ≥ 0.1 mV J-point elevation in at least two contiguous inferior and/or lateral ECG leads. A total of 616 children were included. There was a trend toward a higher frequency of ER in the Africans compared to the Caucasians (23.3% vs. 17.1%, respectively, p = 0.053). The subtype (slurred vs. notched) and location of ER (lateral, inferior, or inferior-lateral) were significantly different in the two groups (p < 0.001 and p = 0.020, respectively). There was no significant difference in the number of high-risk ECG features of ERP (i.e., horizontal/descendent pattern, inferior or inferior-lateral location or J-waves ≥ 2 mm) between African and Caucasian children. On the multivariate analysis, African ethnicity was an independent predictive factor of ER (OR 3.57, 95% CI 2.04-6.25, p < 0.001). African children have an increased risk of ER compared to Caucasian counterparts. Future studies should clarify the clinical and prognostic significance of ER in the pediatric population, and whether ethnicity has an impact on the outcomes.
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10
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Howes RE, Franchard T, Rakotomanga TA, Ramiranirina B, Zikursh M, Cramer EY, Tisch DJ, Kang SY, Ramboarina S, Ratsimbasoa A, Zimmerman PA. Risk Factors for Malaria Infection in Central Madagascar: Insights from a Cross-Sectional Population Survey. Am J Trop Med Hyg 2019; 99:995-1002. [PMID: 30182923 DOI: 10.4269/ajtmh.18-0417] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Community prevalence of infection is a widely used, standardized metric for evaluating malaria endemicity. Conventional methods for measuring prevalence include light microscopy and rapid diagnostic tests (RDTs), but their detection thresholds are inadequate for diagnosing low-density infections. The significance of submicroscopic malaria infections is poorly understood in Madagascar, a country of heterogeneous malaria epidemiology. A cross-sectional community survey in the western foothills of Madagascar during the March 2014 transmission season found malaria infection to be predominantly submicroscopic and asymptomatic. Prevalence of Plasmodium infection diagnosed by microscopy, RDT, and molecular diagnosis was 2.4%, 4.1%, and 13.8%, respectively. This diagnostic discordance was greatest for Plasmodium vivax infection, which was 98.5% submicroscopic. Village location, insecticide-treated bednet ownership, and fever were significantly associated with infection outcomes, as was presence of another infected individual in the household. Duffy-negative individuals were diagnosed with P. vivax, but with reduced odds relative to Duffy-positive hosts. The observation of high proportions of submicroscopic infections calls for a wider assessment of the parasite reservoir in other regions of the island, particularly given the country's current focus on malaria elimination and the poorly documented distribution of the non-P. falciparum parasite species.
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Affiliation(s)
- Rosalind E Howes
- Malaria Atlas Project, Nuffield Department of Medicine, Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom.,The Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Thierry Franchard
- National Malaria Control Programme of Madagascar, Ministry of Health, Antananarivo, Madagascar
| | | | - Brune Ramiranirina
- National Malaria Control Programme of Madagascar, Ministry of Health, Antananarivo, Madagascar
| | - Melinda Zikursh
- The Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Estee Y Cramer
- The Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Daniel J Tisch
- The Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Su Y Kang
- Malaria Atlas Project, Nuffield Department of Medicine, Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Stéphanie Ramboarina
- National Malaria Control Programme of Madagascar, Ministry of Health, Antananarivo, Madagascar.,The Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Arsène Ratsimbasoa
- Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar.,Faculty of Medicine, University of Antananarivo, Antananarivo, Madagascar.,National Malaria Control Programme of Madagascar, Ministry of Health, Antananarivo, Madagascar
| | - Peter A Zimmerman
- The Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
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11
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Tabata R, Kawaguchi F, Sasazaki S, Yamamoto Y, Rakotondraparany F, Ratsoavina FM, Yonezawa T, Mannen H. Phylogeographic Analysis of Madagascan Goats Using mtDNA Control Region and SRY Gene Sequences. Zoolog Sci 2019; 36:294-298. [DOI: 10.2108/zs180184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/21/2019] [Indexed: 11/17/2022]
Affiliation(s)
- Risa Tabata
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Yoshio Yamamoto
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Felix Rakotondraparany
- Mention Zoologie et Biodiversité Animale, Faculty of Sciences, Antananarivo University, BP 906 Ankatso, Antananarivo 101, Madagascar
| | - Fanomezana Mihaja Ratsoavina
- Mention Zoologie et Biodiversité Animale, Faculty of Sciences, Antananarivo University, BP 906 Ankatso, Antananarivo 101, Madagascar
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa 243-0034, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
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12
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Brucato N, Fernandes V, Kusuma P, Černý V, Mulligan CJ, Soares P, Rito T, Besse C, Boland A, Deleuze JF, Cox MP, Sudoyo H, Stoneking M, Pereira L, Ricaut FX. Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia. Genome Biol Evol 2019; 11:748-758. [PMID: 30715341 PMCID: PMC6423374 DOI: 10.1093/gbe/evz028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2019] [Indexed: 12/31/2022] Open
Abstract
The Austronesian dispersal across the Indonesian Ocean to Madagascar and the Comoros has been well documented, but in an unexplained anomaly, few to no traces have been found of the Austronesian expansion in East Africa or the Arabian Peninsula. To revisit this peculiarity, we surveyed the Western Indian Ocean rim populations to identify potential Austronesian genetic ancestry. We generated full mitochondrial DNA genomes and genome-wide genotyping data for these individuals and compared them with the Banjar, the Indonesian source population of the westward Austronesian dispersal. We find strong support for Asian genetic contributions to maternal lineages and autosomal variation in modern day Somalia and Yemen. Surprisingly, this input reveals two apparently different geographic origins and timings of admixture for the Austronesian contact; one at a very early phase (likely associated with the early Austronesian dispersals), and a later movement dating to the end of nineteenth century. These Austronesian gene flows come, respectively, from Madagascar and directly from an unidentified location in Island Southeast Asia. This result reveals a far more complex dynamic of Austronesian dispersals through the Western Indian Ocean than has previously been understood and suggests that Austronesian movements within the Indian Ocean may have been part of a lengthy process, probably continuing well into the modern era.
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Affiliation(s)
- Nicolas Brucato
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, Toulouse, France
| | - Veronica Fernandes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Porto, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Porto, Portugal
| | - Pradiptajati Kusuma
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Viktor Černý
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | | | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Porto, Portugal.,Centro de Biologia Molecular e Ambiental (CBMA), Departamento de Biologia, Universidade do Minho, Braga, Portugal
| | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Porto, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Medicine & ICVS/3B, PT Government Associate Laboratory, University of Minho, Braga, Portugal
| | - Céline Besse
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Murray P Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luisa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Porto, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Porto, Portugal
| | - François-Xavier Ricaut
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, Toulouse, France
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13
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Brucato N, Fernandes V, Mazières S, Kusuma P, Cox MP, Ng'ang'a JW, Omar M, Simeone-Senelle MC, Frassati C, Alshamali F, Fin B, Boland A, Deleuze JF, Stoneking M, Adelaar A, Crowther A, Boivin N, Pereira L, Bailly P, Chiaroni J, Ricaut FX. The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor. Am J Hum Genet 2018; 102:58-68. [PMID: 29304377 DOI: 10.1016/j.ajhg.2017.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/16/2017] [Indexed: 12/12/2022] Open
Abstract
At the dawn of the second millennium, the expansion of the Indian Ocean trading network aligned with the emergence of an outward-oriented community along the East African coast to create a cosmopolitan cultural and trading zone known as the Swahili Corridor. On the basis of analyses of new genome-wide genotyping data and uniparental data in 276 individuals from coastal Kenya and the Comoros islands, along with large-scale genetic datasets from the Indian Ocean rim, we reconstruct historical population dynamics to show that the Swahili Corridor is largely an eastern Bantu genetic continuum. Limited gene flows from the Middle East can be seen in Swahili and Comorian populations at dates corresponding to historically documented contacts. However, the main admixture event in southern insular populations, particularly Comorian and Malagasy groups, occurred with individuals from Island Southeast Asia as early as the 8th century, reflecting an earlier dispersal from this region. Remarkably, our results support recent archaeological and linguistic evidence-based suggestions that the Comoros archipelago was the earliest location of contact between Austronesian and African populations in the Swahili Corridor.
