Publications by authors named "Kendra Sirak"

23 Publications

  • Page 1 of 1

Integrating buccal and occlusal dental microwear with isotope analyses for a complete paleodietary reconstruction of Holocene populations from Hungary.

Sci Rep 2021 Mar 29;11(1):7034. Epub 2021 Mar 29.

Department of Evolutionary Anthropology, University of Vienna, AltrantraBe 14, Vienna, Austria.

Dietary reconstruction is used to make inferences about the subsistence strategies of ancient human populations, but it may also serve as a proxy to characterise their diverse cultural and technological manifestations. Dental microwear and stable isotope analyses have been shown to be successful techniques for paleodietary reconstruction of ancient populations but, despite yielding complementary dietary information, these techniques have rarely been combined within the same study. Here we present for the first time a comprehensive approach to interpreting ancient lifeways through the results of buccal and occlusal microwear, and δC and δN isotope analyses applied to the same individuals of prehistoric populations of Hungary from the Middle Neolithic to the Late Bronze Age periods. This study aimed to (a) assess if the combination of techniques yields a more precise assessment of past dietary and subsistence practices, and (b) contribute to our understanding of the dietary patterns of the prehistoric Hungarian populations. Overall, no correlations between microwear and δC and δN isotope variables were observed, except for a relationship between nitrogen and the vertical and horizontal index. However, we found that diachronic differences are influenced by the variation within the period. Particularly, we found differences in microwear and isotope variables between Middle Neolithic sites, indicating that there were different dietary practices among those populations. Additionally, microwear results suggest no changes in the abrasiveness of the diet, neither food processing methods, despite higher C plant resource consumption shown by carbon isotopic signal. Thus, we demonstrate that the integration of dental microwear and carbon and nitrogen stable isotope methodologies can provide complementary information for making inferences about paleodietary habits.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-021-86369-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8007593PMC
March 2021

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

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

Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia.

PLoS One 2019 21;14(8):e0216366. Epub 2019 Aug 21.

School of Archaeology, University College Dublin, Dublin, Ireland.

Three individuals dating to the Great Migration Period (5th century CE) were discovered in a pit at the Hermanov vinograd site in Osijek, Croatia. We were inspired to study these individuals based on their unusual burial context as well as the identification of two different types of artificial cranial deformation in two of the individuals. We combine bioarchaeological analysis with radiographic imaging, stable isotopes analysis, and ancient DNA to analyze their dietary patterns, molecular sex, and genetic affinities in the context of the archaeological data and their bioarchaeological attributes. While all three individuals were adolescent males with skeletal evidence of severe malnutrition and similar diets, the most striking observation is that they had major differences in their genetic ancestry. Results of the genetic analyses of the nuclear ancient DNA data for these individuals indicate that the individual without artificial cranial deformation shows broadly West Eurasian associated-ancestry, the individual with tabular oblique-type has East Asian ancestry and the third individual with circular erect-type has Near Eastern associated-ancestry. Based on these results, we speculate that artificial cranial deformation type may have been a visual indicator membership in a specific cultural group, and that these groups were interacting intimately on the Pannonian Plain during the Migration Period.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216366PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6703674PMC
February 2020

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

Isolating the human cochlea to generate bone powder for ancient DNA analysis.

Nat Protoc 2019 04 6;14(4):1194-1205. Epub 2019 Mar 6.

