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Yonezawa T, Mannen H, Honma K, Matsunaga M, Rakotondraparany F, Ratsoavina FM, Wu J, Nishibori M, Yamamoto Y. Origin and spatial population structure of Malagasy native chickens based on mitochondrial DNA. Sci Rep 2024; 14:569. [PMID: 38177203 PMCID: PMC10766636 DOI: 10.1038/s41598-023-50708-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/23/2023] [Indexed: 01/06/2024] Open
Abstract
Since Malagasy human culture became established in a multi-layered way by genetic admixture of Austronesian (Indonesia), Bantu (East Africa) and West Asian populations, the Malagasy native livestock should also have originated from these regions. While recent genetic studies revealed that Malagasy native dogs and goats were propagated from Africa, the origin of Malagasy native chickens is still controversial. Here, we conducted a phylogeographic analysis of the native chickens, focusing on the historical relationships among the Indian Ocean rim countries and based on mitochondrial D-loop sequences. Although previous work suggested that the rare Haplogroup D occurs with high frequencies in Island Southeast Asia-Pacific, East Africa and Madagascar, the major mitochondrial lineage in Malagasy populations is actually not Haplogroup D but the Sub-haplogroup C2, which is also observed in East Africa, North Africa, India and West Asia. We demonstrate that the Malagasy native chickens were propagated directly from West Asia (including India and North Africa), and not via East Africa. Furthermore, they display clear genetic differentiation within Madagascar, separated into the Highland and Lowland regions as seen in the human genomic landscape on this island. Our findings provide new insights for better understanding the intercommunion of material/non-material cultures within and around Madagascar.
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Affiliation(s)
- Takahiro Yonezawa
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
- 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
| | - Kaho Honma
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
- Chubu Regional Office, Agriculture and Forestry Bureau, Tottori, 682-0802, Japan
| | - Megumi Matsunaga
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Felix Rakotondraparany
- Department of Zoology and Animal Biodiversity, Faculty of Science, University of Antananarivo, BP 906, 101, Antananarivo, Madagascar
| | - Fanomezana Mihaja Ratsoavina
- Department of Zoology and Animal Biodiversity, Faculty of Science, University of Antananarivo, BP 906, 101, Antananarivo, Madagascar
| | - Jiaqi Wu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimo-Kasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Masahide Nishibori
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
| | - Yoshio Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
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Alva O, Leroy A, Heiske M, Pereda-Loth V, Tisseyre L, Boland A, Deleuze JF, Rocha J, Schlebusch C, Fortes-Lima C, Stoneking M, Radimilahy C, Rakotoarisoa JA, Letellier T, Pierron D. The loss of biodiversity in Madagascar is contemporaneous with major demographic events. Curr Biol 2022; 32:4997-5007.e5. [PMID: 36334586 DOI: 10.1016/j.cub.2022.09.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/13/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Only 400 km off the coast of East Africa, the island of Madagascar is one of the last large land masses to have been colonized by humans. While many questions surround the human occupation of Madagascar, recent studies raise the question of human impact on endemic biodiversity and landscape transformation. Previous genetic and linguistic analyses have shown that the Malagasy population has emerged from an admixture that happened during the last millennium, between Bantu-speaking African populations and Austronesian-speaking Asian populations. By studying the sharing of chromosome segments between individuals (IBD determination), local ancestry information, and simulated genetic data, we inferred that the Malagasy ancestral Asian population was isolated for more than 1,000 years with an effective size of just a few hundred individuals. This isolation ended around 1,000 years before present (BP) by admixture with a small African population. Around the admixture time, there was a rapid demographic expansion due to intrinsic population growth of the newly admixed population, which coincides with extensive changes in Madagascar's landscape and the extinction of all endemic large-bodied vertebrates. Therefore, our approach can provide new insights into past human demography and associated impacts on ecosystems.
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Affiliation(s)
- Omar Alva
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Anaïs Leroy
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Margit Heiske
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Veronica Pereda-Loth
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Lenka Tisseyre
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Anne Boland
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000 Evry, France
| | - Jean-François Deleuze
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000 Evry, France
| | - Jorge Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Cesar Fortes-Lima
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany; Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Villeurbanne, France
| | - Chantal Radimilahy
- Musée d'Art et d'Archéologie, University of Antananarivo, Antananarivo, Madagascar
| | | | - Thierry Letellier
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Denis Pierron
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France.