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Affiliation(s)
- Nicolas Brucato
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse 31073, France.
| | - Veronica Fernandes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto 4200-465, Portugal
| | - Stéphane Mazières
- Groupe Biologie des Groupes Sanguins, Aix Marseille Université, CNRS, Etablissement Francais du Sang, Anthropologie Bio-culturelle, Droit, Éthique et Santé, Marseille 13385, France
| | - Pradiptajati Kusuma
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse 31073, France; Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | | | | | - Marie-Claude Simeone-Senelle
- Langage, Langues et Cultures d'Afrique Noire, UMR 8135, CNRS, Institut National des Langues et Cultures Orientales, Université Sorbonne Paris Cité, BP 8, 94801 Villejuif-Cedex, France
| | - Coralie Frassati
- Groupe Biologie des Groupes Sanguins, Aix Marseille Université, CNRS, Etablissement Francais du Sang, Anthropologie Bio-culturelle, Droit, Éthique et Santé, Marseille 13385, France; Établissement Français du Sang Alpes Méditerranée, Marseille 13272, France
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, PO Box 1493, Dubai, United Arab Emirates
| | - Bertrand Fin
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Commissariat à L'Énergie Atomique et aux Énergies Alternatives, Evry 91000, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Commissariat à L'Énergie Atomique et aux Énergies Alternatives, Evry 91000, France
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Commissariat à L'Énergie Atomique et aux Énergies Alternatives, Evry 91000, France
| | | | - Alexander Adelaar
- Asia Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alison Crowther
- School of Social Science, University of Queensland, Brisbane 4072, Australia; Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Nicole Boivin
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Luisa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto 4200-465, Portugal
| | - Pascal Bailly
- Groupe Biologie des Groupes Sanguins, Aix Marseille Université, CNRS, Etablissement Francais du Sang, Anthropologie Bio-culturelle, Droit, Éthique et Santé, Marseille 13385, France; Établissement Français du Sang Alpes Méditerranée, Marseille 13272, France
| | - Jacques Chiaroni
- Groupe Biologie des Groupes Sanguins, Aix Marseille Université, CNRS, Etablissement Francais du Sang, Anthropologie Bio-culturelle, Droit, Éthique et Santé, Marseille 13385, France; Établissement Français du Sang Alpes Méditerranée, Marseille 13272, France
| | - François-Xavier Ricaut
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse 31073, France.
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14
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Abstract
Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations.
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15
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Arigliani M, Canciani MC, Mottini G, Altomare M, Magnolato A, Loa Clemente SV, Tshilolo L, Cogo P, Quanjer PH. Evaluation of the Global Lung Initiative 2012 Reference Values for Spirometry in African Children. Am J Respir Crit Care Med 2017; 195:229-236. [PMID: 27564235 DOI: 10.1164/rccm.201604-0693oc] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Despite the high burden of respiratory disease, no spirometry reference values for African children are available. OBJECTIVES Investigate whether the Global Lung Initiative (GLI-2012) reference values for spirometry are appropriate for children in sub-Saharan Africa and assess the impact of malnutrition on lung function. METHODS Anthropometry and spirometry were obtained in children aged 6 to 12 years from urban and semiurban schools in three African countries. Spirometry z-scores were derived using the GLI-2012 prediction equations for African Americans. Thinness (body mass index z-score < -2) was a surrogate for malnutrition. Spirometry outcomes were compared with those of African American children from the third National Health and Nutrition Survey. MEASUREMENTS AND MAIN RESULTS Spirometry data were analyzed from 1,082 schoolchildren (51% boys) aged 6.0 to 12.8 years in Angola (n = 306), Democratic Republic of the Congo (n = 377), and Madagascar (n = 399). GLI-2012 provided a good fit with mean (SD) z-scores of -0.11 (0.83) for FEV1, -0.08 (0.86) for FVC, and -0.07 (0.83) for FEV1/FVC. Because of low scatter, the fifth centile corresponded to -1.3 z-scores in boys and -1.5 z-scores in girls. Malnourished African children had a normal FEV1/FVC ratio but significant reductions of ∼0.5 z-scores (∼5%) in FEV1 and FVC compared with African American peers from the third National Health and Nutrition Survey. Children in Angola had the lowest, and those in Madagascar had the highest, zFEV1 and zFVC. CONCLUSIONS The results of this study support the use of GLI-2012 reference values for schoolchildren in sub-Saharan Africa. Malnutrition affects body growth, leading to a proportionately smaller FEV1 and FVC without respiratory impairment, as shown by the normal FEV1/FVC ratio.
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Affiliation(s)
- Michele Arigliani
- 1 Department of Clinical and Experimental Medical Sciences, Unit of Pediatrics, University Hospital of Udine, Udine, Italy
| | - Mario C Canciani
- 1 Department of Clinical and Experimental Medical Sciences, Unit of Pediatrics, University Hospital of Udine, Udine, Italy
| | - Giovanni Mottini
- 2 International Health Cooperation Project, University Campus Bio-Medico, Rome, Italy
| | | | | | | | - Leon Tshilolo
- 6 Service de Pédiatrie, Centre Hospitalier Monkole and Centre de Formation et d'Appui Sanitaire, Kinshasa, Democratic Republic of the Congo; and
| | - Paola Cogo
- 1 Department of Clinical and Experimental Medical Sciences, Unit of Pediatrics, University Hospital of Udine, Udine, Italy
| | - Philip H Quanjer
- 7 Department of Pulmonary Diseases and.,8 Department of Paediatrics-Pulmonary Diseases, Erasmus Medical Centre, Erasmus University, Rotterdam, the Netherlands
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16
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Howes RE, Chan ER, Rakotomanga TA, Schulte S, Gibson J, Zikursh M, Franchard T, Ramiranirina B, Ratsimbasoa A, Zimmerman PA. Prevalence and genetic variants of G6PD deficiency among two Malagasy populations living in Plasmodium vivax-endemic areas. Malar J 2017; 16:139. [PMID: 28376871 PMCID: PMC5381087 DOI: 10.1186/s12936-017-1771-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/08/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The prevalence and variants of G6PD deficiency in the Plasmodium vivax-endemic zones of Madagascar remain unknown. The admixed African-Austronesian origins of the Malagasy population make it probable that a heterogeneous mix of genetic variants with a spectrum of clinical severity will be circulating. This would have implications for the widespread use of P. vivax radical cure therapy. Two study populations in the P. vivax-endemic western foothills region of Madagascar were selected for G6PD screening. Both the qualitative fluorescent spot test and G6PD genotyping were used to screen all participants. RESULTS A total of 365 unrelated male volunteers from the Tsiroanomandidy, Mandoto, and Miandrivazo districts of Madagascar were screened and 12.9% were found to be phenotypically G6PD deficient. Full gene sequencing of 95 samples identified 16 single nucleotide polymorphisms, which were integrated into a genotyping assay. Genotyping (n = 291) found one individual diagnosed with the severe G6PD Mediterranean C563T mutation, while the remaining G6PD deficient samples had mutations of African origin, G6PD A- and G6PD A. CONCLUSIONS Deployment of P. vivax radical cure in Madagascar must be considerate of the risks presented by the observed prevalence of G6PDd prevalence. The potential morbidity associated with cumulative episodes of P. vivax clinical relapses requires a strategy for increasing access to safe radical cure. The observed dominance of African G6PDd haplotypes is surprising given the known mixed African-Austronesian origins of the Malagasy population; more widespread surveying of G6PDd epidemiology across the island would be required to characterize the distribution of G6PD haplotypes across Madagascar.
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Affiliation(s)
- Rosalind E Howes
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA. .,Nuffield Department of Medicine, Oxford Big Data Institute, University of Oxford, Oxford, UK.
| | - Ernest R Chan
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Tovonahary Angelo Rakotomanga
- National Malaria Control Programme, Ministry of Health, Antananarivo, Madagascar.,Faculty of Science, University of Antananarivo, Antananarivo, Madagascar
| | - Seth Schulte
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - John Gibson
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda Zikursh
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Thierry Franchard
- National Malaria Control Programme, Ministry of Health, Antananarivo, Madagascar.,Faculty of Science, University of Antananarivo, Antananarivo, Madagascar
| | - Brune Ramiranirina
- National Malaria Control Programme, Ministry of Health, Antananarivo, Madagascar
| | - Arsène Ratsimbasoa
- National Malaria Control Programme, Ministry of Health, Antananarivo, Madagascar.,University of Antananarivo, Antananarivo, Madagascar
| | - Peter A Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA.
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17
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Herrera MB, Thomson VA, Wadley JJ, Piper PJ, Sulandari S, Dharmayanthi AB, Kraitsek S, Gongora J, Austin JJ. East African origins for Madagascan chickens as indicated by mitochondrial DNA. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160787. [PMID: 28405364 PMCID: PMC5383821 DOI: 10.1098/rsos.160787] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/20/2017] [Indexed: 06/07/2023]
Abstract
The colonization of Madagascar by Austronesian-speaking people during AD 50-500 represents the most westerly point of the greatest diaspora in prehistory. A range of economically important plants and animals may have accompanied the Austronesians. Domestic chickens (Gallus gallus) are found in Madagascar, but it is unclear how they arrived there. Did they accompany the initial Austronesian-speaking populations that reached Madagascar via the Indian Ocean or were they late arrivals with Arabian and African sea-farers? To address this question, we investigated the mitochondrial DNA control region diversity of modern chickens sampled from around the Indian Ocean rim (Southeast Asia, South Asia, the Arabian Peninsula, East Africa and Madagascar). In contrast to the linguistic and human genetic evidence indicating dual African and Southeast Asian ancestry of the Malagasy people, we find that chickens in Madagascar only share a common ancestor with East Africa, which together are genetically closer to South Asian chickens than to those in Southeast Asia. This suggests that the earliest expansion of Austronesian-speaking people across the Indian Ocean did not successfully introduce chickens to Madagascar. Our results further demonstrate the complexity of the translocation history of introduced domesticates in Madagascar.