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

The cortical bone that forms the structure of the cochlea, part of the osseous labyrinth of the inner ear, is now one of the most frequently used skeletal elements in analyses of human ancient DNA. However, there is currently no published, standardized method for its sampling. This protocol describes the preparation of bone powder from the cochlea of fragmented skulls in which the petrous pyramid of the temporal bone is accessible. Using a systematic process of bone removal based on distinct anatomical landmarks and the identification of relevant morphological features, a petrous pyramid is cleaned with a sandblaster, and the cochlea is located, isolated, and reduced to a homogeneous bone powder. All steps are carried out in dedicated ancient DNA facilities, thus reducing the introduction of contamination. This protocol requires an understanding of ancient DNA clean-room procedures and basic knowledge of petrous pyramid anatomy. In 50-65 min, it results in bone powder with endogenous DNA yields that can exceed those from teeth and other bones by up to two orders of magnitude. Compared with drilling methods, this method facilitates a more precise targeting of the cochlea, allows the user to visually inspect the cochlea and remove any residual sediment before the generation of bone powder, and confines the damage to the inner ear region and surface of the petrous portion of fragmentary crania.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41596-019-0137-7DOI Listing
April 2019

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

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 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

Reconstructing Prehistoric African Population Structure.

Cell 2017 Sep;171(1):59-71.e21

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 assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2017.08.049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679310PMC
September 2017

A minimally-invasive method for sampling human petrous bones from the cranial base for ancient DNA analysis.

Biotechniques 2017 06 1;62(6):283-289. Epub 2017 Jun 1.

School of Archaeology and Earth Institute, Belfield, University College Dublin, Ireland.

Ancient DNA (aDNA) research involves invasive and destructive sampling procedures that are often incompatible with anthropological, anatomical, and bioarcheological analyses requiring intact skeletal remains. The osseous labyrinth inside the petrous bone has been shown to yield higher amounts of endogenous DNA than any other skeletal element; however, accessing this labyrinth in cases of a complete or reconstructed skull involves causing major structural damage to the cranial vault or base. Here, we describe a novel cranial base drilling method (CBDM) for accessing the osseous labyrinth from the cranial base that prevents damaging the surrounding cranial features, making it highly complementary to morphological analyses. We assessed this method by comparing the aDNA results from one petrous bone processed using our novel method to its pair, which was processed using established protocols for sampling disarticulated petrous bones. We show a decrease in endogenous DNA and molecular copy numbers when the drilling method is used; however, we also show that this method produces more endogenous DNA and higher copy numbers than any postcranial bone. Our results demonstrate that this minimally-invasive method reduces the loss of genetic data associated with the use of other skeletal elements and enables the combined craniometric and genetic study of individuals with archeological, cultural, and evolutionary value.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2144/000114558DOI Listing
June 2017

The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes.

Sci Rep 2017 01 30;7:41529. Epub 2017 Jan 30.

School of Biology and Environment Science, University College Dublin, Belfield, Dublin 4, Republic of Ireland.

Thomas Kent was an Irish rebel who was executed by British forces in the aftermath of the Easter Rising armed insurrection of 1916 and buried in a shallow grave on Cork prison's grounds. In 2015, ninety-nine years after his death, a state funeral was offered to his living family to honor his role in the struggle for Irish independence. However, inaccuracies in record keeping did not allow the bodily remains that supposedly belonged to Kent to be identified with absolute certainty. Using a novel approach based on homozygous single nucleotide polymorphisms, we identified these remains to be those of Kent by comparing his genetic data to that of two known living relatives. As the DNA degradation found on Kent's DNA, characteristic of ancient DNA, rendered traditional methods of relatedness estimation unusable, we forced all loci homozygous, in a process we refer to as "forced homozygote approach". The results were confirmed using simulated data for different relatedness classes. We argue that this method provides a necessary alternative for relatedness estimations, not only in forensic analysis, but also in ancient DNA studies, where reduced amounts of genetic information can limit the application of traditional methods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep41529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5278401PMC
January 2017

Genomic insights into the peopling of the Southwest Pacific.

Nature 2016 Oct 3;538(7626):510-513. Epub 2016 Oct 3.

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

The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100-2,700 years before present) and one from Tonga (about 2,700-2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians. Today, indigenous people of the South Pacific harbour a mixture of ancestry from Papuans and a population of East Asian origin that no longer exists in unmixed form, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five per cent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, before their further expansion into Remote Oceania. However, our finding that the ancient individuals had little to no Papuan ancestry implies that later human population movements spread Papuan ancestry through the South Pacific after the first peopling of the islands.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature19844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515717PMC
October 2016

Genomic insights into the origin of farming in the ancient Near East.

