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Journal ArticleDOI

Early farmers from across Europe directly descended from Neolithic Aegeans

TL;DR: This study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.
Abstract: Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.
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Journal ArticleDOI
25 Aug 2016-Nature
TL;DR: This paper reported 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, showing 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.
Abstract: 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.

695 citations

Journal ArticleDOI
Iñigo Olalde1, Selina Brace2, Morten E. Allentoft3, Ian Armit4  +166 moreInstitutions (69)
08 Mar 2018-Nature
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

Journal ArticleDOI
Iain Mathieson1, Songül Alpaslan-Roodenberg1, Cosimo Posth2, Cosimo Posth3, Anna Szécsényi-Nagy4, Nadin Rohland1, Swapan Mallick1, Swapan Mallick5, Iñigo Olalde1, Nasreen Broomandkhoshbacht1, Nasreen Broomandkhoshbacht5, Francesca Candilio6, Olivia Cheronet7, Olivia Cheronet6, Daniel Fernandes6, Daniel Fernandes8, Matthew Ferry5, Matthew Ferry1, Beatriz Gamarra6, Gloria G. Fortes9, Wolfgang Haak3, Wolfgang Haak10, Eadaoin Harney5, Eadaoin Harney1, Eppie R. Jones11, Eppie R. Jones12, Denise Keating6, Ben Krause-Kyora3, Isil Kucukkalipci2, Megan Michel5, Megan Michel1, Alissa Mittnik3, Alissa Mittnik2, Kathrin Nägele3, Mario Novak6, Jonas Oppenheimer5, Jonas Oppenheimer1, Nick Patterson13, Saskia Pfrengle2, Kendra Sirak14, Kendra Sirak6, Kristin Stewardson1, Kristin Stewardson5, Stefania Vai15, Stefan Alexandrov16, Kurt W. Alt17, Radian Andreescu, Dragana Antonović, Abigail Ash6, Nadezhda Atanassova16, Krum Bacvarov16, Mende Balázs Gusztáv4, Hervé Bocherens2, Michael Bolus2, Adina Boroneanţ18, Yavor Boyadzhiev16, Alicja Budnik, Josip Burmaz, Stefan Chohadzhiev, Nicholas J. Conard2, Richard Cottiaux, Maja Čuka, Christophe Cupillard19, Dorothée G. Drucker2, Nedko Elenski, Michael Francken2, Borislava Galabova, Georgi Ganetsovski, Bernard Gély, Tamás Hajdu20, Veneta Handzhyiska21, Katerina Harvati2, Thomas Higham22, Stanislav Iliev, Ivor Janković23, Ivor Karavanić24, Ivor Karavanić23, Douglas J. Kennett25, Darko Komšo, Alexandra Kozak26, Damian Labuda27, Martina Lari15, Cătălin Lazăr28, Maleen Leppek29, Krassimir Leshtakov21, Domenico Lo Vetro15, Dženi Los, Ivaylo Lozanov21, Maria Malina2, Fabio Martini15, Kath McSweeney30, Harald Meller, Marko Menđušić, Pavel Mirea, Vyacheslav Moiseyev, Vanya Petrova21, T. Douglas Price31, Angela Simalcsik18, Luca Sineo32, Mario Šlaus33, Vladimir Slavchev, Petar Stanev, Andrej Starović, Tamás Szeniczey20, Sahra Talamo3, Maria Teschler-Nicola7, Maria Teschler-Nicola34, Corinne Thevenet, Ivan Valchev21, Frédérique Valentin19, Sergey Vasilyev35, Fanica Veljanovska, Svetlana Venelinova, Elizaveta Veselovskaya35, Bence Viola35, Bence Viola36, Cristian Virag, Joško Zaninović, Steve Zäuner, Philipp W. Stockhammer29, Philipp W. Stockhammer3, Giulio Catalano32, Raiko Krauß2, David Caramelli15, Gunita Zariņa37, Bisserka Gaydarska38, Malcolm Lillie39, Alexey G. Nikitin40, Inna Potekhina26, Anastasia Papathanasiou, Dusan Boric41, Clive Bonsall30, Johannes Krause3, Johannes Krause2, Ron Pinhasi6, Ron Pinhasi7, David Reich13, David Reich1, David Reich5 
08 Mar 2018-Nature
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