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Affiliation(s)
- Michael B. Herrera
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia, Australia
| | - Vicki A. Thomson
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia, Australia
| | - Jessica J. Wadley
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia, Australia
| | - Philip J. Piper
- School of Archaeology and Anthropology, Faculty of Arts, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sri Sulandari
- Genetic Laboratory, Division of Zoology, Research Center for Biology, The Indonesian Institute of Sciences (LIPI), Jl Raya Jakarta-Bogor Km.46, Cibinong 16911, Indonesia
| | - Anik Budhi Dharmayanthi
- Genetic Laboratory, Division of Zoology, Research Center for Biology, The Indonesian Institute of Sciences (LIPI), Jl Raya Jakarta-Bogor Km.46, Cibinong 16911, Indonesia
| | - Spiridoula Kraitsek
- Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jaime Gongora
- Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jeremy J. Austin
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia, Australia
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18
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Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM. Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. BMC Evol Biol 2016; 16:246. [PMID: 27832758 PMCID: PMC5105315 DOI: 10.1186/s12862-016-0816-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022] Open
Abstract
Background From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia. Results The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side. Conclusions The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Marrero
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain.
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19
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Mathias RA, Taub MA, Gignoux CR, Fu W, Musharoff S, O'Connor TD, Vergara C, Torgerson DG, Pino-Yanes M, Shringarpure SS, Huang L, Rafaels N, Boorgula MP, Johnston HR, Ortega VE, Levin AM, Song W, Torres R, Padhukasahasram B, Eng C, Mejia-Mejia DA, Ferguson T, Qin ZS, Scott AF, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Kumar R, Avila PC, Williams LK, Watson H, Ware LB, Olopade C, Olopade O, Oliveira R, Ober C, Nicolae DL, Meyers D, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker E, Araujo MI, Herrera-Paz EF, Gietzen K, Grus WE, Bamshad M, Bustamante CD, Kenny EE, Hernandez RD, Beaty TH, Ruczinski I, Akey J, Barnes KC. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nat Commun 2016; 7:12522. [PMID: 27725671 PMCID: PMC5062574 DOI: 10.1038/ncomms12522] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/12/2016] [Indexed: 01/20/2023] Open
Abstract
The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas. We summarize genetic variation in these populations, quantifying the postcolonial sex-biased European gene flow across multiple regions. Moreover, we refine estimates on the burden of deleterious variants carried across populations and how this varies with African ancestry. Our data are an important resource for empowering disease mapping studies in African-admixed individuals and will facilitate gene discovery for diseases disproportionately affecting individuals of African ancestry.
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Affiliation(s)
- Rasika Ann Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
- Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
| | - Christopher R. Gignoux
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Wenqing Fu
- Department of Genomic Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Shaila Musharoff
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Timothy D. O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Candelaria Vergara
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Dara G. Torgerson
- Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Suyash S. Shringarpure
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lili Huang
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Nicholas Rafaels
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | | | - Henry Richard Johnston
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia 30322, USA
| | - Victor E. Ortega
- Center for Human Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Albert M. Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan 48202, USA
| | - Wei Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Raul Torres
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California 94158, USA
| | - Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan 48202, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Delmy-Aracely Mejia-Mejia
- Centro de Neumologia y Alergias, San Pedro Sula 21102, Honduras
- Faculty of Medicine, Centro Medico de la Familia, San Pedro Sula 21102, Honduras
| | - Trevor Ferguson
- Tropical Medicine Research Institute, The University of the West Indies, St. Michael BB11115, Barbados
| | - Zhaohui S. Qin
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia 30322, USA
| | - Alan F. Scott
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, Leiden 2333ZA, The Netherlands
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
| | - Javier Marrugo
- Instituto de Investigaciones Immunologicas, Universidad de Cartagena, Cartagena 130000, Colombia
| | - Leslie A. Lange
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Rajesh Kumar
- Department of Pediatrics, Northwestern University, Chicago, Illinois 60637, USA
- The Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60637, USA
| | - Pedro C. Avila
- Department of Medicine, Northwestern University, Chicago, Illinois 60637, USA
| | - L. Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan 48202, USA
- Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan 48202, USA
| | - Harold Watson
- Faculty of Medical Sciences Cave Hill Campus, The University of the West Indies, Bridgetown BB11000, Barbados
- Queen Elizabeth Hospital, The University of the West Indies, St. Michael BB11115, Barbados
| | - Lorraine B. Ware
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Christopher Olopade
- Department of Medicine and Center for Global Health, University of Chicago, Chicago, Illinois 60637, USA
| | | | - Ricardo Oliveira
- Laboratório de Patologia Experimental, Centro de Pesquisas Gonçalo Moniz, Salvador 40296-710, Brazil
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Dan L. Nicolae
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
- Department of Statistics, University of Chicago, Chicago, Illinois 60637, USA
| | - Deborah Meyers
- Center for Human Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Alvaro Mayorga
- Centro de Neumologia y Alergias, San Pedro Sula 21102, Honduras
| | - Jennifer Knight-Madden
- Tropical Medicine Research Institute, The University of the West Indies, St. Michael BB11115, Barbados
| | - Tina Hartert
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Nadia N. Hansel
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Marilyn G. Foreman
- Pulmonary and Critical Care Medicine, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
| | - Jean G. Ford
- Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
- Department of Medicine, The Brooklyn Hospital Center, Brooklyn, New York 11201, USA
| | - Mezbah U. Faruque
- National Human Genome Center, Howard University College of Medicine, Washington DC 20059, USA
| | - Georgia M. Dunston
- National Human Genome Center, Howard University College of Medicine, Washington DC 20059, USA
- Department of Microbiology, Howard University College of Medicine, Washington DC 20059, USA
| | - Luis Caraballo
- Institute for Immunological Research, Universidad de Cartagena, Cartagena 130000, Colombia
| | - Esteban G. Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Eugene Bleecker
- Center for Human Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Maria Ilma Araujo
- Immunology Service, Universidade Federal da Bahia, Salvador 401110170, Brazil
| | - Edwin Francisco Herrera-Paz
- Centro de Neumologia y Alergias, San Pedro Sula 21102, Honduras
- Faculty of Medicine, Centro Medico de la Familia, San Pedro Sula 21102, Honduras
- Facultad de Medicina, Universidad Catolica de Honduras, San Pedro Sula 21102, Honduras
| | | | | | - Michael Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Eimear E. Kenny
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, California 94143, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
| | - Joshua Akey
- Department of Genomic Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Kathleen C. Barnes
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
- Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
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20
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Brucato N, Kusuma P, Cox MP, Pierron D, Purnomo GA, Adelaar A, Kivisild T, Letellier T, Sudoyo H, Ricaut FX. Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo. Mol Biol Evol 2016; 33:2396-400. [PMID: 27381999 PMCID: PMC4989113 DOI: 10.1093/molbev/msw117] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Malagasy genetic diversity results from an exceptional protoglobalization process that took place over a thousand years ago across the Indian Ocean. Previous efforts to locate the Asian origin of Malagasy highlighted Borneo broadly as a potential source, but so far no firm source populations were identified. Here, we have generated genome-wide data from two Southeast Borneo populations, the Banjar and the Ngaju, together with published data from populations across the Indian Ocean region. We find strong support for an origin of the Asian ancestry of Malagasy among the Banjar. This group emerged from the long-standing presence of a Malay Empire trading post in Southeast Borneo, which favored admixture between the Malay and an autochthonous Borneo group, the Ma’anyan. Reconciling genetic, historical, and linguistic data, we show that the Banjar, in Malay-led voyages, were the most probable Asian source among the analyzed groups in the founding of the Malagasy gene pool.