Nature 2016 08 25;536(7617):419-24. Epub 2016 Jul 25.

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature19310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003663PMC
August 2016

Genome-wide patterns of selection in 230 ancient Eurasians.

Nature 2015 Dec 23;528(7583):499-503. Epub 2015 Nov 23.

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

Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature16152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918750PMC
December 2015

Developmental patterns of bilateral asymmetry in ancestral puebloans.

Am J Hum Biol 2016 05 14;28(3):421-30. Epub 2015 Nov 14.

Department of Anthropology, Emory University, Atlanta, Georgia, 30322.

Objectives: Producing and maintaining a bilaterally symmetric phenotype throughout the lifespan is energetically demanding. Over the course of an individual's life, various intrinsic and external stressors impact the growth trajectory. These perturbations can compromise the allocation of energetic resources to processes that maintain developmental precision, potentially resulting in bilateral asymmetry (BA). Because different stressors are present during the lifespan, BA is a valuable tool for examining the unique factors impacting symmetrical growth and development. This study examines BA in paired long bones across a developmental skeletal series.

Methods: The humeri, radii, femora, and tibiae of 198 individuals from Ancestral Puebloan New Mexico (919-1670 CE) are analyzed to explore BA across development. Individuals are separated into five age categories, and by sex when possible, to explore patterns of BA.

Results: Significant BA is found in the bones of the upper limb when the interaction between bone and age is examined. Results suggest that BA in the humerus and radius becomes more right-biased with age. These directional trends are not observed in the lower limbs. Division into age categories illuminates patterns of asymmetry associated with age-related activities and physiological maturity, indicating that BA is differentially affected by varying environmental stressors across development.

Conclusions: Our findings support the hypothesis that BA in long bones is influenced by environmental stressors that impact an individual's ability to produce symmetric morphological traits over the lifespan. Right-biased BA in the upper limb bones indicates that this variation from a symmetric ideal is strongly influenced by handedness resulting from habitual manual activities. Am. J. Hum. Biol. 28:421-430, 2016. © 2015 Wiley Periodicals, Inc.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ajhb.22804DOI Listing
May 2016

Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.

PLoS One 2015 18;10(6):e0129102. Epub 2015 Jun 18.

Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknechtstr. 24-25, 14476 Potsdam Golm, Germany; Department of Biology, University of York, Wentworth Way, Heslington, York, United Kingdom.

The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129102PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472748PMC
April 2016

Analysis of nutritional disease in prehistory: The search for scurvy in antiquity and today.

Int J Paleopathol 2014 Jun 15;5:9-17. Epub 2013 Nov 15.

Georgia State University, Atlanta, GA 30302-3998, United States.

In this paper, we discuss the issues surrounding the study of scurvy, or vitamin C deficiency, in paleopathology, and highlight the work of Donald Ortner in advancing this area of research. This micronutrient deficiency impacts collagen formation and results in damage to a variety of bodily tissues. While clinical manifestations are observed routinely, the lack of specific signatures on bone makes paleopathological diagnosis difficult. Rapid growth in infants, children, and subadults provides abundant remodeled tissue and an increase in vascularization that makes identification possible in younger segments of the population. However, diagnosis of scurvy in adults remains problematic, given that diagnostic lesions are strikingly similar to those associated with rickets, osteomalacia, and other conditions. We argue that this confounding factor underscores the need for a broader anthropological approach to scurvy research that expands beyond differential diagnosis to include more accurate reconstruction of diets and available resources, greater consideration of the possibility - even likelihood - of multiple nutrient deficiencies simultaneously affecting an individual, and the patterning of these deficiencies along lines of status, sex, and age.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijpp.2013.09.007DOI Listing
June 2014