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The Last Sea Nomads of the Indonesian Archipelago: Genomic Origins and Dispersal European Journal of Human Genetics (2017) 25, 1004–1010 Official journal of The European Society of Human Genetics www.nature.com/ejhg ARTICLE The last sea nomads of the Indonesian archipelago: genomic origins and dispersal Pradiptajati Kusuma1,2, Nicolas Brucato1, Murray P Cox3, Thierry Letellier1, Abdul Manan4, Chandra Nuraini5, Philippe Grangé5, Herawati Sudoyo2,6 and François-Xavier Ricaut*,1 The Bajo, the world’s largest remaining sea nomad group, are scattered across hundreds of recently settled communities in Island Southeast Asia, along the coasts of Indonesia, Malaysia and the Philippines. With a significant role in historical trading, the Bajo lived until recently as nomads, spending their entire lives on houseboats while moving long distances to fish and trade. Along the routes they traveled, the Bajo settled and intermarried with local land-based groups, leading to ‘maritime creolization’, a process whereby Bajo communities retained their culture, but assimilated – and frequently married into – local groups. The origins of the Bajo have remained unclear despite several hypotheses from oral tradition, culture and language, all currently without supporting genetic evidence. Here, we report genome-wide SNP analyses on 73 Bajo individuals from three communities across Indonesia – the Derawan of Northeast Borneo, the Kotabaru of Southeast Borneo and the Kendari of Southeast Sulawesi, with 87 new samples from three populations surrounding the area where these Bajo peoples live. The Bajo likely share a common connection with Southern Sulawesi, but crucially, each Bajo community also exhibits unique genetic contributions from neighboring populations. European Journal of Human Genetics (2017) 25, 1004–1010; doi:10.1038/ejhg.2017.88; published online 17 May 2017 INTRODUCTION biodiversity in the world, thus underpinning the Bajo economy based Rapid advances in sea faring technologies in Island Southeast Asia on exploiting marine resources including fish, tortoise shell and sea (ISEA) around 5000 years ago created an intricate network of cucumber. Within Indonesia, the Bajo presence extends over a wide maritime interactions, the leading example being the well-known geographical area (Figure 1). Historically, Bajo were frequently – expansion of Austronesian peoples.1 3 Triggering inter-continental associated with Sulawesi Bugis traders and ship owners12,17 and were maritime connections linking ISEA with East Africa and Remote well known for traveling with their families, even for long-distance 2,4–8 Oceania, these contacts drove exchanges of goods, ideas, cultures journeys reaching as far as New Guinea and Australia.21 The Bajo may fi 9,10 and people around the Indo-Paci cregion. Sea-orientated popula- have mediated westward dispersals into the Indian Ocean, perhaps tions, including sea nomads, emerged from this milieu, dominating even having a role in the Indonesian settlement of Madagascar.22 trade within ISEA for centuries and helping to structure population Although some Bajo communities live far apart today, they still have interactions across Indonesia and beyond. Today, the Indonesian similar social and cultural features, including shared shipbuilding and 11 archipelago hosts ~ 600 ethnic groups, of which only a handful are fishing culture, traditions and myths.17,23,24 Their languages belong to known for their sea-based lifestyles. Some, like the Bugis and Makassar a single subfamily, the Sama-Bajau subgroup on the West Malayo- of Southern Sulawesi,12 are maritime inter-regional traders that arose Polynesian branch of the Austronesian language family.25,26 This within the framework of regional empires, such as Malay/Hindu subgroup includes at least nine languages,11,18 with its highest diversity Śrīvijaya and Majapahit. However, these groups still have homeland in Sabah (North Borneo) and the Southern Philippines.18 However, territories on land. Far more extreme are ethnic groups that subsist the Sama-Bajau languages of Indonesia are poorly documented, and entirely detached from the land, living their whole lives aboard small fi boats, and as recently as 40 years ago, living as nomadic seafarers.13–15 an ongoing survey has identi ed at least three unrecognized languages The biggest group, the Bajo (also Bajaw, Bajau or Sama-Bajau),16,17 (Grangé, personal communication). Some of these languages are number approximately one million people, who today live in mutually unintelligible, suggesting that the Bajo diaspora started fi numerous scattered hamlets and villages recently created by the centuries ago, tting with oral tradition. Numerous loanwords indicate fl Indonesian government along the coasts of the Indonesian archi- that the languages spoken by the Bajo were in uenced by neighboring pelago, as well as Sabah in Malaysia, and the Sulu archipelago and ethnic groups with whom the Bajo interacted and socialized, in a South-Western Mindanao in the Southern Philippines.13,18–20 The process called ‘maritime creolization’.24 However, the extent of these geographical distribution of Bajo communities overlaps large parts of social interactions on the genetic composition of Bajo communities the coral triangle, which contains one of the highest rates of marine remains unknown. 