Author
Matthew Ferry
Other affiliations: Broad Institute, Harvard University
Bio: Matthew Ferry is an academic researcher from Howard Hughes Medical Institute. The author has contributed to research in topics: Population & Bronze Age. The author has an hindex of 15, co-authored 24 publications receiving 1823 citations. Previous affiliations of Matthew Ferry include Broad Institute & Harvard University.
Topics: Population, Bronze Age, Chalcolithic, Ancient DNA, Steppe
Papers
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TL;DR: Genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans is presented, finding limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and excludes migration as an important mechanism of spread between these two regions.
Abstract: 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.
479 citations
Harvard University1, Max Planck Society2, University of Tübingen3, Hungarian Academy of Sciences4, Howard Hughes Medical Institute5, University College Dublin6, University of Vienna7, University of Coimbra8, University of Ferrara9, University of Adelaide10, Trinity College, Dublin11, University of Cambridge12, Broad Institute13, Emory University14, University of Florence15, Bulgarian Academy of Sciences16, Danube Private University17, Romanian Academy18, Centre national de la recherche scientifique19, Eötvös Loránd University20, Sofia University21, University of Oxford22, University of Wyoming23, University of Zagreb24, Pennsylvania State University25, National Academy of Sciences of Ukraine26, Université de Montréal27, University of Bucharest28, Ludwig Maximilian University of Munich29, University of Edinburgh30, University of Wisconsin-Madison31, University of Palermo32, Croatian Academy of Sciences and Arts33, Naturhistorisches Museum34, Russian Academy of Sciences35, University of Toronto36, University of Latvia37, Durham University38, University of Hull39, Grand Valley State University40, Columbia University41
TL;DR: It is shown 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.
Abstract: 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 und ...
447 citations
Harvard University1, Hungarian Academy of Sciences2, Broad Institute3, University of Mainz4, Howard Hughes Medical Institute5, University of Adelaide6, Eötvös Loránd University7, Hungarian National Museum8, University of Pécs9, University of the Basque Country10, Free University of Berlin11, Deutsches Archäologisches Institut12, University of Basel13, Danube Private University14, Spanish National Research Council15, Max Planck Society16
TL;DR: Investigating the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples finds 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.
Abstract: In European Neolithic populations, the arrival of farmers prompted admixture with local hunter-gatherers over many centuries, resulting in distinct signatures in each region due to a complex series of interactions. David Reich and colleagues analyse genome-wide data from 180 individuals from the Neolithic and Chalcolithic periods of Hungary, Germany and Spain to study the population dynamics of Neolithization in European prehistory. They examine how gene flow reshaped European populations during the Neolithic period, including pervasive admixture—the interbreeding between previously isolated populations—between groups with different ancestry profiles. In each region, they find that the arrival of farmers prompted admixture with local hunter-gatherers, over the course of 3,000 years. Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants1,2,3,4,5,6,7,8 who received a limited amount of admixture from resident hunter-gatherers3,4,5,9. 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.
278 citations
Harvard University1, Emory University2, Radcliffe Institute for Advanced Study3, Max Planck Society4, University College Dublin5, University of Cape Town6, Broad Institute7, University of Tübingen8, Howard Hughes Medical Institute9, California State Polytechnic University, Pomona10, University of Queensland11, University of Wisconsin–La Crosse12, University College London13, Canterbury Archaeological Trust14, University of Bristol15, McDonald Institute for Archaeological Research16, University of Pretoria17, Leiden University18, University of Sydney19, Garvan Institute of Medical Research20, Pennsylvania State University21, University of Vienna22
TL;DR: 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.
272 citations
Max Planck Society1, University of Tübingen2, Harvard University3, Massachusetts Institute of Technology4, Francis Crick Institute5, Howard Hughes Medical Institute6, Broad Institute7, University of Pavia8, University of Adelaide9, Pennsylvania State University10, University of São Paulo11, University of California, Santa Cruz12, Xiamen University13, Catholic University of the North14, Ohio State University15, Pontifical Catholic University of Peru16, Michigan State University17, University of Exeter18, University of New Mexico19, University of the Basque Country20, Federal University of Rio de Janeiro21, Universidade Federal do Rio Grande do Sul22, National University of Central Buenos Aires23, Field Museum of Natural History24, University of Magallanes25, Federal University of São Paulo26, University of Buenos Aires27, National Scientific and Technical Research Council28, Naturhistorisches Museum29, Deutsches Archäologisches Institut30
TL;DR: Genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone suggests a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.
