Kinship structures create persistent channels for language transmission.

Languages are transmitted through channels created by kinship systems. Given sufficient time, these kinship channels can change the genetic and linguistic structure of populations. In traditional societies of eastern Indonesia, finely resolved cophylogenies of languages and genes reveal persistent movements between stable speech communities facilitated by kinship rules. When multiple languages are present in a region and postmarital residence rules encourage sustained directional movement between speech communities, then languages should be channeled along uniparental lines. We find strong evidence for this pattern in 982 individuals from 25 villages on two adjacent islands, where different kinship rules have been followed. Core groups of close relatives have stayed together for generations, while remaining in contact with, and marrying into, surrounding groups. Over time, these kinship systems shaped their gene and language phylogenies: Consistently following a postmarital residence rule turned social communities into speech communities

The Role of Traditional Knowledge About and Management of Seaworms (Polychaeta) in Making Austronesian Worlds

This paper discusses how Kodi make their worlds cognitively as well as experientially, and how these worlds relate to sustainability and wellbeing. Kodi construct their cognitive worlds as well as their biophysical landscapes whilst interacting with many other species. This presentation focuses on human-polychaete interactions in order to illustrate world making processes. Seaworm traditions have deep historical roots in Austronesian societies and continue to be crucial for the wellbeing of contemporary communities. World-making processes are evident in what Kodi people say about seaworms and how they move through space relative to seaworms. While Kodi construct time they simultaneously construct space around seaworms and the many associated entities and processes. Kodi people have done and continue to do difficult intellectual work of translating knowledge gained from sensing, perceiving, observing, and experiencing their worlds into their space-time culture, and this is reflected in the ecology of their homelands

Genetic continuity across a deeply divergent linguistic contact zone in North Maluku, Indonesia

<p>Abstract</p> <p>Background</p> <p>The islands of North Maluku, Indonesia occupy a central position in the major prehistoric dispersal streams that shaped the peoples of Island Southeast Asia and the Pacific. Within this region a linguistic contact zone exists where speakers of Papuan and Austronesian languages reside in close proximity. Here we use population genetic data to assess the extent to which North Maluku populations experienced admixture of Asian genetic material, and whether linguistic boundaries reflect genetic differentiation today.</p> <p>Results</p> <p>Autosomal and X-linked markers reveal overall Asian admixture of 67% in North Maluku, demonstrating a substantial contribution of genetic material into the region from Asia. We observe no evidence of population structure associated with ethnicity or language affiliation.</p> <p>Conclusions</p> <p>Our data support a model of widespread Asian admixture in North Maluku, likely mediated by the expansion of Austronesian-speaking peoples into the region during the mid Holocene. In North Maluku there is no genetic differentiation in terms of Austronesian- versus Papuan-speakers, suggesting extensive gene flow across linguistic boundaries. In a regional context, our results illuminate a major genetic divide at the Molucca Sea, between the islands of Sulawesi and North Maluku. West of this divide, populations exhibit predominantly Asian ancestry, with very little contribution of Papuan genetic material. East of the Molucca Sea, populations show diminished rates of Asian admixture and substantial persistence of Papuan genetic diversity.</p

Geological Approach In Order to Distinguish the Preference Source of the Raw Material from the Megalithic Tombs in East Sumba, Indonesia

Pulau Sumba sudah lama dikenal dengan tradisi makam megalitiknya yang dijumpai tersebar hampir di semua area di Sumba. Makam megalitik ini dibangun dari potongan-potongan batuan berukuran besar. Berdasarkan aspek geologi, penelitian ini mencoba untuk mencari tahu asal batuan bahan pembuat makam megalitik dan apa yang menjadi alasan untuk memilih suatu batuan untuk bahan makam megalitik. Metode yang digunakan meliputi beberapa tahap. Tahap pertama merupakan pendeskripsian sampel di lapangan. Tahap kedua, analisis geologi digunakan untuk memetakan titik-titik observasi dan singkapan batuan di lapangan. Tahap ketiga, variabel hasil pengamatan kemudian dianalisa menggunakan metode Principle Components Analysis (PCA). Empat variabel digunakan dalam penelitian ini, yaitu: variabel jarak dari sumber, variabel litologi, variabel tekstur dan variabel tingkat kekerasan. Hasil penelitian mengindikasikan bahwa tekstur batuan merupakan pertimbangan utama dalam memilih jenis batuan untuk bahan makam megalitik. Jarak dan tingat kekerasan batuannya juga menjadi alasan penting lainnya dalam mengambil bahan material untuk makam megalitik terlepas apapun jenis batunya. Secara geologi bahan batuan berasal dari batugamping Formasi Kaliangga dan batupasir Formasi Kananggar. Sumba is well known for its megalithic tradition, surviving evidence for which can be observed throughout the island in the form of tombs built from enormous stone slabs. The current study is aimed at identifying the sources of the raw material used to manufacture megalithic tombs and factors underlying the choice of raw material based on geological properties. We report the results of our field observations and geological analysis, including mapping of megalithic tomb sites and geological outcrops. Concerning the latter, field-datasets were analyzed using a Principle Components Analysis (PCA). Based on a sample of 11 megalithic tombs from several different locations, four variables were employed to distinguish the preferred source of the raw material used in tomb construction: 1) distance from the source; 2) lithology; 3) rock texture; and 4) rock hardness. Analytical results indicate that raw material texture was the key factor in the construction of megalithic tombs, followed by distance from source and hardness of the stone selected for making this structures. Finally, we establish that raw materials used for constructing sampled megalithic tomb sites on Sumba included Kaliangga Formation limestone and Kananggar Formation sandstone