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Affiliation(s)
- Nicolas Brucato
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse, France
| | - Pradiptajati Kusuma
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse, France Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Denis Pierron
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse, France
| | - Gludhug A Purnomo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Toomas Kivisild
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom Estonian Biocentre, Tartu, Estonia
| | - Thierry Letellier
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse, France
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - François-Xavier Ricaut
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse, France
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21
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Busby GB, Band G, Si Le Q, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM, Manjurano A, Nyirongo V, Doumba O, Rockett KA, Kwiatkowski DP, Spencer CC. Admixture into and within sub-Saharan Africa. eLife 2016; 5. [PMID: 27324836 PMCID: PMC4915815 DOI: 10.7554/elife.15266] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/17/2016] [Indexed: 12/27/2022] Open
Abstract
Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology. DOI:http://dx.doi.org/10.7554/eLife.15266.001 Our genomes contain a record of historical events. This is because when groups of people are separated for generations, the DNA sequence in the two groups’ genomes will change in different ways. Looking at the differences in the genomes of people from the same population can help researchers to understand and reconstruct the historical interactions that brought their ancestors together. The mixing of two populations that were previously separate is known as admixture. Africa as a continent has few written records of its history. This means that it is somewhat unknown which important movements of people in the past generated the populations found in modern-day Africa. Busby et al. have now attempted to use DNA to look into this and reconstruct the last 4000 years of genetic history in African populations. As has been shown in other regions of the world, the new analysis showed that all African populations are the result of historical admixture events. However, Busby et al. could characterize these events to unprecedented level of detail. For example, multiple ethnic groups from The Gambia and Mali all show signs of sharing the same set of ancestors from West Africa, Europe and Asia who mixed around 2000 years ago. Evidence of a migration of people from Central West Africa, known as the Bantu expansion, could also be detected, and was shown to carry genes to the south and east. An important next step will be to now look at the consequences of the observed gene-flow, and ask if it has contributed to spreading beneficial, or detrimental, mutations around Africa. DOI:http://dx.doi.org/10.7554/eLife.15266.002
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Affiliation(s)
- George Bj Busby
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Quang Si Le
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Muminatou Jallow
- Medical Research Council Unit, Serrekunda, The Gambia.,Royal Victoria Teaching Hospital, Banjul, The Gambia
| | - Edith Bougama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Valentina D Mangano
- Dipartimento di Sanita Publica e Malattie Infettive, University of Rome La Sapienza, Rome, Italy
| | | | | | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | | | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Vysaul Nyirongo
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Ogobara Doumba
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Chris Ca Spencer
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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22
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Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy. Sci Rep 2016; 6:26066. [PMID: 27188237 PMCID: PMC4870696 DOI: 10.1038/srep26066] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/26/2016] [Indexed: 12/23/2022] Open
Abstract
The Austronesian expansion, one of the last major human migrations, influenced regions as distant as tropical Asia, Remote Oceania and Madagascar, off the east coast of Africa. The identity of the Asian groups that settled Madagascar is particularly mysterious. While language connects Madagascar to the Ma’anyan of southern Borneo, haploid genetic data are more ambiguous. Here, we screened genome-wide diversity in 211 individuals from the Ma’anyan and surrounding groups in southern Borneo. Surprisingly, the Ma’anyan are characterized by a distinct, high frequency genomic component that is not found in Malagasy. This novel genetic layer occurs at low levels across Island Southeast Asia and hints at a more complex model for the Austronesian expansion in this region. In contrast, Malagasy show genomic links to a range of Island Southeast Asian groups, particularly from southern Borneo, but do not have a clear genetic connection with the Ma’anyan despite the obvious linguistic association.
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23
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African origin of the malaria parasite Plasmodium vivax. Nat Commun 2015; 5:3346. [PMID: 24557500 PMCID: PMC4089193 DOI: 10.1038/ncomms4346] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/29/2014] [Indexed: 01/12/2023] Open
Abstract
Plasmodium vivax is the leading cause of human malaria in Asia and Latin America but is absent from most of central Africa due to the near fixation of a mutation that inhibits the expression of its receptor, the Duffy antigen, on human erythrocytes. The emergence of this protective allele is not understood because P. vivax is believed to have originated in Asia. Here we show, using a non-invasive approach, that wild chimpanzees and gorillas throughout central Africa are endemically infected with parasites that are closely related to human P. vivax. Sequence analyses reveal that ape parasites lack host specificity and are much more diverse than human parasites, which form a monophyletic lineage within the ape parasite radiation. These findings indicate that human P. vivax is of African origin and likely selected for the Duffy-negative mutation. All extant human P. vivax parasites are derived from a single ancestor that escaped out of Africa.
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24
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Tofanelli S, Brisighelli F, Anagnostou P, Busby GBJ, Ferri G, Thomas MG, Taglioli L, Rudan I, Zemunik T, Hayward C, Bolnick D, Romano V, Cali F, Luiselli D, Shepherd GB, Tusa S, Facella A, Capelli C. The Greeks in the West: genetic signatures of the Hellenic colonisation in southern Italy and Sicily. Eur J Hum Genet 2015; 24:429-36. [PMID: 26173964 DOI: 10.1038/ejhg.2015.124] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/29/2015] [Accepted: 05/06/2015] [Indexed: 11/09/2022] Open
Abstract
Greek colonisation of South Italy and Sicily (Magna Graecia) was a defining event in European cultural history, although the demographic processes and genetic impacts involved have not been systematically investigated. Here, we combine high-resolution surveys of the variability at the uni-parentally inherited Y chromosome and mitochondrial DNA in selected samples of putative source and recipient populations with forward-in-time simulations of alternative demographic models to detect signatures of that impact. Using a subset of haplotypes chosen to represent historical sources, we recover a clear signature of Greek ancestry in East Sicily compatible with the settlement from Euboea during the Archaic Period (eighth to fifth century BCE). We inferred moderate sex-bias in the numbers of individuals involved in the colonisation: a few thousand breeding men and a few hundred breeding women were the estimated number of migrants. Last, we demonstrate that studies aimed at quantifying Hellenic genetic flow by the proportion of specific lineages surviving in present-day populations may be misleading.
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Affiliation(s)
| | - Francesca Brisighelli
- Department of Zoology, University of Oxford, Oxford, UK.,Sezione di Medicina Legale-Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Università "La Sapienza", Roma, Italy.,Istituto Italiano di Antropologia, Roma, Italy
| | - George B J Busby
- Department of Zoology, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Gianmarco Ferri
- Dipartimento ad Attività Integrata di Laboratori, Anatomia Patologica, Medicina Legale, U.O. Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Luca Taglioli
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Igor Rudan
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Scotland, UK
| | - Tatijana Zemunik
- Department of Medical Biology, University of Split, School of Medicine, Split, Croatia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Deborah Bolnick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Valentino Romano
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, Italy.,Laboratorio di Genetica Molecolare, I.R.C.C.S. Associazione Oasi Maria SS., Troina, Italy
| | - Francesco Cali
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, Italy
| | - Donata Luiselli
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Gillian B Shepherd
- A.D. Trendall Research Centre for Ancient Mediterranean Studies, La Trobe University, Melbourne, Victoria, Australia
| | | | - Antonino Facella
- Soprintendenza per i Beni Archeologici della Calabria, Reggio Calabria, Italy
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25
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Randrianandrasana M, Berenbaum MR. Edible Non-Crustacean Arthropods in Rural Communities of Madagascar. J ETHNOBIOL 2015. [DOI: 10.2993/etbi-35-02-354-383.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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26
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Sarno S, Tofanelli S, De Fanti S, Quagliariello A, Bortolini E, Ferri G, Anagnostou P, Brisighelli F, Capelli C, Tagarelli G, Sineo L, Luiselli D, Boattini A, Pettener D. Shared language, diverging genetic histories: high-resolution analysis of Y-chromosome variability in Calabrian and Sicilian Arbereshe. Eur J Hum Genet 2015; 24:600-6. [PMID: 26130483 PMCID: PMC4929864 DOI: 10.1038/ejhg.2015.138] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/02/2015] [Accepted: 04/14/2015] [Indexed: 11/25/2022] Open
Abstract
The relationship between genetic and linguistic diversification in human populations has been often explored to interpret some specific issues in human history. The Albanian-speaking minorities of Sicily and Southern Italy (Arbereshe) constitute an important portion of the ethnolinguistic variability of Italy. Their linguistic isolation from neighboring Italian populations and their documented migration history, make such minorities particularly effective for investigating the interplay between cultural, geographic and historical factors. Nevertheless, the extent of Arbereshe genetic relationships with the Balkan homeland and the Italian recipient populations has been only partially investigated. In the present study we address the genetic history of Arbereshe people by combining highly resolved analyses of Y-chromosome lineages and extensive computer simulations. A large set of slow- and fast-evolving molecular markers was typed in different Arbereshe communities from Sicily and Southern Italy (Calabria), as well as in both the putative Balkan source and Italian sink populations. Our results revealed that the considered Arbereshe groups, despite speaking closely related languages and sharing common cultural features, actually experienced diverging genetic histories. The estimated proportions of genetic admixture confirm the tight relationship of Calabrian Arbereshe with modern Albanian populations, in accordance with linguistic hypotheses. On the other hand, population stratification and/or an increased permeability of linguistic and geographic barriers may be hypothesized for Sicilian groups, to account for their partial similarity with Greek populations and their higher levels of local admixture. These processes ultimately resulted in the differential acquisition or preservation of specific paternal lineages by the present-day Arbereshe communities.
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Affiliation(s)
- Stefania Sarno
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | | | - Sara De Fanti
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Andrea Quagliariello
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Eugenio Bortolini
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Gianmarco Ferri
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Università degli Studi di Modena e Reggio Emilia, Modena, Italia
| | - Paolo Anagnostou
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Roma, Italia.,Istituto Italiano di Antropologia, Roma, Italia
| | - Francesca Brisighelli
- Department of Zoology, University of Oxford, Oxford, UK.,Sezione di medicina Legale-Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | | | | | - Luca Sineo
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italia
| | - Donata Luiselli
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Alessio Boattini
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Davide Pettener
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
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27
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Hodgson JA, Pickrell JK, Pearson LN, Quillen EE, Prista A, Rocha J, Soodyall H, Shriver MD, Perry GH. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar. Proc Biol Sci 2015; 281:20140930. [PMID: 24990677 DOI: 10.1098/rspb.2014.0930] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa.
