Publications by authors named "Swapan Mallick"

76 Publications

Genomic insights into the formation of human populations in East Asia.

Nature 2021 03 22;591(7850):413-419. Epub 2021 Feb 22.

Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.

The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.
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http://dx.doi.org/10.1038/s41586-021-03336-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7993749PMC
March 2021

Mitochondrial genome diversity on the Central Siberian Plateau with particular reference to the prehistory of northernmost Eurasia.

PLoS One 2021 28;16(1):e0244228. Epub 2021 Jan 28.

Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk, Russian Federation.

The Central Siberian Plateau was the last geographic area in Eurasia to become habitable by modern humans after the Last Glacial Maximum (LGM). Through a comprehensive dataset of mitochondrial DNA (mtDNA) genomes retained in the remnats of earlier ("Old") Siberians, primarily the Ket, Tofalar, and Todzhi, we explored genetic links between the Yenisei-Sayan region and Northeast Eurasia (best represented by the Yukaghir) over the last 10,000 years. We generated 218 new complete mtDNA sequences and placed them into compound phylogenies with 7 newly obtained and 70 published ancient mitochondrial genomes. We have considerably extended the mtDNA sequence diversity (at the entire mtDNA genome level) of autochthonous Siberians, which remain poorly sampled, and these new data may have a broad impact on the study of human migration. We compared present-day mtDNA diversity in these groups with complete mitochondrial genomes from ancient samples from the region and placed the samples into combined genealogical trees. The resulting components were used to clarify the origins and expansion history of mtDNA lineages that evolved in the refugia of south-central Siberia and beyond, as well as multiple phases of connection between this region and distant parts of Eurasia.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244228PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7842996PMC
April 2021

A genetic history of the pre-contact Caribbean.

Nature 2021 02 23;590(7844):103-110. Epub 2020 Dec 23.

Department of Genetics, Harvard Medical School, Boston, MA, USA.

Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500-1,500 and a maximum of 1,530-8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large. Confirming a small and interconnected Ceramic Age population, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world.
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http://dx.doi.org/10.1038/s41586-020-03053-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7864882PMC
February 2021

ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium.

Genome Biol 2020 08 10;21(1):199. Epub 2020 Aug 10.

Department of Genetics, New Research Building, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA.

We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA. ContamLD leverages the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors: for example, less than 1.5% standard error in cases with less than 10% contamination and 500,000 sequences covering SNPs. This method is optimized for application to aDNA, taking advantage of characteristic aDNA damage patterns to provide calibrated contamination estimates, and is available at https://github.com/nathan-nakatsuka/ContamLD .
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http://dx.doi.org/10.1186/s13059-020-02111-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418405PMC
August 2020

Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography.

Nat Commun 2020 08 3;11(1):3868. Epub 2020 Aug 3.

Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.

Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700-2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200-1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.
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http://dx.doi.org/10.1038/s41467-020-17656-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7400565PMC
August 2020

The Genomic History of the Bronze Age Southern Levant.

Cell 2020 05;181(5):1146-1157.e11

Department of Statistics, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel.

We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the "Canaanite" material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations and (2) populations related to the Chalcolithic Zagros or the Bronze Age Caucasus. The non-local contribution increased over time, as evinced by three outliers who can be modeled as descendants of recent migrants. We show evidence that different "Canaanite" groups genetically resemble each other more than other populations. We find that Levant-related modern populations typically have substantial ancestry coming from populations related to the Chalcolithic Zagros and the Bronze Age Southern Levant. These groups also harbor ancestry from sources we cannot fully model with the available data, highlighting the critical role of post-Bronze-Age migrations into the region over the past 3,000 years.
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http://dx.doi.org/10.1016/j.cell.2020.04.024DOI Listing
May 2020

A Paleogenomic Reconstruction of the Deep Population History of the Andes.

Cell 2020 05 7;181(5):1131-1145.e21. Epub 2020 May 7.

Harvard Peabody Museum, Harvard University, Cambridge, MA 02138, USA.

