The population history of northeastern Siberia since the Pleistocene

ABSTRACTFar northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we analyze 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of “Ancient North Siberians” (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry related to present-day East Asians, giving rise to ancestral Native Americans and “Ancient Paleosiberians” (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the “Neosiberians” from which many contemporary Siberians derive. We detect gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic throughout the Late Pleistocene and Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.

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Helicobacter pylori’s historical journey through Siberia and the Americas

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2015523118 ◽

2021 ◽

Vol 118 (25) ◽

pp. e2015523118

Author(s):

Yoshan Moodley ◽

Andrea Brunelli ◽

Silvia Ghirotto ◽

Andrey Klyubin ◽

Ayas S. Maady ◽

...

Keyword(s):

Native Americans ◽

Ethnically Diverse ◽

Northern Eurasia ◽

Human Populations ◽

Bering Strait ◽

Demographic Bottleneck ◽

History Of ◽

Low Levels ◽

Approximate Bayesian ◽

H Pylori

The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.

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A Large-scale Analysis of Human Mitochondrial DNA Sequences with Special Reference to the Population History of East Eurasian.

Anthropological Science ◽

10.1537/ase.110.293 ◽

2002 ◽

Vol 110 (3) ◽

pp. 293-312 ◽

Cited By ~ 4

Author(s):

H. Oota ◽

N. Saitou ◽

S. Ueda

Keyword(s):

Mitochondrial Dna ◽

Special Reference ◽

Dna Sequences ◽

Large Scale ◽

Population History ◽

Scale Analysis ◽

Human Mitochondrial Dna ◽

Large Scale Analysis ◽

History Of

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Denisovan ancestry and population history of early East Asians

10.1101/2020.06.03.131995 ◽

2020 ◽

Cited By ~ 1

Author(s):

Diyendo Massilani ◽

Laurits Skov ◽

Mateja Hajdinjak ◽

Byambaa Gunchinsuren ◽

Damdinsuren Tseveendorj ◽

...

Keyword(s):

Gene Flow ◽

Human Population ◽

Modern Human ◽

Population History ◽

East Asians ◽

Aboriginal Australians ◽

North East ◽

History Of ◽

Female Member ◽

Admixture Event

AbstractWe present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in North East Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

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Denisovan ancestry and population history of early East Asians

Science ◽

10.1126/science.abc1166 ◽

2020 ◽

Vol 370 (6516) ◽

pp. 579-583

Author(s):

Diyendo Massilani ◽

Laurits Skov ◽

Mateja Hajdinjak ◽

Byambaa Gunchinsuren ◽

Damdinsuren Tseveendorj ◽

...

Keyword(s):

Gene Flow ◽

Human Population ◽

Modern Human ◽

Population History ◽

East Asians ◽

Aboriginal Australians ◽

History Of ◽

East And West ◽

Female Member ◽

Admixture Event

We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in northeastern Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

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Genomic insights into the recent population history of Mapuche Native Americans

10.1101/2021.11.25.470066 ◽

2021 ◽

Author(s):

Lucas Vicuña ◽

Anastasia Mikhailova ◽

Tomás Norambuena ◽

Anna Ilina ◽

Olga Klimenkova ◽

...

Keyword(s):

Native American ◽

Native Americans ◽

Amazon Basin ◽

Genomic Data ◽

Population History ◽

Ancestral Population ◽

Effective Population ◽

Southern Patagonia ◽

History Of ◽

Demographic Shifts

The last few years have witnessed an explosive generation of genomic data from ancient and modern Native American populations. These data shed light on key demographic shifts that occurred in geographically diverse territories of South America, such as the Andean highlands, Southern Patagonia and the Amazon basin. We used genomic data to study the recent population history of the Mapuche, who are the major Native population from the Southern Cone (Chile and Argentina). We found evidence of specific shared genetic ancestry between the Mapuche and ancient populations from Southern Patagonia, Central Chile and the Argentine Pampas. Despite previous evidence of cultural influence of Inca and Tiwanaku polities over the Mapuche, we did not find evidence of specific shared ancestry between them, nor with Amazonian groups. We estimated the effective population size dynamics of the Mapuche ancestral population during the last millennia, identifying a population bottleneck around 1650 AD, coinciding with a period of Spaniards invasions into the territory inhabited by the Mapuche. Finally, we show that admixed Chileans underwent post-admixture adaptation in their Mapuche subancestry component in genes related with lipid metabolism, suggesting adaptation to scarce food availability.

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Whole genome sequence of Mapuche-Huilliche Native Americans

10.1101/252619 ◽

2018 ◽

Cited By ~ 1

Author(s):

Elena A. Vidal ◽

Tomás C. Moyano ◽

Bernabé I. Bustos ◽

Eduardo Pérez-Palma ◽

Carol Moraga ◽

...

Keyword(s):

Native American ◽

Native Americans ◽

Latin American ◽

Genome Sequence ◽

Large Scale ◽

Genomic Structure ◽

Southern Cone ◽

Population History ◽

Whole Genome Sequence ◽

Single Nucleotide Variants

AbstractBackgroundWhole human genome sequencing initiatives provide a compendium of genetic variants that help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations and information on the genomic structure of Native Americans, especially those from the Southern Cone is scant.ResultsHere we present a high-quality complete genome sequence of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile (85% genomic and 98% exonic coverage at > 30X), with 96–97% high confidence calls. We found approximately 3.1×106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs that are not included in current sequencing databases. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a marginally admixed population from the Southern Cone, whose genetic component is derived from early Native American ancestors. In addition, we found that HUI genomes display highly divergent and novel variants with potential functional impact that converge in ontological categories essential in cell metabolic processes.ConclusionsMapuche-Huilliche genomes contain a unique set of small– and large-scale genomic variants in functionally linked genes, which may contribute to susceptibility for the development of common complex diseases or traits in admixed Latinos and Native American populations. Our data represents an ancestral reference panel for population-based studies in Native and admixed Latin American populations.