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Affiliation(s)
- Jason A Hodgson
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - Joseph K Pickrell
- New York Genome Center, New York, NY 10013, USA Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Laurel N Pearson
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ellen E Quillen
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - António Prista
- Faculdade de Educação Física e Desporto, Universidade Pedagógica, Maputo, Moçambique
| | - Jorge Rocha
- Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto (CIBIO), Vairão, Portugal Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Himla Soodyall
- Human Genomic Diversity and Disease Research Unit, Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Mark D Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - George H Perry
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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28
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Ardalan A, Oskarsson MCR, van Asch B, Rabakonandriania E, Savolainen P. African origin for Madagascan dogs revealed by mtDNA analysis. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140552. [PMID: 26064658 PMCID: PMC4453261 DOI: 10.1098/rsos.140552] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 04/17/2015] [Indexed: 06/04/2023]
Abstract
Madagascar was one of the last major land masses to be inhabited by humans. It was initially colonized by Austronesian speaking Indonesians 1500-2000 years ago, but subsequent migration from Africa has resulted in approximately equal genetic contributions from Indonesia and Africa, and the material culture has mainly African influences. The dog, along with the pig and the chicken, was part of the Austronesian Neolithic culture, and was furthermore the only domestic animal to accompany humans to every continent in ancient times. To illuminate Madagascan cultural origins and track the initial worldwide dispersal of dogs, we here investigated the ancestry of Madagascan dogs. We analysed mtDNA control region sequences in dogs from Madagascar (n=145) and compared it with that from potential ancestral populations in Island Southeast Asia (n=219) and sub-Saharan Africa (n=493). We found that 90% of the Madagascan dogs carried a haplotype that was also present in sub-Saharan Africa and that the remaining lineages could all be attributed to a likely origin in Africa. By contrast, only 26% of Madagascan dogs shared haplotypes with Indonesian dogs, and one haplotype typical for Austronesian dogs, carried by more than 40% of Indonesian and Polynesian dogs, was absent among the Madagascan dogs. Thus, in contrast to the human population, Madagascan dogs seem to trace their origin entirely from Africa. These results suggest that dogs were not brought to Madagascar by the initial Austronesian speaking colonizers on their transoceanic voyage, but were introduced at a later stage, together with human migration and cultural influence from Africa.
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Affiliation(s)
- Arman Ardalan
- Department of Gene Technology, KTH–Royal Institute of Technology, Science for Life Laboratory, Solna 171 21, Sweden
- Division of Animal Biotechnology and Genomics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Mattias C. R. Oskarsson
- Department of Gene Technology, KTH–Royal Institute of Technology, Science for Life Laboratory, Solna 171 21, Sweden
| | - Barbara van Asch
- IPATIMUP, Rua Dr Roberto Frias s/n, Porto 4200–465, Portugal
- Department of Genetics, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7601, South Africa
| | - Elisabeth Rabakonandriania
- Département de Biologie et Écologie Végétales, Faculté des Sciences Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Peter Savolainen
- Department of Gene Technology, KTH–Royal Institute of Technology, Science for Life Laboratory, Solna 171 21, Sweden
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29
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Eppley TM, Ganzhorn JU, Donati G. Cathemerality in a small, folivorous primate: proximate control of diel activity in Hapalemur meridionalis. Behav Ecol Sociobiol 2015. [DOI: 10.1007/s00265-015-1911-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kusuma P, Cox MP, Pierron D, Razafindrazaka H, Brucato N, Tonasso L, Suryadi HL, Letellier T, Sudoyo H, Ricaut FX. Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations. BMC Genomics 2015; 16:191. [PMID: 25880430 PMCID: PMC4373124 DOI: 10.1186/s12864-015-1394-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/24/2015] [Indexed: 11/18/2022] Open
Abstract
Background Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy language branches from the Southeast Barito language family of southern Borneo, Indonesia, with the closest language spoken today by the Ma’anyan. To test for a genetic link between Malagasy and these linguistically related Indonesian populations, we studied the Ma’anyan and other Indonesian ethnic groups (including the sea nomad Bajo) that, from their historical and linguistic contexts, may be modern descendants of the populations that helped enact the settlement of Madagascar. Result A combination of phylogeographic analysis of genetic distances, haplotype comparisons and inference of parental populations by linear optimization, using both maternal and paternal DNA lineages, suggests that Malagasy derive from multiple regional sources in Indonesia, with a focus on eastern Borneo, southern Sulawesi and the Lesser Sunda islands. Conclusion Settlement may have been mediated by ancient sea nomad movements because the linguistically closest population, Ma’anyan, has only subtle genetic connections to Malagasy, whereas genetic links with other sea nomads are more strongly supported. Our data hint at a more complex scenario for the Indonesian settlement of Madagascar than has previously been recognized. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1394-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pradiptajati Kusuma
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France. .,Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
| | - Denis Pierron
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Harilanto Razafindrazaka
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Nicolas Brucato
- Center for Linguistics, University of Leiden, Leiden, Netherlands.
| | - Laure Tonasso
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Helena Loa Suryadi
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
| | - Thierry Letellier
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia. .,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.
| | - François-Xavier Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
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Randrianaivo JB, Anholt RM, Tendrisoa DL, Margiano NJ, Courtright P, Lewallen S. Blindness and cataract surgical services in Atsinanana region, Madagascar. Middle East Afr J Ophthalmol 2014; 21:153-7. [PMID: 24791107 PMCID: PMC4005180 DOI: 10.4103/0974-9233.129767] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Purpose: To assess the prevalence and causes of avoidable blindness in Atsinanana Region, Madagascar, with the Rapid Assessment of Avoidable Blindness (RAAB) survey. We analyzed the hospital records to supplement the findings for public health care planning. Materials and Methods: Only villages within a two-hour walk from a road, about half of the population of Atsinanana was included. Seventy-two villages were selected by population-proportional-to-size sampling. In each village, compact segment sampling was used to select 50 people over age 50 for eye examination using standard RAAB methods. Records at the two hospitals providing cataract surgery in the region were analyzed for information on patients who underwent cataract surgery in 2010. Cataract incidence rate and target cataract surgery rate (CSR) was modeled from age-specific prevalence of cataract. Results: The participation rate was 87% and the sample prevalence of blindness was 1.96%. Cataract was responsible for 64% and 85.7% of blindness and severe visual impairment, respectively. Visual impairment was due to cataract (69.4%) and refractive error (14.1%). There was a strong positive correlation between cataract surgical rate by district and the proportion of people living within 2 hours of a road. There were marked differences in the profiles of the cataract patients at the two facilities. The estimated incidence of cataract at the 6/18 level was 2.4 eyes per 100 people over age 50 per year. Conclusions: Although the survey included only people with reasonable access, the main cause of visual impairment was still cataract. The incidence of cataract is such that it ought to be possible to eliminate it as a cause of visual impairment, but changes in service delivery at hospitals and strategies to improve access will be necessary for this change.
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Affiliation(s)
| | - R Michele Anholt
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
| | | | | | - Paul Courtright
- Kilimanjaro Centre for Community Ophthalmology Tanzania, Moshi, Tanzania ; Kilimanjaro Centre for Community Ophthalmology International, University of Cape Town, Cape Town, South Africa
| | - Susan Lewallen
- Kilimanjaro Centre for Community Ophthalmology Tanzania, Moshi, Tanzania ; Kilimanjaro Centre for Community Ophthalmology International, University of Cape Town, Cape Town, South Africa
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Trejaut JA, Poloni ES, Yen JC, Lai YH, Loo JH, Lee CL, He CL, Lin M. Taiwan Y-chromosomal DNA variation and its relationship with Island Southeast Asia. BMC Genet 2014; 15:77. [PMID: 24965575 PMCID: PMC4083334 DOI: 10.1186/1471-2156-15-77] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 06/10/2014] [Indexed: 01/12/2023] Open
Abstract
Background Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned. Results We examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South. Conclusion The geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15,000 years ago. The branches of the pincer contributed separately to the paternal gene pool of the Philippines and conjointly to the gene pools of Madagascar and the Solomon Islands. The North to South increase in diversity found for Taiwanese Austronesian speaking groups contrasts with observations based on mitochondrial DNA, thus hinting to a differentiated demographic history of men and women in these populations.
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Affiliation(s)
- Jean A Trejaut
- Mackay Memorial Hospital, Taipei, Molecular Anthropology Laboratory, 45 Min-Sheng Road,225115 Tamsui, New Taipei city, Taiwan.
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Fregel R, Seetah K, Betancor E, Suárez NM, Calaon D, Čaval S, Janoo A, Pestano J. Multiple ethnic origins of mitochondrial DNA lineages for the population of Mauritius. PLoS One 2014; 9:e93294. [PMID: 24676463 PMCID: PMC3968120 DOI: 10.1371/journal.pone.0093294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 03/04/2014] [Indexed: 11/18/2022] Open
Abstract
This article reports on the first genetic assessment of the contemporary Mauritian population. Small island nodes such as Mauritius played a critical role in historic globalization processes and revealing high-resolution details of labour sourcing is crucial in order to better understand early-modern diaspora events. Mauritius is a particularly interesting case given detailed historic accounts attesting to European (Dutch, French and British), African and Asian points of origin. Ninety-seven samples were analysed for mitochondrial DNA to begin unravelling the complex dynamics of the island's modern population. In corroboration with general demographic information, the majority of maternal lineages were derived from South Asia (58.76%), with Malagasy (16.60%), East/Southeast Asian (11.34%) and Sub-Saharan African (10.21%) also making significant contributions. This study pinpoints specific regional origins for the South Asian genetic contribution, showing a greater influence on the contemporary population from northern and southeast India. Moreover, the analysis of lineages related to the slave trade demonstrated that Madagascar and East Asia were the main centres of origin, with less influence from West Africa.