222 citations
Cited by
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Daniel Taliun1, Daniel N. Harris2, Michael D. Kessler2, Jedidiah Carlson1 +202 more•Institutions (61)
TL;DR: The Trans-Omics for Precision Medicine (TOPMed) project as discussed by the authors aims to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases.
Abstract: The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1 In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals) These rare variants provide insights into mutational processes and recent human evolutionary history The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 001% The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history
801 citations
Daniel Taliun1, Daniel N. Harris2, Michael D. Kessler2, Jedidiah Carlson1 +191 more•Institutions (61)
TL;DR: The nearly complete catalog of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and non-coding sequence variants to phenotypic variation as well as resources and early insights from the sequence data.
Abstract: Summary paragraph The Trans-Omics for Precision Medicine (TOPMed) program seeks to elucidate the genetic architecture and disease biology of heart, lung, blood, and sleep disorders, with the ultimate goal of improving diagnosis, treatment, and prevention. The initial phases of the program focus on whole genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here, we describe TOPMed goals and design as well as resources and early insights from the sequence data. The resources include a variant browser, a genotype imputation panel, and sharing of genomic and phenotypic data via dbGaP. In 53,581 TOPMed samples, >400 million single-nucleotide and insertion/deletion variants were detected by alignment with the reference genome. Additional novel variants are detectable through assembly of unmapped reads and customized analysis in highly variable loci. Among the >400 million variants detected, 97% have frequency
662 citations
TL;DR: Genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans is presented, finding limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and excludes migration as an important mechanism of spread between these two regions.
Abstract: 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.
479 citations
Harvard University1, University of Tübingen2, Max Planck Society3, Hungarian Academy of Sciences4, Howard Hughes Medical Institute5, University College Dublin6, University of Vienna7, University of Coimbra8, University of Ferrara9, University of Adelaide10, University of Cambridge11, Trinity College, Dublin12, Broad Institute13, Emory University14, University of Florence15, Bulgarian Academy of Sciences16, Danube Private University17, Romanian Academy18, Centre national de la recherche scientifique19, Eötvös Loránd University20, Sofia University21, University of Oxford22, University of Wyoming23, University of Zagreb24, Pennsylvania State University25, National Academy of Sciences of Ukraine26, Université de Montréal27, University of Bucharest28, Ludwig Maximilian University of Munich29, University of Edinburgh30, University of Wisconsin-Madison31, University of Palermo32, Croatian Academy of Sciences and Arts33, Naturhistorisches Museum34, Russian Academy of Sciences35, University of Toronto36, University of Latvia37, Durham University38, University of Hull39, Grand Valley State University40, Columbia University41
TL;DR: It is shown 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.
Abstract: 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 und ...
447 citations
Broad Institute1, Harvard University2, University of Tübingen3, Max Planck Society4, University of Mainz5, University of Washington6, University of California, Berkeley7, Massachusetts Institute of Technology8, Stockholm University9, University of Adelaide10, The Heritage Foundation11, National Museum of Natural History12, Sultan Qaboos University13, University of Edinburgh14, University of Costa Rica15, University of Antioquia16, Rambam Health Care Campus17, University of Pécs18, Al Akhawayn University19, Catholic University of the Sacred Heart20, University of Oxford21, Belgorod State University22, University of Toronto23, University of Buenos Aires24, University of Bern25, Russian Academy of Sciences26, Paul Sabatier University27, North-Eastern Federal University28, University of Chicago29, University of Arizona30, Stony Brook University31, University of Bergen32, Illumina33, Sofia Medical University34, Bashkir State University35, University of Cambridge36, Vilnius University37, Estonian Biocentre38, University of Strasbourg39, University College London40, Amgen41, Gladstone Institutes42, University of Tartu43, University of Oulu44, Muhimbili University of Health and Allied Sciences45, University of Palermo46, University of Tarapacá47, University of Chile48, Academy of Sciences of Uzbekistan49, Armenian National Academy of Sciences50, University of North Texas51, University of Santiago de Compostela52, University of Kharkiv53, Higher University of San Andrés54, Novosibirsk State University55, Leidos56, Lebanese American University57, University of Split58, University of Pennsylvania59, Banaras Hindu University60, Centre for Cellular and Molecular Biology61, Estonian Academy of Sciences62, Pompeu Fabra University63, Howard Hughes Medical Institute64
TL;DR: The authors showed that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunters-gatherer related ancestry.
Abstract: We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
442 citations