Publications by authors named "Nasreen Broomandkhoshbacht"

22 Publications

  • Page 1 of 1

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

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

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

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-021-03336-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7993749PMC
March 2021

A minimally destructive protocol for DNA extraction from ancient teeth.

Genome Res 2021 Mar 12;31(3):472-483. Epub 2021 Feb 12.

Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria.

Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.267534.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919446PMC
March 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-020-03053-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7864882PMC
February 2021

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

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

Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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.

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

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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.

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

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-020-1929-1DOI Listing
January 2020

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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.

Authors:
Vagheesh M Narasimhan Nick Patterson Priya Moorjani Nadin Rohland Rebecca Bernardos Swapan Mallick Iosif Lazaridis Nathan Nakatsuka Iñigo Olalde Mark Lipson Alexander M Kim Luca M Olivieri Alfredo Coppa Massimo Vidale James Mallory Vyacheslav Moiseyev Egor Kitov Janet Monge Nicole Adamski Neel Alex Nasreen Broomandkhoshbacht Francesca Candilio Kimberly Callan Olivia Cheronet Brendan J Culleton Matthew Ferry Daniel Fernandes Suzanne Freilich Beatriz Gamarra Daniel Gaudio Mateja Hajdinjak Éadaoin Harney Thomas K Harper Denise Keating Ann Marie Lawson Matthew Mah Kirsten Mandl Megan Michel Mario Novak Jonas Oppenheimer Niraj Rai Kendra Sirak Viviane Slon Kristin Stewardson Fatma Zalzala Zhao Zhang Gaziz Akhatov Anatoly N Bagashev Alessandra Bagnera Bauryzhan Baitanayev Julio Bendezu-Sarmiento Arman A Bissembaev Gian Luca Bonora Temirlan T Chargynov Tatiana Chikisheva Petr K Dashkovskiy Anatoly Derevianko Miroslav Dobeš Katerina Douka Nadezhda Dubova Meiram N Duisengali Dmitry Enshin Andrey Epimakhov Alexey V Fribus Dorian Fuller Alexander Goryachev Andrey Gromov Sergey P Grushin Bryan Hanks Margaret Judd Erlan Kazizov Aleksander Khokhlov Aleksander P Krygin Elena Kupriyanova Pavel Kuznetsov Donata Luiselli Farhod Maksudov Aslan M Mamedov Talgat B Mamirov Christopher Meiklejohn Deborah C Merrett Roberto Micheli Oleg Mochalov Samariddin Mustafokulov Ayushi Nayak Davide Pettener Richard Potts Dmitry Razhev Marina Rykun Stefania Sarno Tatyana M Savenkova Kulyan Sikhymbaeva Sergey M Slepchenko Oroz A Soltobaev Nadezhda Stepanova Svetlana Svyatko Kubatbek Tabaldiev Maria Teschler-Nicola Alexey A Tishkin Vitaly V Tkachev Sergey Vasilyev Petr Velemínský Dmitriy Voyakin Antonina Yermolayeva Muhammad Zahir Valery S Zubkov Alisa Zubova Vasant S Shinde Carles Lalueza-Fox Matthias Meyer David Anthony Nicole Boivin Kumarasamy Thangaraj Douglas J Kennett Michael Frachetti Ron Pinhasi David Reich

Science 2019 09;365(6457)

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

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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 Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-019-1251-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6942545PMC
June 2019

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.

Science 2019 07 30;365(6448). Epub 2019 May 30.

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

How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aaw6275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6827346PMC
July 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41559-019-0912-4DOI Listing
June 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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.