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Affiliation(s)
- Rosa Fregel
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain
- Department of Anthropology, Stanford University, Stanford, California, United States of America
- * E-mail:
| | - Krish Seetah
- Department of Anthropology, Stanford University, Stanford, California, United States of America
| | - Eva Betancor
- Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas, Spain
| | - Nicolás M. Suárez
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Diego Calaon
- Department of Anthropology, Stanford University, Stanford, California, United States of America
- IDEAS Interdepartmental Centre, Ca'Foscari University, Venice, Italy
| | - Saša Čaval
- Department of Anthropology, Stanford University, Stanford, California, United States of America
| | - Anwar Janoo
- Department of History, University of Mauritius, Reduit, Mauritius
| | - Jose Pestano
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain
- Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas, Spain
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Pierron D, Razafindrazaka H, Pagani L, Ricaut FX, Antao T, Capredon M, Sambo C, Radimilahy C, Rakotoarisoa JA, Blench RM, Letellier T, Kivisild T. Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar. Proc Natl Acad Sci U S A 2014; 111:936-41. [PMID: 24395773 PMCID: PMC3903192 DOI: 10.1073/pnas.1321860111] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Linguistic and cultural evidence suggest that Madagascar was the final point of two major dispersals of Austronesian- and Bantu-speaking populations. Today, the Mikea are described as the last-known Malagasy population reported to be still practicing a hunter-gatherer lifestyle. It is unclear, however, whether the Mikea descend from a remnant population that existed before the arrival of Austronesian and Bantu agriculturalists or whether it is only their lifestyle that separates them from the other contemporary populations of South Madagascar. To address these questions we have performed a genome-wide analysis of >700,000 SNP markers on 21 Mikea, 24 Vezo, and 24 Temoro individuals, together with 50 individuals from Bajo and Lebbo populations from Indonesia. Our analyses of these data in the context of data available from other Southeast Asian and African populations reveal that all three Malagasy populations are derived from the same admixture event involving Austronesian and Bantu sources. In contrast to the fact that most of the vocabulary of the Malagasy speakers is derived from the Barito group of the Austronesian language family, we observe that only one-third of their genetic ancestry is related to the populations of the Java-Kalimantan-Sulawesi area. Because no additional ancestry components distinctive for the Mikea were found, it is likely that they have adopted their hunter-gatherer way of life through cultural reversion, and selection signals suggest a genetic adaptation to their new lifestyle.
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Affiliation(s)
- Denis Pierron
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Unité Mixte de Recherche 5288, Centre National de la Recherche Scientifique, Université de Toulouse, 31073 Toulouse, France
- Plateforme Technologique d'Innovation Biomédicale, Institut National de la Santé et de la Recherche Médicale, 33600 Pessac, France
| | - Harilanto Razafindrazaka
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Unité Mixte de Recherche 5288, Centre National de la Recherche Scientifique, Université de Toulouse, 31073 Toulouse, France
- Plateforme Technologique d'Innovation Biomédicale, Institut National de la Santé et de la Recherche Médicale, 33600 Pessac, France
| | - Luca Pagani
- Division of Biological Anthropology, University of Cambridge, Cambridge CB2 3DZ, United Kingdom
| | - François-Xavier Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Unité Mixte de Recherche 5288, Centre National de la Recherche Scientifique, Université de Toulouse, 31073 Toulouse, France
| | - Tiago Antao
- Division of Biological Anthropology, University of Cambridge, Cambridge CB2 3DZ, United Kingdom
| | - Mélanie Capredon
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Unité Mixte de Recherche 5288, Centre National de la Recherche Scientifique, Université de Toulouse, 31073 Toulouse, France
| | - Clément Sambo
- Ecole Normale Supérieure, Université de Toliara, Toliara 601, Madagascar
| | - Chantal Radimilahy
- Institut de Civilisations/Musée d'Art et d'Archéologie, Isoraka, Antananarivo 101, Madagascar; and
| | - Jean-Aimé Rakotoarisoa
- Institut de Civilisations/Musée d'Art et d'Archéologie, Isoraka, Antananarivo 101, Madagascar; and
| | - Roger M. Blench
- Kay Williamson Educational Foundation, Cambridge CB1 2AL, United Kingdom
| | - Thierry Letellier
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Unité Mixte de Recherche 5288, Centre National de la Recherche Scientifique, Université de Toulouse, 31073 Toulouse, France
- Plateforme Technologique d'Innovation Biomédicale, Institut National de la Santé et de la Recherche Médicale, 33600 Pessac, France
| | - Toomas Kivisild
- Division of Biological Anthropology, University of Cambridge, Cambridge CB2 3DZ, United Kingdom
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Capredon M, Brucato N, Tonasso L, Choesmel-Cadamuro V, Ricaut FX, Razafindrazaka H, Rakotondrabe AB, Ratolojanahary MA, Randriamarolaza LP, Champion B, Dugoujon JM. Tracing Arab-Islamic inheritance in Madagascar: study of the Y-chromosome and mitochondrial DNA in the Antemoro. PLoS One 2013; 8:e80932. [PMID: 24278350 PMCID: PMC3838347 DOI: 10.1371/journal.pone.0080932] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/08/2013] [Indexed: 11/19/2022] Open
Abstract
Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.
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Affiliation(s)
- Mélanie Capredon
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
- Centre de recherche littéraire et historique de l’Océan Indien (CRLHOI), Département d’ethnologie, Université de La Réunion, Saint-Denis, France
- Department of Pediatrics, CHU Sainte Justine, Faculty of Medecine, University of Montreal, Quebec, Canada
- *
| | - Nicolas Brucato
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Laure Tonasso
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - Valérie Choesmel-Cadamuro
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - François-Xavier Ricaut
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - Harilanto Razafindrazaka
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | | | - Mamisoa Adelta Ratolojanahary
- Laboratoire d'Anthropologie Patrimoine -Transformations sociales- Transculturalité (LAP2T), Université Antananarivo, Antananarivo, Madagascar
| | - Louis-Paul Randriamarolaza
- Laboratoire d'Anthropologie Patrimoine -Transformations sociales- Transculturalité (LAP2T), Université Antananarivo, Antananarivo, Madagascar
| | - Bernard Champion
- Centre de recherche littéraire et historique de l’Océan Indien (CRLHOI), Département d’ethnologie, Université de La Réunion, Saint-Denis, France
| | - Jean-Michel Dugoujon
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
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Stone tools and foraging in northern Madagascar challenge Holocene extinction models. Proc Natl Acad Sci U S A 2013; 110:12583-8. [PMID: 23858456 DOI: 10.1073/pnas.1306100110] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Past research on Madagascar indicates that village communities were established about AD 500 by people of both Indonesian and East African heritage. Evidence of earlier visits is scattered and contentious. Recent archaeological excavations in northern Madagascar provide evidence of occupational sites with microlithic stone technologies related to foraging for forest and coastal resources. A forager occupation of one site dates to earlier than 2000 B.C., doubling the length of Madagascar's known occupational history, and thus the time during which people exploited Madagascar's environments. We detail stratigraphy, chronology, and artifacts from two rock shelters. Ambohiposa near Iharana (Vohémar) on the northeast coast, yielded a stratified assemblage with small flakes, microblades, and retouched crescentic and trapezoidal tools, probably projectile elements, made on cherts and obsidian, some brought more that 200 km. (14)C dates are contemporary with the earliest villages. No food remains are preserved. Lakaton'i Anja near Antsiranana in the north yielded several stratified assemblages. The latest assemblage is well dated to A.D. 1050-1350, by (14)C and optically stimulated luminescence dating and pottery imported from the Near East and China. Below is a series of stratified assemblages similar to Ambohiposa. (14)C and optically stimulated luminescence dates indicate occupation from at least 2000 B.C. Faunal remains indicate a foraging pattern. Our evidence shows that foragers with a microlithic technology were active in Madagascar long before the arrival of farmers and herders and before many Late Holocene faunal extinctions. The differing effects of historically distinct economies must be identified and understood to reconstruct Holocene histories of human environmental impact.
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Poetsch M, Wiegand A, Harder M, Blöhm R, Rakotomavo N, Freitag-Wolf S, von Wurmb-Schwark N. Determination of population origin: a comparison of autosomal SNPs, Y-chromosomal and mtDNA haplogroups using a Malagasy population as example. Eur J Hum Genet 2013; 21:1423-8. [PMID: 23612573 DOI: 10.1038/ejhg.2013.51] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 02/13/2013] [Accepted: 02/20/2013] [Indexed: 11/09/2022] Open
Abstract
Y-chromosomal and mitochondrial DNA (mtDNA) polymorphisms have been used for population studies for a long time. However, there is another possibility to define the origin of a population: autosomal single-nucleotide polymorphisms (SNPs) whose allele frequencies differ considerably in different populations. In an attempt to compare the usefulness of these approaches we studied a population from Madagascar using all the three mentioned approaches. Former investigations of Malagasy maternal (mtDNA) and paternal (Y chromosome) lineages have led to the assumption that the Malagasy are an admixed population with an African and Asian-Indonesian heritage. Our additional study demonstrated that more than two-third of the Malagasy investigated showed clearly a West African genotype regarding only the autosomal SNPs despite the fact that 64% had an Asian mtDNA and more than 70% demonstrated an Asian-Indonesian heritage in either mtDNA or Y-chromosomal haplogroup or both. Nonetheless, the admixture of the Malagasy could be confirmed. A clear African or Asian-Indonesian heritage according to all the three DNA approaches investigated was only found in 14% and 1% of male samples, respectively. Not even the European or Northern African influences, detected in 9% of males (Y-chromosomal analysis) and 11% of samples (autosomal SNPs) were consistent. No Malagasy in our samples showed a European or Northern African origin in both categories. So, the analysis of autosomal SNPs could confirm the admixed character of the Malagasy population, even if it pointed to a greater African influence as detectable by Y-chromosomal or mtDNA analysis.