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Estrada A, Garber PA, Gouveia S, Fernández-Llamazares Á, Ascensão F, Fuentes A, Garnett ST, Shaffer C, Bicca-Marques J, Fa JE, Hockings K, Shanee S, Johnson S, Shepard GH, Shanee N, Golden CD, Cárdenas-Navarrete A, Levey DR, Boonratana R, Dobrovolski R, Chaudhary A, Ratsimbazafy J, Supriatna J, Kone I, Volampeno S. Global importance of Indigenous Peoples, their lands, and knowledge systems for saving the world's primates from extinction. SCIENCE ADVANCES 2022; 8:eabn2927. [PMID: 35947670 PMCID: PMC9365284 DOI: 10.1126/sciadv.abn2927] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 06/28/2022] [Indexed: 06/02/2023]
Abstract
Primates, represented by 521 species, are distributed across 91 countries primarily in the Neotropic, Afrotropic, and Indo-Malayan realms. Primates inhabit a wide range of habitats and play critical roles in sustaining healthy ecosystems that benefit human and nonhuman communities. Approximately 68% of primate species are threatened with extinction because of global pressures to convert their habitats for agricultural production and the extraction of natural resources. Here, we review the scientific literature and conduct a spatial analysis to assess the significance of Indigenous Peoples' lands in safeguarding primate biodiversity. We found that Indigenous Peoples' lands account for 30% of the primate range, and 71% of primate species inhabit these lands. As their range on these lands increases, primate species are less likely to be classified as threatened or have declining populations. Safeguarding Indigenous Peoples' lands, languages, and cultures represents our greatest chance to prevent the extinction of the world's primates.
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Affiliation(s)
- Alejandro Estrada
- Institute of Biology, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Paul A. Garber
- Department of Anthropology and Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sidney Gouveia
- Department of Ecology, Federal University of Sergipe, São Cristóvão - SE, Brazil
| | | | - Fernando Ascensão
- cE3c—Center for Ecology, Evolution and Environmental Changes and CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, 5° Piso, Sala 2.5.46, Campo Grande, 1749-016 Lisboa, Portugal
| | - Agustin Fuentes
- Department of Anthropology, Princeton University, Princeton, NJ 08544, USA
| | - Stephen T. Garnett
- Research Institute for the Environment and Livelihoods, College of Engineering, Casuarina, Northern Territory 0909, Australia
| | - Christopher Shaffer
- Department of Anthropology, Grand Valley State University, Allendale, MI 49401, USA
| | | | - Julia E. Fa
- School of Natural Sciences, Manchester Metropolitan University, Manchester, UK
- Center for International Forestry Research (CIFOR), CIFOR Headquarters, Bogor 16115, Indonesia
| | | | - Sam Shanee
- Neotropical Primate Conservation, London, UK
| | - Steig Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Glenn H. Shepard
- Museu Paraense Emilio Goeldi, Belém do Para, Brazil
- Programa de Pós Graduação em Antropologia Social, Universidade Federal do Amazonas, Manaus, Brazil
- Department of Anthropology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5102, USA
| | | | - Christopher D. Golden
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Dallas R. Levey
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- National Autonomous University of Mexico, Institute of Biology, Mexico City 04510, Mexico
| | - Ramesh Boonratana
- Mahidol University International College, Salaya, Nakhon Pathom, Thailand
| | | | - Abhishek Chaudhary
- Department of Civil Engineering, Indian Institute of Technology, Kanpur, India
| | - Jonah Ratsimbazafy
- Groupe d’étude et de recherche sur les primates (Gerp), Antananarivo, Madagascar
| | - Jatna Supriatna
- Graduate Program in Conservation Biology, Department of Biology, University of Indonesia, Depok, Indonesia
| | - Inza Kone
- Centre Suisse des Recherches Scientifiques, Université de Cocody, Abidjan, Côte d’Ivoire
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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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