scholarly journals Reconstructing Austronesian population history in Island Southeast Asia

2014 ◽  
Author(s):  
Mark Lipson ◽  
Po-Ru Loh ◽  
Nick Patterson ◽  
Priya Moorjani ◽  
Ying-Chin Ko ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Population History ◽  
Austronesian Languages ◽  
Ancestral Gene ◽  
Mainland Population ◽  
Island Southeast Asia ◽  
New Methods ◽  
Asian Populations ◽  
Genome Wide ◽  
Genome Wide Data

Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the "Austronesian expansion," which began 4-5 thousand years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, focusing primarily on Island Southeast Asia, we analyze genome-wide data from 56 populations using new methods for tracing ancestral gene flow. We show that all sampled Austronesian groups harbor ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.

scholarly journals Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity

2020 ◽  
Vol 37 (9) ◽  
pp. 2503-2519 ◽  
Author(s):  
Dang Liu ◽  
Nguyen Thuy Duong ◽  
Nguyen Dang Ton ◽  
Nguyen Van Phong ◽  
Brigitte Pakendorf ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Southeast Asia ◽  
Linguistic Diversity ◽  
Published Data ◽  
Multiple Sources ◽  
Austronesian Languages ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
Mainland Southeast Asia

Abstract Vietnam features extensive ethnolinguistic diversity and occupies a key position in Mainland Southeast Asia. Yet, the genetic diversity of Vietnam remains relatively unexplored, especially with genome-wide data, because previous studies have focused mainly on the majority Kinh group. Here, we analyze newly generated genome-wide single-nucleotide polymorphism data for the Kinh and 21 additional ethnic groups in Vietnam, encompassing all five major language families in Mainland Southeast Asia. In addition to analyzing the allele and haplotype sharing within the Vietnamese groups, we incorporate published data from both nearby modern populations and ancient samples for comparison. In contrast to previous studies that suggested a largely indigenous origin for Vietnamese genetic diversity, we find that Vietnamese ethnolinguistic groups harbor multiple sources of genetic diversity that likely reflect different sources for the ancestry associated with each language family. However, linguistic diversity does not completely match genetic diversity: There have been extensive interactions between the Hmong-Mien and Tai-Kadai groups; different Austro-Asiatic groups show different affinities with other ethnolinguistic groups; and we identified a likely case of cultural diffusion in which some Austro-Asiatic groups shifted to Austronesian languages during the past 2,500 years. Overall, our results highlight the importance of genome-wide data from dense sampling of ethnolinguistic groups in providing new insights into the genetic diversity and history of an ethnolinguistically diverse region, such as Vietnam.

scholarly journals Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

2021 ◽  
Author(s):  
Sandra Oliveira ◽  
Kathrin Nägele ◽  
Selina Carlhoff ◽  
Irina Pugach ◽  
Toetik Koesbardiati ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Demographic History ◽  
Island Southeast Asia ◽  
The North ◽  
Complex Interactions ◽  
Time Estimates ◽  
Continental Shelves ◽  
Genome Wide ◽  
Timor Leste ◽  
Genome Wide Data

Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this region's demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estimates for the Austronesian arrival into the region than are admixture time estimates for present-day groups. The decreasing trend in admixture times exhibited by younger individuals supports a scenario of multiple or continuous admixture involving Papuan- and Asian-related groups. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

The role of contact and language shift in the spread of Austronesian languages across Island Southeast Asia

2020 ◽  
pp. 167-194
Author(s):  
Mark Donohue ◽  
Tim Denham
Keyword(s):  
Southeast Asia ◽  
Marine Environment ◽  
Language Shift ◽  
Language Family ◽  
Austronesian Languages ◽  
Island Southeast Asia ◽  
South West ◽  
The Pacific ◽  
European Colonization

The spread of modern humans into and across Island Southeast Asia and the Pacific represents the earliest confirmed dispersal of humans across a marine environment, and involved numerous associated technologies that indicate sophisticated societies on the move. The later spread of ‘Austronesian’ over the region shows language replacement on a scale that is reminiscent of the period of state-sponsored European colonization, and yet the Austronesian languages present a typological profile that is more diverse than any other large language family. These facts require investigation. This chapter examines the separate, but intertwined, histories of the region. It shows that the dispersal of Austronesian languages, originating in Taiwan, should not be portrayed as a technological and demographic steamroller. This involves discussion of the nature of pre-Austronesian society and language in the south-west Pacific, and the degree to which it has and has not changed following ‘Austronesianization’.