Iosif Lazaridis1, Iosif Lazaridis2, Nick Patterson1, Alissa Mittnik3, Gabriel Renaud4, Swapan Mallick1, Swapan Mallick2, Karola Kirsanow5, Peter H. Sudmant6, Joshua G. Schraiber7, Joshua G. Schraiber6, Sergi Castellano4, Mark Lipson8, Bonnie Berger8, Bonnie Berger1, Christos Economou9, Ruth Bollongino5, Qiaomei Fu4, Kirsten I. Bos3, Susanne Nordenfelt2, Susanne Nordenfelt1, Heng Li2, Heng Li1, Cesare de Filippo4, Kay Prüfer4, Susanna Sawyer4, Cosimo Posth3, Wolfgang Haak10, Fredrik Hallgren11, Elin Fornander11, Nadin Rohland1, Nadin Rohland2, Dominique Delsate12, Michael Francken3, Jean-Michel Guinet12, Joachim Wahl, George Ayodo, Hamza A. Babiker13, Hamza A. Babiker14, Graciela Bailliet, Elena Balanovska, Oleg Balanovsky, Ramiro Barrantes15, Gabriel Bedoya16, Haim Ben-Ami17, Judit Bene18, Fouad Berrada19, Claudio M. Bravi, Francesca Brisighelli20, George B.J. Busby21, Francesco Calì, Mikhail Churnosov22, David E. C. Cole23, Daniel Corach24, Larissa Damba, George van Driem25, Stanislav Dryomov26, Jean-Michel Dugoujon27, Sardana A. Fedorova28, Irene Gallego Romero29, Marina Gubina, Michael F. Hammer30, Brenna M. Henn31, Tor Hervig32, Ugur Hodoglugil33, Aashish R. Jha29, Sena Karachanak-Yankova34, Rita Khusainova35, Elza Khusnutdinova35, Rick A. Kittles30, Toomas Kivisild36, William Klitz7, Vaidutis Kučinskas37, Alena Kushniarevich38, Leila Laredj39, Sergey Litvinov38, Theologos Loukidis40, Theologos Loukidis41, Robert W. Mahley42, Béla Melegh18, Ene Metspalu43, Julio Molina, Joanna L. Mountain, Klemetti Näkkäläjärvi44, Desislava Nesheva34, Thomas B. Nyambo45, Ludmila P. Osipova, Jüri Parik43, Fedor Platonov28, Olga L. Posukh, Valentino Romano46, Francisco Rothhammer47, Francisco Rothhammer48, Igor Rudan13, Ruslan Ruizbakiev49, Hovhannes Sahakyan50, Hovhannes Sahakyan38, Antti Sajantila51, Antonio Salas52, Elena B. Starikovskaya26, Ayele Tarekegn, Draga Toncheva34, Shahlo Turdikulova49, Ingrida Uktveryte37, Olga Utevska53, René Vasquez54, Mercedes Villena54, Mikhail Voevoda55, Cheryl A. Winkler56, Levon Yepiskoposyan50, Pierre Zalloua2, Pierre Zalloua57, Tatijana Zemunik58, Alan Cooper10, Cristian Capelli21, Mark G. Thomas41, Andres Ruiz-Linares41, Sarah A. Tishkoff59, Lalji Singh60, Kumarasamy Thangaraj61, Richard Villems62, Richard Villems43, Richard Villems38, David Comas63, Rem I. Sukernik26, Mait Metspalu38, Matthias Meyer4, Evan E. Eichler6, Joachim Burger5, Montgomery Slatkin7, Svante Pääbo4, Janet Kelso4, David Reich2, David Reich64, David Reich1, Johannes Krause4, Johannes Krause3 
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, University of Edinburgh13, Sultan Qaboos University14, 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, Amgen40, University College London41, 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
01 Sep 2014
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