Reconstructing Social Prehistory from Genomic Data in the Indo-Pacific Region

Reconstructing the evolutionary history of our species has traditionally been the purview of archeology and linguistics, but is now increasingly influenced by genetics. However, the information held in our DNA cannot be read like a book, but must instead be extracted using population genetic theory, advanced statistical methods and computational tools that can handle large genome-scale datasets. In this series of published studies, these approaches have been applied to reconstruct human prehistory, with a special focus on the social features of past communities in the Indo-Pacific region. They reveal that marriage between Asian women and Melanesian men was favored during the spread of farming populations in the Neolithic period, that Madagascar was settled by a small number of Indonesian families with close female relatives, and that extremely complex marriage rules continue to define and structure small traditional communities in the Indo-Pacific region even today. These studies are largely unique in moving beyond a traditional emphasis in molecular anthropology of identifying and dating human migrations to instead reveal key aspects of the social rules by which those communities lived

Lack of gene-language correlation due to reciprocal female but directional male admixture in Austronesians and non-Austronesians of East Timor

Nusa Tenggara, including East Timor, located at the crossroad between Island Southeast Asia, Near Oceania, and Australia, are characterized by a complex cultural structure harbouring speakers from two different major linguistic groups of different geographic origins (Austronesian (AN) and non-Austronesian (NAN)). This provides suitable possibilities to study gene-language relationship; however, previous studies from other parts of Nusa Tenggara reported conflicting evidence about gene-language correlation in this region. Aiming to investigate gene-language relationships including sex-mediated aspects in East Timor, we analysed the paternally inherited non-recombining part of the Y chromosome (NRY) and the maternally inherited mitochondrial (mt) DNA in a representative collection of AN-and NAN-speaking groups. Y-SNP (single-nucleotide polymorphism) data were newly generated for 273 samples and combined with previously established Y-STR (short tandem repeat) data of the same samples, and with previously established mtDNA data of 290 different samples with, however, very similar representation of geographic and linguistic coverage of the country. We found NRY and mtDNA haplogroups of previously described putative East/Southeast Asian (E/SEA) and Near Oceanian (NO) origins in both AN and NAN speakers of East Timor, albeit in different proportions, suggesting reciprocal genetic admixture between both linguistic groups for females, but directional admixture for males. Our data underline the dual genetic origin of East Timorese in E/SEA and NO, and highlight that substantial genetic admixtur

Climate Change Influenced Female Population Sizes through Time across the Indonesian Archipelago

Lying at the crossroads of Asia and the Pacific world, the Indonesian archipelago hosts one of the world’s richest accumulations of cultural, linguistic, and genetic variation. While the role of human migration into and around the archipelago is now known in some detail, other aspects of Indonesia’s complex history are less understood. Here, we focus on population size changes from the first settlement of Indonesia nearly 50 kya up to the historic era. We reconstructed the past effective population sizes of Indonesian women using mitochondrial DNA sequences from 2,104 individuals in 55 village communities on four islands spanning the Indonesian archipelago (Bali, Flores, Sumba, and Timor). We found little evidence for large fluctuations in effective population size. Most communities grew slowly during the late Pleistocene, peaked 15–20 kya, and subsequently declined slowly into the Holocene. This unexpected pattern may reflect population declines caused by the flooding of lowland hunter/gatherer habitat during sea-level rises following the last glacial maximum

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago.

Indonesia is the world's fourth most populous country, host to striking levels of human diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10.55% of tested genes are differentially expressed between the islands of Sumba and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.80% of genes correlating with nearby promoter CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia's tropical role as a source of infectious disease diversity and the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by fine-scale environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes

Paternal genetic affinity between western Austronesians and Daic populations

<p>Abstract</p> <p>Background</p> <p>Austronesian is a linguistic family spread in most areas of the Southeast Asia, the Pacific Ocean, and the Indian Ocean. Based on their linguistic similarity, this linguistic family included Malayo-Polynesians and Taiwan aborigines. The linguistic similarity also led to the controversial hypothesis that Taiwan is the homeland of all the Malayo-Polynesians, a hypothesis that has been debated by ethnologists, linguists, archaeologists, and geneticists. It is well accepted that the Eastern Austronesians (Micronesians and Polynesians) derived from the Western Austronesians (Island Southeast Asians and Taiwanese), and that the Daic populations on the mainland are supposed to be the headstream of all the Austronesian populations.</p> <p>Results</p> <p>In this report, we studied 20 SNPs and 7 STRs in the non-recombining region of the 1,509 Y chromosomes from 30 China Daic populations, 23 Indonesian and Vietnam Malayo-Polynesian populations, and 11 Taiwan aboriginal populations. These three groups show many resemblances in paternal lineages. Admixture analyses demonstrated that the Daic populations are hardly influenced by Han Chinese genetically, and that they make up the largest proportion of Indonesians. Most of the population samples contain a high frequency of haplogroup O1a-M119, which is nearly absent in other ethnic families. The STR network of haplogroup O1a* illustrated that Indonesian lineages did not derive from Taiwan aborigines as linguistic studies suggest, but from Daic populations.</p> <p>Conclusion</p> <p>We show that, in contrast to the Taiwan homeland hypothesis, the Island Southeast Asians do not have a Taiwan origin based on their paternal lineages. Furthermore, we show that both Taiwan aborigines and Indonesians likely derived from the Daic populations based on their paternal lineages. These two populations seem to have evolved independently of each other. Our results indicate that a super-phylum, which includes Taiwan aborigines, Daic, and Malayo-Polynesians, is genetically educible.</p