Authors:
Iñigo Olalde Swapan Mallick Nick Patterson Nadin Rohland Vanessa Villalba-Mouco Marina Silva Katharina Dulias Ceiridwen J Edwards Francesca Gandini Maria Pala Pedro Soares Manuel Ferrando-Bernal Nicole Adamski Nasreen Broomandkhoshbacht Olivia Cheronet Brendan J Culleton Daniel Fernandes Ann Marie Lawson Matthew Mah Jonas Oppenheimer Kristin Stewardson Zhao Zhang Juan Manuel Jiménez Arenas Isidro Jorge Toro Moyano Domingo C Salazar-García Pere Castanyer Marta Santos Joaquim Tremoleda Marina Lozano Pablo García Borja Javier Fernández-Eraso José Antonio Mujika-Alustiza Cecilio Barroso Francisco J Bermúdez Enrique Viguera Mínguez Josep Burch Neus Coromina David Vivó Artur Cebrià Josep Maria Fullola Oreto García-Puchol Juan Ignacio Morales F Xavier Oms Tona Majó Josep Maria Vergès Antònia Díaz-Carvajal Imma Ollich-Castanyer F Javier López-Cachero Ana Maria Silva Carmen Alonso-Fernández Germán Delibes de Castro Javier Jiménez Echevarría Adolfo Moreno-Márquez Guillermo Pascual Berlanga Pablo Ramos-García José Ramos-Muñoz Eduardo Vijande Vila Gustau Aguilella Arzo Ángel Esparza Arroyo Katina T Lillios Jennifer Mack Javier Velasco-Vázquez Anna Waterman Luis Benítez de Lugo Enrich María Benito Sánchez Bibiana Agustí Ferran Codina Gabriel de Prado Almudena Estalrrich Álvaro Fernández Flores Clive Finlayson Geraldine Finlayson Stewart Finlayson Francisco Giles-Guzmán Antonio Rosas Virginia Barciela González Gabriel García Atiénzar Mauro S Hernández Pérez Armando Llanos Yolanda Carrión Marco Isabel Collado Beneyto David López-Serrano Mario Sanz Tormo António C Valera Concepción Blasco Corina Liesau Patricia Ríos Joan Daura María Jesús de Pedro Michó Agustín A Diez-Castillo Raúl Flores Fernández Joan Francès Farré Rafael Garrido-Pena Victor S Gonçalves Elisa Guerra-Doce Ana Mercedes Herrero-Corral Joaquim Juan-Cabanilles Daniel López-Reyes Sarah B McClure Marta Merino Pérez Arturo Oliver Foix Montserrat Sanz Borràs Ana Catarina Sousa Julio Manuel Vidal Encinas Douglas J Kennett Martin B Richards Kurt Werner Alt Wolfgang Haak Ron Pinhasi Carles Lalueza-Fox David Reich

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

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

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aav4040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436108PMC
March 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 Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2018.10.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327247PMC
November 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aat3188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6476732PMC
July 2018

Erratum: The Beaker phenomenon and the genomic transformation of northwest Europe.

Authors:
Iñigo Olalde Selina Brace Morten E Allentoft Ian Armit Kristian Kristiansen Thomas Booth Nadin Rohland Swapan Mallick Anna Szécsényi-Nagy Alissa Mittnik Eveline Altena Mark Lipson Iosif Lazaridis Thomas K Harper Nick Patterson Nasreen Broomandkhoshbacht Yoan Diekmann Zuzana Faltyskova Daniel Fernandes Matthew Ferry Eadaoin Harney Peter de Knijff Megan Michel Jonas Oppenheimer Kristin Stewardson Alistair Barclay Kurt Werner Alt Corina Liesau Patricia Ríos Concepción Blasco Jorge Vega Miguel Roberto Menduiña García Azucena Avilés Fernández Eszter Bánffy Maria Bernabò-Brea David Billoin Clive Bonsall Laura Bonsall Tim Allen Lindsey Büster Sophie Carver Laura Castells Navarro Oliver E Craig Gordon T Cook Barry Cunliffe Anthony Denaire Kirsten Egging Dinwiddy Natasha Dodwell Michal Ernée Christopher Evans Milan Kuchařík Joan Francès Farré Chris Fowler Michiel Gazenbeek Rafael Garrido Pena María Haber-Uriarte Elżbieta Haduch Gill Hey Nick Jowett Timothy Knowles Ken Massy Saskia Pfrengle Philippe Lefranc Olivier Lemercier Arnaud Lefebvre César Heras Martínez Virginia Galera Olmo Ana Bastida Ramírez Joaquín Lomba Maurandi Tona Majó Jacqueline I McKinley Kathleen McSweeney Balázs Gusztáv Mende Alessandra Modi Gabriella Kulcsár Viktória Kiss András Czene Róbert Patay Anna Endrődi Kitti Köhler Tamás Hajdu Tamás Szeniczey János Dani Zsolt Bernert Maya Hoole Olivia Cheronet Denise Keating Petr Velemínský Miroslav Dobeš Francesca Candilio Fraser Brown Raúl Flores Fernández Ana-Mercedes Herrero-Corral Sebastiano Tusa Emiliano Carnieri Luigi Lentini Antonella Valenti Alessandro Zanini Clive Waddington Germán Delibes Elisa Guerra-Doce Benjamin Neil Marcus Brittain Mike Luke Richard Mortimer Jocelyne Desideri Marie Besse Günter Brücken Mirosław Furmanek Agata Hałuszko Maksym Mackiewicz Artur Rapiński Stephany Leach Ignacio Soriano Katina T Lillios João Luís Cardoso Michael Parker Pearson Piotr Włodarczak T Douglas Price Pilar Prieto Pierre-Jérôme Rey Roberto Risch Manuel A Rojo Guerra Aurore Schmitt Joël Serralongue Ana Maria Silva Václav Smrčka Luc Vergnaud João Zilhão David Caramelli Thomas Higham Mark G Thomas Douglas J Kennett Harry Fokkens Volker Heyd Alison Sheridan Karl-Göran Sjögren Philipp W Stockhammer Johannes Krause Ron Pinhasi Wolfgang Haak Ian Barnes Carles Lalueza-Fox David Reich