Journal ArticleDOI
Iñigo Olalde1, Swapan Mallick1, Swapan Mallick2, Swapan Mallick3, Nick Patterson2, Nadin Rohland1, Vanessa Villalba-Mouco4, Vanessa Villalba-Mouco5, Marina Silva6, Katharina Dulias6, Ceiridwen J. Edwards6, Francesca Gandini6, Maria Pala6, Pedro Soares7, Manuel Ferrando-Bernal8, Nicole Adamski3, Nicole Adamski1, Nasreen Broomandkhoshbacht3, Nasreen Broomandkhoshbacht1, Olivia Cheronet9, Brendan J. Culleton10, Daniel Fernandes11, Daniel Fernandes9, Ann Marie Lawson1, Ann Marie Lawson3, Matthew Mah3, Matthew Mah2, Matthew Mah1, Jonas Oppenheimer1, Jonas Oppenheimer3, Kristin Stewardson1, Kristin Stewardson3, Zhao Zhang1, Juan Manuel Jiménez Arenas12, Juan Manuel Jiménez Arenas13, Isidro Jorge Toro Moyano, Domingo C. Salazar-García14, Pere Castanyer, Marta Santos, Joaquim Tremoleda, Marina Lozano15, Pablo García Borja16, Javier Fernández-Eraso14, José Antonio Mujika-Alustiza14, Cecilio Barroso, Francisco J. Bermúdez, Enrique Viguera Mínguez17, Josep Burch, Neus Coromina, David Vivó, Artur Cebrià18, Josep Maria Fullola18, Oreto García-Puchol19, Juan Ignacio Morales18, F. Xavier Oms18, Tona Majó20, Josep Maria Vergès15, Antonia Díaz-Carvajal18, Imma Ollich-Castanyer18, F. Javier López-Cachero18, Ana Maria Silva11, Ana Maria Silva21, Carmen Alonso-Fernández, Germán Delibes de Castro22, Javier Jiménez Echevarría, Adolfo Moreno-Márquez23, Adolfo Moreno-Márquez24, Guillermo Pascual Berlanga13, Pablo Ramos-García13, José Ramos-Muñoz23, Eduardo Vijande Vila23, Gustau Aguilella Arzo, Ángel Esparza Arroyo25, Katina T. Lillios26, Jennifer E. Mack26, Javier Velasco-Vázquez27, Anna J. Waterman28, Luis Benítez de Lugo Enrich16, Luis Benítez de Lugo Enrich29, María Benito Sánchez30, Bibiana Agustí, Ferran Codina, Gabriel de Prado, Almudena Estalrrich31, Álvaro Fernández Flores, Clive Finlayson, Geraldine Finlayson32, Geraldine Finlayson33, Stewart Finlayson33, Stewart Finlayson34, Francisco Giles-Guzmán33, Antonio Rosas35, Virginia Barciela González22, Gabriel García Atiénzar22, Mauro S. Hernández Pérez22, Armando Llanos, Yolanda Carrión Marco19, Isabel Collado Beneyto, David López-Serrano, Mario Sanz Tormo36, António Carlos Valera, Concepción Blasco29, Corina Liesau29, Patricia Ríos29, Joan Daura18, María Jesús de Pedro Michó, Agustín Diez Castillo19, Raúl Flores Fernández37, Raúl Flores Fernández38, Joan Francès Farré, Rafael Garrido-Pena29, Victor S. Gonçalves21, Elisa Guerra-Doce22, Ana Mercedes Herrero-Corral30, Joaquim Juan-Cabanilles, Daniel López-Reyes, Sarah B. McClure36, Marta Pérez18, Arturo Oliver Foix, Montserrat Sanz Borràs18, Ana Catarina Sousa21, Julio Manuel Vidal Encinas, Douglas J. Kennett10, Douglas J. Kennett36, Martin B. Richards6, Kurt W. Alt38, Kurt W. Alt37, Wolfgang Haak4, Wolfgang Haak39, Ron Pinhasi9, Carles Lalueza-Fox8, David Reich2, David Reich1, David Reich3 
15 Mar 2019-Science
TL;DR: It is revealed that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia, and how the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean is document.
Abstract: J.M.F., F.J.L.-C., J.I.M., F.X.O., J.D., and M.S.B. were supported by HAR2017-86509-P, HAR2017-87695-P, and SGR2017-11 from the Generalitat de Catalunya, AGAUR agency. C.L.-F. was supported by Obra Social La Caixa and by FEDER-MINECO (BFU2015- 64699-P). L.B.d.L.E. was supported by REDISCO-HAR2017-88035-P (Plan Nacional I+D+I, MINECO). C.L., P.R., and C.Bl. were supported by MINECO (HAR2016-77600-P). A.Esp., J.V.-V., G.D., and D.C.S.-G. were supported by MINECO (HAR2009-10105 and HAR2013-43851-P). D.J.K. and B.J.C. were supported by NSF BCS-1460367. K.T.L., A.W., and J.M. were supported by NSF BCS-1153568. J.F.-E. and J.A.M.-A. were supported by IT622-13 Gobierno Vasco, Diputacion Foral de Alava, and Diputacion Foral de Gipuzkoa. We acknowledge support from the Portuguese Foundation for Science and Technology (PTDC/EPH-ARQ/4164/2014) and the FEDER-COMPETE 2020 project 016899. P.S. was supported by the FCT Investigator Program (IF/01641/2013), FCT IP, and ERDF (COMPETE2020 – POCI). M.Si. and K.D. were supported by a Leverhulme Trust Doctoral Scholarship awarded to M.B.R. and M.P. D.R. was supported by an Allen Discovery Center grant from the Paul Allen Foundation, NIH grant GM100233, and the Howard Hughes Medical Institute. V.V.-M. and W.H. were supported by the Max Planck Society.

