title: Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations.
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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France. pradiptajati.kusuma@univ-tlse3.fr.|Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia. pradiptajati.kusuma@univ-tlse3.fr.
authors.forename: Pradiptajati
authors.initials: P
authors.lastname: Kusuma
authors.affiliation: Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand. m.p.cox@massey.ac.nz.
authors.forename: Murray P
authors.initials: MP
authors.lastname: Cox
authors.affiliation: Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France. denis.pierron@cnrs.fr.
authors.forename: Denis
authors.initials: D
authors.lastname: Pierron
authors.affiliation: Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France. razafindrazaka.harilanto@gmail.com.
authors.forename: Harilanto
authors.initials: H
authors.lastname: Razafindrazaka
authors.affiliation: Center for Linguistics, University of Leiden, Leiden, Netherlands. nicolasbrucato@hotmail.fr.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Brucato
authors.affiliation: Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France. laure.calviere-tonasso@univ-tlse3.fr.
authors.forename: Laure
authors.initials: L
authors.lastname: Tonasso
authors.affiliation: Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia. helena@eijkman.go.id.
authors.forename: Helena Loa
authors.initials: HL
authors.lastname: Suryadi
authors.affiliation: Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France. thierry.letellier@u-bordeaux2.fr.
authors.forename: Thierry
authors.initials: T
authors.lastname: Letellier
authors.affiliation: Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia. herawati@eijkman.go.id.|Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia. herawati@eijkman.go.id.
authors.forename: Herawati
authors.initials: H
authors.lastname: Sudoyo
authors.affiliation: Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France. francois-xavier.ricaut@univ-tlse3.fr.
authors.forename: François-Xavier
authors.initials: FX
authors.lastname: Ricaut
mesh_terms: D044466:Asian People / Q000235:genetics*; D041322:Chromosomes, Human, Y / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000145:classification / Q000235:genetics*; D008040:Genetic Linkage; D005828:Genetics, Population; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D007214:Indonesia; D008270:Madagascar; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial