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

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.

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Reconstructing Austronesian population history in Island Southeast Asia

10.1101/005603 ◽

2014 ◽

Cited By ~ 1

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.

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Genomic divergence in allopatric Northern Cardinals of the North American warm deserts is associated with behavioral differentiation

10.1101/347492 ◽

2018 ◽

Author(s):

Kaiya L. Provost ◽

William M. Mauck ◽

Brian Tilston Smith

Keyword(s):

Gene Flow ◽

Sonoran Desert ◽

Demographic History ◽

Isolation With Migration ◽

Song Recognition ◽

Behavioral Isolation ◽

The North ◽

Genome Wide ◽

Behavioral Differentiation ◽

Northern Cardinals

ABSTRACTBiogeographic barriers are thought to be important in initiating speciation through geographic isolation, but they rarely indiscriminately and completely reduce gene flow across the entire community. Understanding which species’ attributes regulate a barrier could help elucidate how speciation is initiated. Here, we investigated the association of behavioral isolation on population differentiation in Northern Cardinals (Cardinalis cardinalis) distributed across the Cochise Filter Barrier, a region of transitional habitat which separates the Sonoran and Chihuahuan deserts. Using genome-wide markers, we modeled demographic history by fitting the data to isolation and isolation-with-migration models. The best-fit model indicated that desert populations diverged in the mid-Pleistocene and there has been historically low, unidirectional gene flow into the Sonoran Desert. We then tested song recognition using reciprocal call-broadcast experiments to compare song recognition between deserts, controlling for song dialect changes within deserts. We found that male Northern Cardinals in both deserts were most aggressive to local songs and failed to recognize across-barrier songs. A correlation of genomic differentiation despite historic introgression and strong song discrimination is consistent with a model where speciation is initiated across a barrier and maintained by behavioral isolation.

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Genetic substructure and complex demographic history of South African Bantu speakers

Nature Communications ◽

10.1038/s41467-021-22207-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Dhriti Sengupta ◽

◽

Ananyo Choudhury ◽

Cesar Fortes-Lima ◽

Shaun Aron ◽

...

Keyword(s):

South Africa ◽

Population Structure ◽

Iron Age ◽

Association Studies ◽

Demographic History ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Scale Population ◽

Genome Wide Data ◽

Genetic Substructure

AbstractSouth Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.

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Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity

Molecular Biology and Evolution ◽

10.1093/molbev/msaa099 ◽

2020 ◽

Vol 37 (9) ◽

pp. 2503-2519 ◽

Cited By ~ 4

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.

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Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data

Scientific Reports ◽

10.1038/s41598-020-66953-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Guilherme Debortoli ◽

Cristina Abbatangelo ◽

Francisco Ceballos ◽

Cesar Fortes-Lima ◽

Heather L. Norton ◽

...

Keyword(s):

Demographic History ◽

Genome Wide ◽

Genome Wide Data ◽

History Of ◽

Caste Groups

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More rule than exception: Parallel evidence of ancient migrations in grammars and genomes of Finno-Ugric speakers

10.1101/2020.11.02.364521 ◽

2020 ◽

Author(s):

Patrícia Santos ◽

Gloria Gonzalez-Fortes ◽

Emiliano Trucchi ◽

Andrea Ceolin ◽

Guido Cordoni ◽

...

Keyword(s):

Demographic History ◽

Comparative Method ◽

Population Level ◽

Syntactic Analysis ◽

Complex Relation ◽

Human Demographic History ◽

Genome Wide ◽

Genome Wide Data ◽

Demographic Processes ◽

North Western

AbstractTo reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method exclusively based on syntactic data, here we focus on the complex relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis supports three distinct clusters corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL-speakers. Therefore, our study indicates plausible secondary convergence in the syntax of languages of different families, providing evidence that such interference effects were accompanied, and possibly caused, by recognizable processes at the population level. In particular, based on the comparison of modern and ancient genomes, our analysis identified the Pontic-Caspian steppes as the possible origin of the demographic processes that led to the expansion of the FU into Europe.

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Demographic History of Oceania Inferred from Genome-wide Data

Current Biology ◽

10.1016/j.cub.2010.10.040 ◽

2010 ◽

Vol 20 (22) ◽

pp. 1983-1992 ◽

Cited By ~ 118

Author(s):

Andreas Wollstein ◽

Oscar Lao ◽

Christian Becker ◽

Silke Brauer ◽

Ronald J. Trent ◽

...

Keyword(s):

Demographic History ◽

Genome Wide ◽

Genome Wide Data ◽

History Of

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Fataluku

Journal of the International Phonetic Association ◽

10.1017/s0025100316000190 ◽

2016 ◽

Vol 49 (3) ◽

pp. 419-425

Author(s):

Tyler M. Heston ◽

Stephanie Locke

Keyword(s):

Southeast Asia ◽

New Guinea ◽

East Timor ◽

The West ◽

Island Southeast Asia ◽

Timor Leste ◽

West Timor ◽

Eastern Half

Fataluku ([fataluku], ISO 639-3: ddg) is a language spoken by approximately 37,000 people on the eastern end of Timor-Leste (Lewis, Simons & Fennig 2016). Timor-Leste, also known as East Timor, is an independent nation that occupies the eastern half of the island of Timor in island Southeast Asia, which it shares politically with Indonesia in the west. Timor is located north of Australia, between the Indonesian islands of Sumatra and Bali in the west and New Guinea in the east.

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More Rule than Exception: Parallel Evidence of Ancient Migrations in Grammars and Genomes of Finno-Ugric Speakers

Genes ◽

10.3390/genes11121491 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1491

Author(s):

Patrícia Santos ◽

Gloria Gonzàlez-Fortes ◽

Emiliano Trucchi ◽

Andrea Ceolin ◽

Guido Cordoni ◽

...

Keyword(s):

Demographic History ◽

Comparative Method ◽

Syntactic Analysis ◽

Interference Effects ◽

Human Demographic History ◽

Genome Wide ◽

Linguistic Interference ◽

Genome Wide Data ◽

Demographic Processes ◽

North Western

To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method based on syntactic data, here we focus on the non-straightforward relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis, in agreement with the indications of more traditional linguistic levels, supports at least three distinct clusters, corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL speakers. Therefore, our analysis indicates that plausible cross-family linguistic interference effects were accompanied, and possibly caused, by recognizable demographic processes. In particular, based on the comparison of modern and ancient genomes, our study identified the Pontic-Caspian steppes as the possible origin of the demographic processes that led to the expansion of FU languages into Europe.

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