Nature 2018 03;555(7697):543

This corrects the article DOI: 10.1038/nature25738.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature26164DOI Listing
March 2018

Population Turnover in Remote Oceania Shortly after Initial Settlement.

Curr Biol 2018 04 28;28(7):1157-1165.e7. Epub 2018 Feb 28.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA. Electronic address:

Ancient DNA from Vanuatu and Tonga dating to about 2,900-2,600 years ago (before present, BP) has revealed that the "First Remote Oceanians" associated with the Lapita archaeological culture were directly descended from the population that, beginning around 5000 BP, spread Austronesian languages from Taiwan to the Philippines, western Melanesia, and eventually Remote Oceania. Thus, ancestors of the First Remote Oceanians must have passed by the Papuan-ancestry populations they encountered in New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture [1]. However, all present-day populations in Near and Remote Oceania harbor >25% Papuan ancestry, implying that additional eastward migration must have occurred. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu from 2900-150 BP, as well as 185 present-day individuals from 18 islands. We find that people of almost entirely Papuan ancestry arrived in Vanuatu by around 2300 BP, most likely reflecting migrations a few hundred years earlier at the end of the Lapita period, when there is also evidence of changes in skeletal morphology and cessation of long-distance trade between Near and Remote Oceania [2, 3]. Papuan ancestry was subsequently diluted through admixture but remains at least 80%-90% in most islands. Through a fine-grained analysis of ancestry profiles, we show that the Papuan ancestry in Vanuatu derives from the Bismarck Archipelago rather than the geographically closer Solomon Islands. However, the Papuan ancestry in Polynesia-the most remote Pacific islands-derives from different sources, documenting a third stream of migration from Near to Remote Oceania.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cub.2018.02.051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5882562PMC
April 2018

The Beaker phenomenon and the genomic transformation of northwest Europe.

Authors:
Iñigo Olalde Selina Brace Morten E Allentoft Ian Armit Kristian Kristiansen Thomas Booth Nadin Rohland Swapan Mallick Anna Szécsényi-Nagy Alissa Mittnik Eveline Altena Mark Lipson Iosif Lazaridis Thomas K Harper Nick Patterson Nasreen Broomandkhoshbacht Yoan Diekmann Zuzana Faltyskova Daniel Fernandes Matthew Ferry Eadaoin Harney Peter de Knijff Megan Michel Jonas Oppenheimer Kristin Stewardson Alistair Barclay Kurt Werner Alt Corina Liesau Patricia Ríos Concepción Blasco Jorge Vega Miguel Roberto Menduiña García Azucena Avilés Fernández Eszter Bánffy Maria Bernabò-Brea David Billoin Clive Bonsall Laura Bonsall Tim Allen Lindsey Büster Sophie Carver Laura Castells Navarro Oliver E Craig Gordon T Cook Barry Cunliffe Anthony Denaire Kirsten Egging Dinwiddy Natasha Dodwell Michal Ernée Christopher Evans Milan Kuchařík Joan Francès Farré Chris Fowler Michiel Gazenbeek Rafael Garrido Pena María Haber-Uriarte Elżbieta Haduch Gill Hey Nick Jowett Timothy Knowles Ken Massy Saskia Pfrengle Philippe Lefranc Olivier Lemercier Arnaud Lefebvre César Heras Martínez Virginia Galera Olmo Ana Bastida Ramírez Joaquín Lomba Maurandi Tona Majó Jacqueline I McKinley Kathleen McSweeney Balázs Gusztáv Mende Alessandra Modi Gabriella Kulcsár Viktória Kiss András Czene Róbert Patay Anna Endrődi Kitti Köhler Tamás Hajdu Tamás Szeniczey János Dani Zsolt Bernert Maya Hoole Olivia Cheronet Denise Keating Petr Velemínský Miroslav Dobeš Francesca Candilio Fraser Brown Raúl Flores Fernández Ana-Mercedes Herrero-Corral Sebastiano Tusa Emiliano Carnieri Luigi Lentini Antonella Valenti Alessandro Zanini Clive Waddington Germán Delibes Elisa Guerra-Doce Benjamin Neil Marcus Brittain Mike Luke Richard Mortimer Jocelyne Desideri Marie Besse Günter Brücken Mirosław Furmanek Agata Hałuszko Maksym Mackiewicz Artur Rapiński Stephany Leach Ignacio Soriano Katina T Lillios João Luís Cardoso Michael Parker Pearson Piotr Włodarczak T Douglas Price Pilar Prieto Pierre-Jérôme Rey Roberto Risch Manuel A Rojo Guerra Aurore Schmitt Joël Serralongue Ana Maria Silva Václav Smrčka Luc Vergnaud João Zilhão David Caramelli Thomas Higham Mark G Thomas Douglas J Kennett Harry Fokkens Volker Heyd Alison Sheridan Karl-Göran Sjögren Philipp W Stockhammer Johannes Krause Ron Pinhasi Wolfgang Haak Ian Barnes Carles Lalueza-Fox David Reich