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.
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http://dx.doi.org/10.1016/j.cell.2020.04.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304944PMC
May 2020

Insights into human genetic variation and population history from 929 diverse genomes.

Science 2020 03;367(6484)

Wellcome Sanger Institute, Hinxton CB10 1SA, UK.

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.
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http://dx.doi.org/10.1126/science.aay5012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115999PMC
March 2020

Differential DNA methylation of vocal and facial anatomy genes in modern humans.

Nat Commun 2020 03 4;11(1):1189. Epub 2020 Mar 4.

Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel.

Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.
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http://dx.doi.org/10.1038/s41467-020-15020-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7055320PMC
March 2020

Human auditory ossicles as an alternative optimal source of ancient DNA.

Genome Res 2020 03 25;30(3):427-436. Epub 2020 Feb 25.

Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary.

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.
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http://dx.doi.org/10.1101/gr.260141.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111520PMC
March 2020

The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean.

Nat Ecol Evol 2020 03 24;4(3):334-345. Epub 2020 Feb 24.

Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria-Gobierno de Cantabria-Banco Santander, Santander, Spain.

Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.
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http://dx.doi.org/10.1038/s41559-020-1102-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080320PMC
March 2020

Ancient West African foragers in the context of African population history.

Nature 2020 01 22;577(7792):665-670. Epub 2020 Jan 22.

UCL Genetics Institute, University College London, London, UK.

Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children-two of whom were buried approximately 8,000 years ago and two 3,000 years ago-from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today-as well as speakers of Bantu languages from across the continent-are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.
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http://dx.doi.org/10.1038/s41586-020-1929-1DOI Listing
January 2020

Correction to: African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations.

Genome Biol 2019 Oct 9;20(1):204. Epub 2019 Oct 9.

Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.

Following publication of the original article [1], a typographical error in the formula for calculating d in the "Scans for local adaptation" subsection in the Method section, was identified. The correct formula should be.
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http://dx.doi.org/10.1186/s13059-019-1821-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6784328PMC
October 2019

An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers.

Cell 2019 10 5;179(3):729-735.e10. Epub 2019 Sep 5.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.
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http://dx.doi.org/10.1016/j.cell.2019.08.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800651PMC
October 2019

The formation of human populations in South and Central Asia.

Science 2019 09;365(6457)

Earth Institute, University College Dublin, Dublin 4, Ireland.

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.
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http://dx.doi.org/10.1126/science.aat7487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822619PMC
September 2019

Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India.

Nat Commun 2019 08 20;10(1):3670. Epub 2019 Aug 20.

CSIR Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.

Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups.
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http://dx.doi.org/10.1038/s41467-019-11357-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6702210PMC
August 2019

Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America.

Nature 2019 06 5;570(7760):236-240. Epub 2019 Jun 5.

Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.

Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup'ik. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup'ik and Aleut populations remains uncertain. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyse these data with data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Using methods based on rare-allele and haplotype sharing, as well as established techniques, we show that Palaeo-Eskimo-related ancestry is ubiquitous among people who speak Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that Na-Dene-speaking peoples, people of the Aleutian Islands, and Yup'ik and Inuit across the Arctic region all share ancestry from a single Palaeo-Eskimo-related Siberian source.
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http://dx.doi.org/10.1038/s41586-019-1251-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6942545PMC
June 2019

Author Correction: Ancient genomes indicate population replacement in Early Neolithic Britain.

Nat Ecol Evol 2019 Jun;3(6):986-987

Department of Earth Sciences, Natural History Museum, London, UK.

In the version of this Article originally published, there were errors in the colour ordering of the legend in Fig. 5b, and in the positions of the target and surrogate populations in Fig. 5c. This has now been corrected. The conclusions of the study are in no way affected. The errors have been corrected in the HTML and PDF versions of the article.
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http://dx.doi.org/10.1038/s41559-019-0912-4DOI Listing
June 2019

African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations.

Genome Biol 2019 04 26;20(1):82. Epub 2019 Apr 26.

Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.