287 citations

References
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Journal ArticleDOI
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Abstract: Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: [email protected]

45,957 citations

Journal ArticleDOI
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Abstract: Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ~10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: [email protected]

43,862 citations


"Early farmers from across Europe di..." refers methods in this paper

  • ...All sequences were aligned against the human reference build GRCh37/hg19 using BWA (35) and realigned using the Genome Analysis Toolkit (36) (SI Appendix, SI3....

    [...]

Journal ArticleDOI
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
Abstract: Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes nearly five terabases—make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.

20,557 citations


"Early farmers from across Europe di..." refers methods in this paper

  • ...Following GATK [116], we calculate the Phred-scaled quality of the call as the likelihood difference ∆LL between the ML and the second most likely genotype....

    [...]

  • ...Here we adopt a similar strategy as implemented in the Base Quality Score Recalibration (BQSR) tool available in GATK [116], but extend it to ancient DNA by incorporating post-mortem damage....

    [...]

Journal ArticleDOI
TL;DR: A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests.
Abstract: The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.

13,111 citations


"Early farmers from across Europe di..." refers methods in this paper

  • ...We employ the classic substitution model by Felsenstein [118], which expresses the probability of each genotype gi as a function of π and the substitution rate θ = 2Tμ along the genealogy connecting the two alleles of an individual, where T corresponds to the time to the most recent common ancestor of the two lineages and μ the mutation rate....

    [...]

Journal ArticleDOI
Adam Auton1, Gonçalo R. Abecasis2, David Altshuler3, Richard Durbin4  +514 moreInstitutions (90)
01 Oct 2015-Nature
TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

12,661 citations

Related Papers (5)
18 Sep 2014-Nature
Iosif Lazaridis, Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Swapan Mallick, Karola Kirsanow, Peter H. Sudmant, Joshua G. Schraiber, Joshua G. Schraiber, Sergi Castellano, Mark Lipson, Bonnie Berger, Bonnie Berger, Christos Economou, Ruth Bollongino, Qiaomei Fu, Kirsten I. Bos, Susanne Nordenfelt, Susanne Nordenfelt, Heng Li, Heng Li, Cesare de Filippo, Kay Prüfer, Susanna Sawyer, Cosimo Posth, Wolfgang Haak, Fredrik Hallgren, Elin Fornander, Nadin Rohland, Nadin Rohland, Dominique Delsate, Michael Francken, Jean-Michel Guinet, Joachim Wahl, George Ayodo, Hamza A. Babiker, Hamza A. Babiker, Graciela Bailliet, Elena Balanovska, Oleg Balanovsky, Ramiro Barrantes, Gabriel Bedoya, Haim Ben-Ami, Judit Bene, Fouad Berrada, Claudio M. Bravi, Francesca Brisighelli, George B.J. Busby, Francesco Calì, Mikhail Churnosov, David E. C. Cole, Daniel Corach, Larissa Damba, George van Driem, Stanislav Dryomov, Jean-Michel Dugoujon, Sardana A. Fedorova, Irene Gallego Romero, Marina Gubina, Michael F. Hammer, Brenna M. Henn, Tor Hervig, Ugur Hodoglugil, Aashish R. Jha, Sena Karachanak-Yankova, Rita Khusainova, Elza Khusnutdinova, Rick A. Kittles, Toomas Kivisild, William Klitz, Vaidutis Kučinskas, Alena Kushniarevich, Leila Laredj, Sergey Litvinov, Theologos Loukidis, Theologos Loukidis, Robert W. Mahley, Béla Melegh, Ene Metspalu, Julio Molina, Joanna L. Mountain, Klemetti Näkkäläjärvi, Desislava Nesheva, Thomas B. Nyambo, Ludmila P. Osipova, Jüri Parik, Fedor Platonov, Olga L. Posukh, Valentino Romano, Francisco Rothhammer, Francisco Rothhammer, Igor Rudan, Ruslan Ruizbakiev, Hovhannes Sahakyan, Hovhannes Sahakyan, Antti Sajantila, Antonio Salas, Elena B. Starikovskaya, Ayele Tarekegn, Draga Toncheva, Shahlo Turdikulova, Ingrida Uktveryte, Olga Utevska, René Vasquez, Mercedes Villena, Mikhail Voevoda, Cheryl A. Winkler, Levon Yepiskoposyan, Pierre Zalloua, Pierre Zalloua, Tatijana Zemunik, Alan Cooper, Cristian Capelli, Mark G. Thomas, Andres Ruiz-Linares, Sarah A. Tishkoff, Lalji Singh, Kumarasamy Thangaraj, Richard Villems, Richard Villems, Richard Villems, David Comas, Rem I. Sukernik, Mait Metspalu, Matthias Meyer, Evan E. Eichler, Joachim Burger, Montgomery Slatkin, Svante Pääbo, Janet Kelso, David Reich, David Reich, David Reich, Johannes Krause, Johannes Krause