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Patterns in the Population History of Northern Eurasia from the Mesolithic to the Early Bronze Age, Based on Craniometry and Genetics

Archaeology Ethnology and Anthropology of Eurasia (Russian-language) ◽

10.17746/1563-0102.2021.49.4.140-151 ◽

2021 ◽

Vol 49 (4) ◽

pp. 140-151

Author(s):

A. G. Kozintsev ◽

Keyword(s):

Bronze Age ◽

Population History ◽

Early Bronze Age ◽

Northern Eurasia ◽

History Of

Цель исследования — рассмотреть краниометрические данные о популяционной изменчивости на территории Северной Евразии под углом зрения генетических и отчасти лингвистических фактов. Измерения 66 серий мужских черепов разных эпох (от мезолита до раннего бронзового века) с этой территории обработаны статистическими методами, специально предназначенными для изучения пространственных закономерностей, в частности градиентов. С помощью неметрического многомерного шкалирования матрицы расстояний D2 (с поправкой на численность) получена двумерная проекция взаимоположения групп, построено минимальное остовное дерево, показывающее кратчайший путь между точками в многомерном пространстве. Обнаруживаемые генетическими и краниометрическими данными восточно-западные градиенты на территории Северной Евразии свидетельствуют, видимо, не столько о смешении, сколько о незавершенности процесса дифференциации бореального надрасового ствола. Западный компонент, представленный в Сибири и Центральной Азии носителями афанасьевской культуры, вероятно, мало повлиял на генетический облик местных популяций. Восточный компонент, проникший в неолите из Забайкалья в Прибайкалье, смешался там с автохтонным палеосибирским. Главный генетический маркер коренного населения — аутосомный компонент ANE — присутствовал в Сибири с верхнего палеолита. Автохтонными следует считать и обе евразийские формации — северную и южную. Статистический анализ позволил включить в их состав новые группы, причем границы первой расширились на восток до Кузнецкой котловины, а второй — на запад до Среднего Прииртышья. Участие восточно-европейских групп в генезисе северной евразийской формации и протоуральской общности обнаружить не удается.

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The population history of northeastern Siberia since the Pleistocene

Nature ◽

10.1038/s41586-019-1279-z ◽

2019 ◽

Vol 570 (7760) ◽

pp. 182-188 ◽

Cited By ~ 56

Author(s):

Martin Sikora ◽

Vladimir V. Pitulko ◽

Vitor C. Sousa ◽

Morten E. Allentoft ◽

Lasse Vinner ◽

...

Keyword(s):

Population History ◽

Northeastern Siberia ◽

History Of

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A New Analysis of Population History in Sabah and Sarawak

GATR Global Journal of Business Social Sciences Review - GATR Global Journal of Business and Social Science Review (GJBSSR) Vol.7(1) Jan-Mar 2019 ◽

10.35609/gjbssr.2018.6.4(1) ◽

2018 ◽

Vol 6 (4) ◽

pp. 106-113

Author(s):

Hashom Mohd Hakim ◽

Japareng Lalung ◽

Suresh Narayanen ◽

Nasha Rodziadi Khaw ◽

Geoffrey Keith Chambers ◽

...

Keyword(s):

Ethnic Groups ◽

Large Scale ◽

Genetic Research ◽

Jel Classification ◽

Population History ◽

Current View ◽

Genetic Lineages ◽

Niah Cave ◽

History Of ◽

Sabah And Sarawak

Objective - This study is a comprehensive account of contemporary knowledge concerning pre-historic communities in Sabah and Sarawak based on newly available evidence from genomic and archaeological research. Methodology/Technique - The data presented in this review was obtained from primary literature including recent reports on several Neolithic excavation sites including Gua Sireh, Bukit Tengkorak, Melanta Tutup, and Bukit Kamiri. Findings - Pre-neolithic populations existed in Borneo long before the arrival of Austronesians as is evident from Niah Cave remains. These considerably pre-date the arrival of the latter new immigrants around 3,500 years ago. Further genetic research is needed, as the current view of the history of the population is based on a limited number of ethnic groups among those currently living in Borneo and to date, no trace has been found of any surviving genetic lineages from the earliest settlers. Novelty - This review paints a contemporary picture from existing information. In particular, it highlights the need for further research on the topic, as the current view of the genetic history of the population in Sabah and Sarawak is only available on a limited number of ethnic groups currently living in Borneo. Developing a conclusive and composite view on this topic will require widespread genetic surveys of many more ethnic groups scattered throughout the Sabah and Sarawak areas. This will require large-scale next-generation techniques (such as genome-wide SNP surveys and whole genome sequencing etc.). These methods should be enhanced by examination of ancient materials including human remains and their associated artefacts. These initiatives will require a number of well-planned excavations of recent settlements (last 10,000 years) and the application of trace and ancient DNA methodology. Type of Paper - Review. Keywords: Population Genetics; Archaeology; Borneo; Sabah and Sarawak; Malaysia; Population History. JEL Classification: N90, Z10.

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