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Affiliation(s)
- Micaela Poetsch
- Institute of Legal Medicine, University Hospital Essen, Essen, Germany
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Pijpe J, de Voogt A, van Oven M, Henneman P, van der Gaag KJ, Kayser M, de Knijff P. Indian Ocean crossroads: human genetic origin and population structure in the Maldives. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 151:58-67. [PMID: 23526367 PMCID: PMC3652038 DOI: 10.1002/ajpa.22256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 02/05/2013] [Indexed: 11/07/2022]
Abstract
The Maldives are an 850 km-long string of atolls located centrally in the northern Indian Ocean basin. Because of this geographic situation, the present-day Maldivian population has potential for uncovering genetic signatures of historic migration events in the region. We therefore studied autosomal DNA-, mitochondrial DNA-, and Y-chromosomal DNA markers in a representative sample of 141 unrelated Maldivians, with 119 from six major settlements. We found a total of 63 different mtDNA haplotypes that could be allocated to 29 mtDNA haplogroups, mostly within the M, R, and U clades. We found 66 different Y-STR haplotypes in 10 Y-chromosome haplogroups, predominantly H1, J2, L, R1a1a, and R2. Parental admixture analysis for mtDNA- and Y-haplogroup data indicates a strong genetic link between the Maldive Islands and mainland South Asia, and excludes significant gene flow from Southeast Asia. Paternal admixture from West Asia is detected, but cannot be distinguished from admixture from South Asia. Maternal admixture from West Asia is excluded. Within the Maldives, we find a subtle genetic substructure in all marker systems that is not directly related to geographic distance or linguistic dialect. We found reduced Y-STR diversity and reduced male-mediated gene flow between atolls, suggesting independent male founder effects for each atoll. Detected reduced female-mediated gene flow between atolls confirms a Maldives-specific history of matrilocality. In conclusion, our new genetic data agree with the commonly reported Maldivian ancestry in South Asia, but furthermore suggest multiple, independent immigration events and asymmetrical migration of females and males across the archipelago.
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Affiliation(s)
- Jeroen Pijpe
- Department of Human Genetics, Leiden University Medical Center, Postzone S5, 2300 RC Leiden, The Netherlands.
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Grant AV, El Baghdadi J, Sabri A, El Azbaoui S, Alaoui-Tahiri K, Abderrahmani Rhorfi I, Gharbaoui Y, Abid A, Benkirane M, Raharimanga V, Richard V, Orlova M, Boland A, Migaud M, Okada S, Nolan DK, Bustamante J, Barreiro LB, Schurr E, Boisson-Dupuis S, Rasolofo V, Casanova JL, Abel L. Age-dependent association between pulmonary tuberculosis and common TOX variants in the 8q12-13 linkage region. Am J Hum Genet 2013; 92:407-14. [PMID: 23415668 DOI: 10.1016/j.ajhg.2013.01.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/12/2012] [Accepted: 01/22/2013] [Indexed: 11/19/2022] Open
Abstract
Only a small fraction of individuals infected with Mycobacterium tuberculosis develop clinical tuberculosis (TB) in their lifetime. Genetic epidemiological evidence suggests a genetic determinism of pulmonary TB (PTB), but the molecular basis of genetic predisposition to PTB remains largely unknown. We used a positional-cloning approach to carry out ultrafine linkage-disequilibrium mapping of a previously identified susceptibility locus in chromosomal region 8q12-13 by genotyping 3,216 SNPs in a family-based Moroccan sample including 286 offspring with PTB. We observed 44 PTB-associated SNPs (p < 0.01), which were genotyped in an independent set of 317 cases and 650 controls from Morocco. A single signal, consisting of two correlated SNPs close to TOX, rs1568952 and rs2726600 (combined p = 1.1 × 10(-5) and 9.2 × 10(-5), respectively), was replicated. Stronger evidence of association was found in individuals who developed PTB before the age of 25 years (combined p for rs1568952 = 4.4 × 10(-8); odds ratio of PTB for AA versus AG/GG = 3.09 [1.99-4.78]). The association with rs2726600 (p = 0.04) was subsequently replicated in PTB-affected subjects under 25 years in a study of 243 nuclear families from Madagascar. Stronger evidence of replication in Madagascar was obtained for additional SNPs in strong linkage disequilibrium with the two initial SNPs (p = 0.003 for rs2726597), further confirming the signal. We thus identified around rs1568952 and rs2726600 a cluster of SNPs strongly associated with early-onset PTB in Morocco and Madagascar. SNP rs2726600 is located in a transcription-factor binding site in the 3' region of TOX, and further functional explorations will focus on CD4 T lymphocytes.
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Affiliation(s)
- Audrey V Grant
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U980, Paris, France
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Mirabal S, Cadenas AM, Garcia-Bertrand R, Herrera RJ. Ascertaining the role of Taiwan as a source for the Austronesian expansion. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:551-64. [PMID: 23440864 DOI: 10.1002/ajpa.22226] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/14/2012] [Indexed: 01/15/2023]
Abstract
Taiwanese aborigines have been deemed the ancestors of Austronesian speakers which are currently distributed throughout two-thirds of the globe. As such, understanding their genetic distribution and diversity as well as their relationship to mainland Asian groups is important to consolidating the numerous models that have been proposed to explain the dispersal of Austronesian speaking peoples into Oceania. To better understand the role played by the aboriginal Taiwanese in this diaspora, we have analyzed a total of 451 individuals belonging to nine of the tribes currently residing in Taiwan, namely the Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, and the Yami from Orchid Island off the coast of Taiwan across 15 autosomal short tandem repeat loci. In addition, we have compared the genetic profiles of these tribes to populations from mainland China as well as to collections at key points throughout the Austronesian domain. While our results suggest that Daic populations from Southern China are the likely forefathers of the Taiwanese aborigines, populations within Taiwan show a greater genetic impact on groups at the extremes of the current domain than populations from Indonesia, Mainland, or Southeast Asia lending support to the "Out of Taiwan" hypothesis. We have also observed that specific Taiwanese aboriginal groups (Paiwan, Puyuma, and Saisiyat), and not all tribal populations, have highly influenced genetic distributions of Austronesian populations in the pacific and Madagascar suggesting either an asymmetric migration out of Taiwan or the loss of certain genetic signatures in some of the Taiwanese tribes due to endogamy, isolation, and/or drift.
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Affiliation(s)
- Sheyla Mirabal
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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Abstract
In mammals, the Y chromosome plays the pivotal role in male sex determination and is essential for normal sperm production. Yet only three Y chromosomes have been completely sequenced to date--those of human, chimpanzee, and rhesus macaque. While Y chromosomes are notoriously difficult to sequence owing to their highly repetitive genomic landscapes, these dedicated sequencing efforts have generated tremendous yields in medical, biological, and evolutionary insight. Knowledge of the complex structural organization of the human Y chromosome and a complete catalog of its gene content have provided a deeper understanding of the mechanisms that generate disease-causing mutations and large-scale rearrangements. Variation among human Y-chromosome sequences has been an invaluable tool for understanding relationships among human populations. Comprehensive comparisons of the human Y-chromosome sequence with those of other primates have illuminated aspects of Y-chromosome evolutionary dynamics over much longer timescales (>25 million years compared with 100,000 years). The future sequencing of additional Y chromosomes will provide a basis for a more comprehensive understanding of the evolution of Y chromosomes and their roles in reproductive biology.