Background: Africa is the origin of modern humans within the past 300 thousand years. To infer the complex demographic history of African populations and adaptation to diverse environments, we sequenced the genomes of 92 individuals from 44 indigenous African populations.

Results: Genetic structure analyses indicate that among Africans, genetic ancestry is largely partitioned by geography and language, though we observe mixed ancestry in many individuals, consistent with both short- and long-range migration events followed by admixture. Phylogenetic analysis indicates that the San genetic lineage is basal to all modern human lineages. The San and Niger-Congo, Afroasiatic, and Nilo-Saharan lineages were substantially diverged by 160 kya (thousand years ago). In contrast, the San and Central African rainforest hunter-gatherer (CRHG), Hadza hunter-gatherer, and Sandawe hunter-gatherer lineages were diverged by ~ 120-100 kya. Niger-Congo, Nilo-Saharan, and Afroasiatic lineages diverged more recently by ~ 54-16 kya. Eastern and western CRHG lineages diverged by ~ 50-31 kya, and the western CRHG lineages diverged by ~ 18-12 kya. The San and CRHG populations maintained the largest effective population size compared to other populations prior to 60 kya. Further, we observed signatures of positive selection at genes involved in muscle development, bone synthesis, reproduction, immune function, energy metabolism, and cell signaling, which may contribute to local adaptation of African populations.

Conclusions: We observe high levels of genomic variation between ethnically diverse Africans which is largely correlated with geography and language. Our study indicates ancient population substructure and local adaptation of Africans.
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http://dx.doi.org/10.1186/s13059-019-1679-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485071PMC
April 2019

Ancient genomes indicate population replacement in Early Neolithic Britain.

Nat Ecol Evol 2019 05 15;3(5):765-771. Epub 2019 Apr 15.

Department of Earth Sciences, Natural History Museum, London, UK.

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.
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http://dx.doi.org/10.1038/s41559-019-0871-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6520225PMC
May 2019

The genomic history of the Iberian Peninsula over the past 8000 years.

Science 2019 03;363(6432):1230-1234

Departamento de Prehistoria e Historia Antigua, Universidad Nacional de Educación a Distancia, Valencia, Spain.

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia's ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European-speaking regions but also into non-Indo-European-speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.
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http://dx.doi.org/10.1126/science.aav4040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436108PMC
March 2019

Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions.

Nat Commun 2019 02 4;10(1):590. Epub 2019 Feb 4.

German Archaeological Institute, Department of Natural Sciences, Im Dol 2-6, D-14195, Berlin, Germany.

Archaeogenetic studies have described the formation of Eurasian 'steppe ancestry' as a mixture of Eastern and Caucasus hunter-gatherers. However, it remains unclear when and where this ancestry arose and whether it was related to a horizon of cultural innovations in the 4 millennium BCE that subsequently facilitated the advance of pastoral societies in Eurasia. Here we generated genome-wide SNP data from 45 prehistoric individuals along a 3000-year temporal transect in the North Caucasus. We observe a genetic separation between the groups of the Caucasus and those of the adjacent steppe. The northern Caucasus groups are genetically similar to contemporaneous populations south of it, suggesting human movement across the mountain range during the Bronze Age. The steppe groups from Yamnaya and subsequent pastoralist cultures show evidence for previously undetected farmer-related ancestry from different contact zones, while Steppe Maykop individuals harbour additional Upper Palaeolithic Siberian and Native American related ancestry.
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http://dx.doi.org/10.1038/s41467-018-08220-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360191PMC
February 2019

Reconstructing the Deep Population History of Central and South America.

Cell 2018 11 8;175(5):1185-1197.e22. Epub 2018 Nov 8.

Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.
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http://dx.doi.org/10.1016/j.cell.2018.10.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327247PMC
November 2018

Publisher Correction: Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation.

Nat Commun 2018 09 20;9(1):3913. Epub 2018 Sep 20.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

In the original version of this Article, references in the format 'First author et al.' were inappropriately deleted. These errors have been corrected in the PDF and HTML versions of the Article.
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http://dx.doi.org/10.1038/s41467-018-06484-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6147797PMC
September 2018

Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation.