Reconnecting Genes, Languages and Material Culture in Island Southeast Asia: Aphorisms on Geography and History

2012 ◽  
Vol 2 (2) ◽  
pp. 184-211 ◽  
Author(s):  
Tim Denham ◽  
Mark Donohue
Keyword(s):  
Material Culture ◽  
Southeast Asia ◽  
Human Genetics ◽  
Southeast Asian ◽  
Archaeological Record ◽  
Austronesian Languages ◽  
The Holocene ◽  
Island Southeast Asia ◽  
Multidisciplinary Data ◽  
History Of

The Holocene history of Island Southeast Asia (ISEA) is dominated by the ‘Out-of-Taiwan’ hypothesis and derivatives, such as the spread of the Island Southeast Asian Neolithic. According to these ideas, approximately 4500–4000 years ago, farmer-voyagers from Taiwan migrated southward into ISEA to subsequently acculturate, assimilate or displace pre-existing inhabitants. These processes are considered to have produced a consilience between human genetics, Austronesian languages and the archaeological record within ISEA, although recurrent critiques have questioned these putative correspondences. These critiques have proposed that each line of evidence should be independently evaluated and considered, rather than assumed to correspond. In this paper, the authors advocate a fuller engagement with and a deeper understanding of the spatial and temporal processes that structure archaeological, genetic and linguistic distributions within Island Southeast Asia. Geography and history are often marginalized in discussions of the Holocene history of ISEA, yet both are fundamental to the interpretation and reconciliation of multidisciplinary data within the region. These themes are discussed using aphorisms that are designed to be illustrative, namely to promote thought and reflection, rather than to be comprehensive.

scholarly journals A COMPRESSED SENSING BASED APPROACH FOR SUBTYPING OF LEUKEMIA FROM GENE EXPRESSION DATA

2011 ◽  
Vol 09 (05) ◽  
pp. 631-645 ◽  
Author(s):  
WENLONG TANG ◽  
HONGBAO CAO ◽  
JUNBO DUAN ◽  
YU-PING WANG
Keyword(s):  
Gene Expression ◽  
Compressed Sensing ◽  
Gene Expression Analysis ◽  
Expression Data ◽  
Data Set ◽  
New Methods ◽  
Genome Wide ◽  
Different Types ◽  
Genome Wide Data ◽  
Improved Accuracy

With the development of genomic techniques, the demand for new methods that can handle high-throughput genome-wide data effectively is becoming stronger than ever before. Compressed sensing (CS) is an emerging approach in statistics and signal processing. With the CS theory, a signal can be uniquely reconstructed or approximated from its sparse representations, which can therefore better distinguish different types of signals. However, the application of CS approach to genome-wide data analysis has been rarely investigated. We propose a novel CS-based approach for genomic data classification and test its performance in the subtyping of leukemia through gene expression analysis. The detection of subtypes of cancers such as leukemia according to different genetic markups is significant, which holds promise for the individualization of therapies and improvement of treatments. In our work, four statistical features were employed to select significant genes for the classification. With our selected genes out of 7,129 ones, the proposed CS method achieved a classification accuracy of 97.4% when evaluated with the cross validation and 94.3% when evaluated with another independent data set. The robustness of the method to noise was also tested, giving good performance. Therefore, this work demonstrates that the CS method can effectively detect subtypes of leukemia, implying improved accuracy of diagnosis of leukemia.

scholarly journals The impact of recent events on human genetic diversity

2012 ◽  
Vol 367 (1590) ◽  
pp. 793-799 ◽  
Author(s):  
Mark A. Jobling
Keyword(s):  
Genetic Diversity ◽  
Historical Record ◽  
Social Selection ◽  
New Methods ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Male Specific ◽  
Demographic Impact ◽  
The Impact ◽  
And Linguistics

The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics.

scholarly journals Reconstructing the human genetic history of mainland Southeast Asia: insights from genome-wide data from Thailand and Laos