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Affiliation(s)
- Jennifer F Hughes
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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Donati G, Santini L, Razafindramanana J, Boitani L, Borgognini-Tarli S. (Un-)expected nocturnal activity in "Diurnal" Lemur catta supports cathemerality as one of the key adaptations of the lemurid radiation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012. [PMID: 23180596 DOI: 10.1002/ajpa.22180] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The ability to operate during the day and at night (i.e., cathemerality) is common among mammals but has rarely been identified in primates. Adaptive hypotheses assume that cathemerality represents a stable adaptation in primates, while nonadaptive hypotheses propose that it is the result of an evolutionary disequilibrium arising from human impacts on natural habitats. Madagascar offers a unique opportunity to study the evolution of activity patterns as there we find a monophyletic primate radiation that shows nocturnal, diurnal, and cathemeral patterns. However, when and why cathemeral activity evolved in lemurs is the subject of intense debate. Thus far, this activity pattern has been regularly observed in only three lemurid genera but the actual number of lemur species exhibiting this activity is as yet unknown. Here we show that the ring-tailed lemur, Lemur catta, a species previously considered to be diurnal, can in fact be cathemeral in the wild. In neighboring but distinct forest areas these lemurs exhibited either mainly diurnal or cathemeral activity. We found that, as in other cathemeral lemurs, activity was entrained by photoperiod and masked by nocturnal luminosity. Our results confirm the relationship between transitional eye anatomy and physiology and 24-h activity, thus supporting the adaptive scenario. Also, on the basis of the most recent strepsirrhine phylogenetic reconstruction, using parsimony criterion, our findings suggest pushing back the emergence of cathemerality to stem lemurids. Flexible activity over 24-h could thus have been one of the key adaptations of the early lemurid radiation possibly driven by Madagascar's island ecology.
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Affiliation(s)
- Giuseppe Donati
- Department of Social Sciences, Oxford Brookes University, UK.
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Simms TM, Wright MR, Martinez E, Regueiro M, McCartney Q, Herrera RJ. Y-STR diversity and sex-biased gene flow among Caribbean populations. Gene 2012. [PMID: 23178184 DOI: 10.1016/j.gene.2012.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In the present study, we report, for the first time, the allele and haplotype frequencies of 17 Y-STR (Y-filer) loci in the populations of Haiti, Jamaica and the Bahamas (Abaco, Eleuthera, Exuma, Grand Bahama, Long Island and New Providence). This investigation was undertaken to assess the paternal genetic structure of the abovementioned Caribbean islands. A total of 607 different haplotypes were identified among the 691 males examined, of which 537 (88.5%) were unique. Haplotype diversities (HD) ranged from 0.989 in Long Island to 1.000 in Grand Bahama, with limited haplotype sharing observed among these Caribbean collections. Discriminatory capacity (DC) values were also high, ranging from 79.1% to 100% in Long Island and Grand Bahama, respectively, illustrating the capacity of this set of markers to differentiate between patrilineal related individuals within each population. Phylogenetic comparison of the Bahamian, Haitian and Jamaican groups with available African, European, East Asian and Native American populations reveals strong genetic ties with the continental African collections, a finding that corroborates our earlier work using autosomal STR and Y-chromosome binary markers. In addition, various degrees of sex-biased gene flow exhibiting disproportionately higher European paternal (as compared to autosomal) influences were detected in all Caribbean islands genotyped except for Abaco and Eleuthera. We attribute the presence or absence of asymmetric gene flow to unique, island specific demographic events and family structures.
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Affiliation(s)
- Tanya M Simms
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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Dewar RE, Richard AF. Madagascar: A History of Arrivals, What Happened, and Will Happen Next. ANNUAL REVIEW OF ANTHROPOLOGY 2012. [DOI: 10.1146/annurev-anthro-092611-145758] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most of the ancestors of today's human and animal populations reached Madagascar over the last 65 million years, by a variety of routes at a variety of times. Settlers encountered a big, isolated island with an unpredictable climate and a wide array of landscapes. Although patterns of diversification were driven by different mechanisms in humans and animals, the complex interplay between historical contingency and responsiveness to local conditions is evident in both. Global climate change will affect Madagascar, although exactly how remains unclear, and the immediate impact of human activity on the island is overtaking that of gradual global change. Three themes in this review bear on the future: the continuing impact of recent, cataclysmic events on modern communities of people, plants, and animals; Madagascar's long and dynamic environmental history; and the complicated history of how people settled and interacted with the island's landscapes. A deeper understanding of all three can contribute to wise decision making in the coming years.
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Affiliation(s)
- Robert E. Dewar
- Department of Anthropology, Yale University, New Haven, Connecticut 06511-8277
| | - Alison F. Richard
- Department of Anthropology, Yale University, New Haven, Connecticut 06511-8277
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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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Randriamanantany ZA, Rajaonatahina DH, Razafimanantsoa FE, Rasamindrakotroka MT, Andriamahenina R, Rasoarilalamanarivo FB, Hanitriniala SP, Herisoa FR, Rasamindrakotroka A, Rakoto Alson OA. Phenotypic and allelic profile of ABO and Rhésus D blood group system among blood donor in Antananarivo. Int J Immunogenet 2012; 39:477-9. [DOI: 10.1111/j.1744-313x.2012.01120.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cox MP, Nelson MG, Tumonggor MK, Ricaut FX, Sudoyo H. A small cohort of Island Southeast Asian women founded Madagascar. Proc Biol Sci 2012; 279:2761-8. [PMID: 22438500 DOI: 10.1098/rspb.2012.0012] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The settlement of Madagascar is one of the most unusual, and least understood, episodes in human prehistory. Madagascar was one of the last landmasses to be reached by people, and despite the island's location just off the east coast of Africa, evidence from genetics, language and culture all attests that it was settled jointly by Africans, and more surprisingly, Indonesians. Nevertheless, extremely little is known about the settlement process itself. Here, we report broad geographical screening of Malagasy and Indonesian genetic variation, from which we infer a statistically robust coalescent model of the island's initial settlement. Maximum-likelihood estimates favour a scenario in which Madagascar was settled approximately 1200 years ago by a very small group of women (approx. 30), most of Indonesian descent (approx. 93%). This highly restricted founding population raises the possibility that Madagascar was settled not as a large-scale planned colonization event from Indonesia, but rather through a small, perhaps even unintended, transoceanic crossing.
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Affiliation(s)
- Murray P Cox
- Institute of Molecular BioSciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
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Interdisciplinary approach to the demography of Jamaica. BMC Evol Biol 2012; 12:24. [PMID: 22360861 PMCID: PMC3299582 DOI: 10.1186/1471-2148-12-24] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/23/2012] [Indexed: 11/22/2022] Open
Abstract
Background The trans-Atlantic slave trade dramatically changed the demographic makeup of the New World, with varying regions of the African coast exploited differently over roughly a 400 year period. When compared to the discrete mitochondrial haplotype distribution of historically appropriate source populations, the unique distribution within a specific source population can prove insightful in estimating the contribution of each population. Here, we analyzed the first hypervariable region of mitochondrial DNA in a sample from the Caribbean island of Jamaica and compared it to aggregated populations in Africa divided according to historiographically defined segments of the continent's coastline. The results from these admixture procedures were then compared to the wealth of historic knowledge surrounding the disembarkation of Africans on the island. Results In line with previous findings, the matriline of Jamaica is almost entirely of West African descent. Results from the admixture analyses suggest modern Jamaicans share a closer affinity with groups from the Gold Coast and Bight of Benin despite high mortality, low fecundity, and waning regional importation. The slaves from the Bight of Biafra and West-central Africa were imported in great numbers; however, the results suggest a deficit in expected maternal contribution from those regions. Conclusions When considering the demographic pressures imposed by chattel slavery on Jamaica during the slave era, the results seem incongruous. Ethnolinguistic and ethnographic evidence, however, may explain the apparent non-random levels of genetic perseverance. The application of genetics may prove useful in answering difficult demographic questions left by historically voiceless groups.
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Bertoncini S, Bulayeva K, Ferri G, Pagani L, Caciagli L, Taglioli L, Semyonov I, Bulayev O, Paoli G, Tofanelli S. The dual origin of Tati-speakers from Dagestan as written in the genealogy of uniparental variants. Am J Hum Biol 2012; 24:391-9. [PMID: 22275152 DOI: 10.1002/ajhb.22220] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/23/2011] [Accepted: 12/03/2011] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES Tat language is classified in an Iranian subbranch of the Indo-European family. It is spoken in the Caucasus and in the West Caspian region by populations with heterogeneous cultural traditions and religion whose ancestry is unknown. The aim of this study is to get a first insight about the genetic history of this peculiar linguistic group. METHODS We investigated the uniparental gene pools, defined by NRY and mtDNA high-resolution markers, in two Tati-speaking communities from Dagestan: Mountain Jews or Juhur, who speak the Judeo-Tat dialect, and the Tats, who speak the Muslim-Tat dialect. The samples have been collected in monoethnic rural villages and selected on the basis of genealogical relationships. A novel approach aimed at resolving cryptic cases in the recent history of human populations, which combines the properties of uniparental genetic markers with the potential of "forward-in-time" computer simulations, is presented. RESULTS Judeo-Tats emerged as a group with tight matrilineal genetic legacy who separated early from other Jewish communities. Tats exhibited genetic signals of a much longer in situ evolution, which appear as substantially unlinked with other Indo-Iranian enclaves in the Caucasus. CONCLUSIONS The independent demographic histories of the two samples, with mutually reversed profiles at paternally and maternally transmitted genetic systems, suggest that geographic proximity and linguistic assimilation of Tati-speakers from Dagestan do not reflect a common ancestry.
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Capredon M, Sanchez-Mazas A, Guitard E, Razafindrazaka H, Chiaroni J, Champion B, Dugoujon JM. The Arabo-Islamic migrations in Madagascar: first genetic study of the GM system in three Malagasy populations. Int J Immunogenet 2011; 39:161-9. [DOI: 10.1111/j.1744-313x.2011.01069.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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