Publications by authors named "Denise Keating"

8 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.
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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

The Genomic History of the Bronze Age Southern Levant.

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

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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

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.
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http://dx.doi.org/10.1126/science.aat7487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822619PMC
September 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.
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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

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.

Department of Archaeogenetics, Max-Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07745, Jena, 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

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.
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http://dx.doi.org/10.1038/nature26164DOI Listing
March 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.
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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.
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http://dx.doi.org/10.1038/nature25778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6091220PMC
March 2018