1Equipe de Médecine Evolutive, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France; 2Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia; 3Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand; 4University of Halu Oleo, Kendari, Indonesia; 5UFR des Lettres, Langues, Arts et Sciences Humaines, Université de La Rochelle, La Rochelle, France; 6Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia *Correspondence: Dr F-X Ricaut, Equipe de Médecine Evolutive, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR-5288, 37 Allées Jules Guesde, Toulouse 31000, France. Tel: +33 5 61 14 55 11; Fax: +33 5 61 14 59 79; E-mail: [email protected] Received 3 February 2017; revised 31 March 2017; accepted 13 April 2017; published online 17 May 2017 Indonesian sea nomad genomic origins and dispersal PKusumaet al 1005 Figure 1 Map showing the distribution of Bajo communities across Island Southeast Asia (yellow), together with the location of sampled Bajo villages (red dots) and sampled historically related communities (blue dots). The Bajo have no written history, instead relying on oral tradition, the Samihim in Eastern Borneo (n = 25), the Bugis of Southern Sulawesi especially epic songs, which say little about their early history. (n = 25), the Mandar of Southern Sulawesi (n = 23) and North Maluku Hypotheses about their origins have been drawn from this folklore, individuals from various linguistic groups (n = 14) as comparative populations. as well as linguistic studies and rare records from European sailors This sampling strategy is relevant for the statistical tests that are described from the 16th century onward.16 The Bajo diaspora may have below, both on population structure and admixture. Genome-wide SNP originated in Johor, Malaysia,13 or even Arabia,23 according to oral genotypes were generated using the Illumina Human Omni5 Bead Chip (Illumina Inc., San Diego, CA, USA), which surveys 4 284 426 single- tradition. Brunei and Southern Sulawesi have also been proposed 23,27,28 nucleotide markers semi-regularly spaced across the genome. Genotype data based on other Bajo stories. Linguistic surveys point toward the from previously published Bajo individuals from the Kendari community of 18 Sulu archipelago of the Philippines, and at an earlier stage, to Southern Sulawesi were also included (n = 32).29 New genotyping data have 26 Southeast Borneo. None of these hypotheses have been tested with been deposited at the European Genome-Phenome Archive (EGA), which is genetic data. hosted by the EBI and CRG, under accession number EGAS00001002246. Here, we undertake a genomic survey to help clarify the history of A comparative data set was built from 110 worldwide populations compris- Bajo sea nomad populations. We present genome-wide analyses from ing an additional 2256 individuals (Supplementary Table S1). Data quality three Bajo communities (n = 73; Supplementary Table S1), represent- controls were performed using PLINK v1.9:30 (i) to avoid close relatives, ing different Sama-Bajaw dialects, together with comparative data relatedness was measured between all pairs of individuals within each from neighboring populations potentially connected historically with population using an identity-by-descent (IBD) estimation with upper threshold of 0.25 (second-degree relatives); (ii) SNPs that failed the Hardy–Weinberg the Bajo. Using this large comparative data set, we investigate the exact test (Po10 − 6) were excluded; (iii) samples with an overall call rate genetic origins and history of the Bajo, and characterize the genetic o 4 ’ 0.99 and individual SNPs with missing rates 0.05 across all samples in each impact of their near-unique lifestyle as some of the world slast population were excluded. The final data set contains 230 833 SNPs. Genotypes remaining sea nomads. were then phased with SHAPEIT v231 using the 1000 Genomes Project phased data32 as a reference panel and the HapMap phase II genetic map. For specific MATERIALS AND METHODS analyses mentioned below, variants in high linkage disequilibrium (LD) (r24 Ethics 0.5; 50
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