2020 ◽  
Author(s):  
Wibhu Kutanan ◽  
Dang Liu ◽  
Jatupol Kampuansai ◽  
Metawee Srikummool ◽  
Suparat Srithawong ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Southeast Asia ◽  
Geographic Region ◽  
Whole Genome Sequence ◽  
Genetic History ◽  
Asian Populations ◽  
Genome Wide ◽  
Population Interactions ◽  
Hill Tribes ◽  
Mainland Southeast Asia

AbstractThailand and Laos, located in the center of Mainland Southeast Asia (MSEA), harbor diverse ethnolinguistic groups encompassing all five language families of MSEA: Tai-Kadai (TK), Austroasiatic (AA), Sino-Tibetan (ST), Hmong-Mien (HM) and Austronesian (AN). Previous genetic studies of Thai/Lao populations have focused almost exclusively on uniparental markers and there is a paucity of genome-wide studies. We therefore generated genome-wide SNP data for 33 ethnolinguistic groups, belonging to the five MSEA language families from Thailand and Laos, and analysed these together with data from modern Asian populations and SEA ancient samples. Overall, we find genetic structure according to language family, albeit with heterogeneity in the AA-, HM- and ST-speaking groups, and in the hill tribes, that reflects both population interactions and genetic drift. For the TK speaking groups, we find localized genetic structure that is driven by different levels of interaction with other groups in the same geographic region. Several Thai groups exhibit admixture from South Asia, which we date to ∼600-1000 years ago, corresponding to a time of intensive international trade networks that had a major cultural impact on Thailand. An AN group from Southern Thailand shows both South Asian admixture as well as overall affinities with AA-speaking groups in the region, suggesting an impact of cultural diffusion. Overall, we provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies.

scholarly journals A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe

2020 ◽  
Author(s):  
Choongwon Jeong ◽  
Ke Wang ◽  
Shevan Wilkin ◽  
William Timothy Treal Taylor ◽  
Bryan K. Miller ◽  
...  
Keyword(s):  
Bronze Age ◽  
Population History ◽  
Complex Interplay ◽  
Cultural Changes ◽  
Genetic History ◽  
Nomadic Pastoralists ◽  
Eurasian Steppe ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of

SummaryThe Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher Eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

scholarly journals Reconstructing Austronesian population history in Island Southeast Asia

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Mark Lipson ◽  
Po-Ru Loh ◽  
Nick Patterson ◽  
Priya Moorjani ◽  
Ying-Chin Ko ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Population History ◽  
Island Southeast Asia

scholarly journals The gateway into Remote Oceania: new insights from genome-wide data

2017 ◽  
Author(s):  
Irina Pugach ◽  
Ana T. Duggan ◽  
D. Andrew Merriwether ◽  
Françoise R. Friedlaender ◽  
Jonathan S. Friedlaender ◽  
...  
Keyword(s):  
Solomon Islands ◽  
Population History ◽  
Indigenous Populations ◽  
Autosomal Snps ◽  
Genome Wide ◽  
A Genome ◽  
Bismarck Archipelago ◽  
Genome Wide Data ◽  
Linguistic Divide ◽  
Founder Event

ABSTRACTA widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration ca 50,000 ya, and one of the most geographically-widespread dispersals of people, known as the Austronesian expansion, which reached the Bismarck Archipelago by about 3,450 ya. While earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic and genetic evidence indicates a more complicated picture of settlement. To study regional variation in Oceania in more detail, we have compiled a genome-wide dataset of 823 individuals from 72 populations (including 50 populations from Oceania) and over 620,000 autosomal SNPs. We show that the initial dispersal of people from the Bismarck Archipelago into Remote Oceania occurred in a “leapfrog” fashion, completely by-passing the main chain of the Solomon Islands, and that the colonization of the Solomon Islands proceeded in a bi-directional manner. Our results also support a divergence between western and eastern Solomons, in agreement with the sharp linguistic divide known as the Tryon-Hackman line. We also report substantial post-Austronesian gene flow across the Solomons. In particular, Santa Cruz (in Remote Oceania) exhibits extraordinarily high levels of Papuan ancestry that cannot be explained by a simple bottleneck/founder event scenario. Finally, we use simulations to show that discrepancies between different methods for dating admixture likely reflect different sensitivities of the methods to multiple admixture events from the same (or similar) sources. Overall, this study points to the importance of fine-scale sampling to understand the complexities of human population history.

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