Nature 2018 03 21;555(7695):190-196. Epub 2018 Feb 21.

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

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature25738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5973796PMC
March 2018

The genomic history of southeastern Europe.

Authors:
Iain Mathieson Songül Alpaslan-Roodenberg Cosimo Posth Anna Szécsényi-Nagy Nadin Rohland Swapan Mallick Iñigo Olalde Nasreen Broomandkhoshbacht Francesca Candilio Olivia Cheronet Daniel Fernandes Matthew Ferry Beatriz Gamarra Gloria González Fortes Wolfgang Haak Eadaoin Harney Eppie Jones Denise Keating Ben Krause-Kyora Isil Kucukkalipci Megan Michel Alissa Mittnik Kathrin Nägele Mario Novak Jonas Oppenheimer Nick Patterson Saskia Pfrengle Kendra Sirak Kristin Stewardson Stefania Vai Stefan Alexandrov Kurt W Alt Radian Andreescu Dragana Antonović Abigail Ash Nadezhda Atanassova Krum Bacvarov Mende Balázs Gusztáv Hervé Bocherens Michael Bolus Adina Boroneanţ Yavor Boyadzhiev Alicja Budnik Josip Burmaz Stefan Chohadzhiev Nicholas J Conard Richard Cottiaux Maja Čuka Christophe Cupillard Dorothée G Drucker Nedko Elenski Michael Francken Borislava Galabova Georgi Ganetsovski Bernard Gély Tamás Hajdu Veneta Handzhyiska Katerina Harvati Thomas Higham Stanislav Iliev Ivor Janković Ivor Karavanić Douglas J Kennett Darko Komšo Alexandra Kozak Damian Labuda Martina Lari Catalin Lazar Maleen Leppek Krassimir Leshtakov Domenico Lo Vetro Dženi Los Ivaylo Lozanov Maria Malina Fabio Martini Kath McSweeney Harald Meller Marko Menđušić Pavel Mirea Vyacheslav Moiseyev Vanya Petrova T Douglas Price Angela Simalcsik Luca Sineo Mario Šlaus Vladimir Slavchev Petar Stanev Andrej Starović Tamás Szeniczey Sahra Talamo Maria Teschler-Nicola Corinne Thevenet Ivan Valchev Frédérique Valentin Sergey Vasilyev Fanica Veljanovska Svetlana Venelinova Elizaveta Veselovskaya Bence Viola Cristian Virag Joško Zaninović Steve Zäuner Philipp W Stockhammer Giulio Catalano Raiko Krauß David Caramelli Gunita Zariņa Bisserka Gaydarska Malcolm Lillie Alexey G Nikitin Inna Potekhina Anastasia Papathanasiou Dušan Borić Clive Bonsall Johannes Krause Ron Pinhasi David Reich

Nature 2018 03 21;555(7695):197-203. Epub 2018 Feb 21.

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

Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west-east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature25778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6091220PMC
March 2018

Parallel palaeogenomic transects reveal complex genetic history of early European farmers.

Nature 2017 11 8;551(7680):368-372. Epub 2017 Nov 8.

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

Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000-2900 bc, n = 100), Germany (5500-3000 bc, n = 42) and Spain (5500-2200 bc, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature24476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5973800PMC
November 2017