Nat Commun 2018 08 20;9(1):3336. Epub 2018 Aug 20.

Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.

The material culture of the Late Chalcolithic period in the southern Levant (4500-3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi'in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi'in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi'in Cave. These results provide an example of how population movements propelled cultural changes in the deep past.
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http://dx.doi.org/10.1038/s41467-018-05649-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6102297PMC
August 2018

Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences.

Eur J Hum Genet 2018 11 10;26(11):1687-1696. Epub 2018 Jul 10.

MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 20043, China.

The expansion of modern humans to the American continent after the Last Glacial Maximum led the way to the present-day distribution of American aborigines. Recent advances in autosomal DNA research and expanded testing of mtDNA lineages has provided a clearer picture of the number and timing of founding lineages. However, both autosomal DNA and mtDNA research have provided unresolved competing theories between the short-term and the long-term models of the Beringian standstill hypothesis. Further, the source of founding paternal lineages of American aborigines and their relationship with ancient Siberia populations remains ambiguous. In this study, we reanalyzed a 7.0 Mbp region of 132 paternal Y-chromosome sequences, including 39 newly reported ones, of male samples from American aborigines and Eurasian populations. Among Eurasian samples, we identified Y-chromosome branches that are most closely related to known American aborigine founding lineages, that is, Q1-L804 links to Q1-M3, Q1-L330 links to Q1-Z780, Q1-M120 links to Q1-B143, and C2-F1756 links to C2-P39. The revised phylogenetic tree and age estimates indicate a narrow timeframe (~15.3-14.3 kya) for the upper time limit of human entry to the American continent. Our analysis suggests that the in situ differentiation of Q-M242 in Central Eurasia and South Siberia region gave rise to numerous sub-lineages older than 15.3 kya, and the founding of Paleo-Indian paternal lineages is part of the great Q1-L53 diffusion throughout the Eurasia after the Last Glacial Maximum. The results of our study will assist in future studies of the history of modern populations in Eurasia and the Americas.
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http://dx.doi.org/10.1038/s41431-018-0211-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6189043PMC
November 2018

Reconstruction of Y-chromosome phylogeny reveals two neolithic expansions of Tibeto-Burman populations.

Mol Genet Genomics 2018 Oct 19;293(5):1293-1300. Epub 2018 Jun 19.

MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 20043, China.

Diffusion of Tibeto-Burman populations across the Tibetan Plateau led to the largest human community in a high-altitude environment and has long been a focus of research on high-altitude adaptation, archeology, genetics, and linguistics. However, much uncertainty remains regarding the origin, diversification, and expansion of Tibeto-Burman populations. In this study, we analyzed a 7.0M bp region of 285 Y-chromosome sequences, including 81 newly reported ones, from male samples from Tibeto-Burman populations and other related Eastern Asian populations. We identified several paternal lineages specific to Tibeto-Burman populations, and most of these lineages emerged between 6000 and 2500 years ago. A phylogenetic tree and lineage dating both support the hypothesis that the establishment of Tibeto-Burman ancestral groups was triggered by Neolithic expansions from the middle Yellow River Basin and admixtures with local populations on the Tibetan Plateau who survived the Paleolithic Age. Furthermore, according to the geographical distributions of the haplogroups, we propose that there are two Neolithic expansion origins for all modern Tibeto-Burman populations. Our research provides a clear scenario about the sources, admixture process and later diffusion process of the ancestor population of all Tibeto-Burman populations.
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http://dx.doi.org/10.1007/s00438-018-1461-2DOI Listing
October 2018

Ancient genomes document multiple waves of migration in Southeast Asian prehistory.

Science 2018 07 17;361(6397):92-95. Epub 2018 May 17.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from 18 Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants.
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http://dx.doi.org/10.1126/science.aat3188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6476732PMC
July 2018

No evidence for unknown archaic ancestry in South Asia.

Nat Genet 2018 05;50(5):632-633

Department of Genetics, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41588-018-0097-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6433599PMC
May 2018
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