Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

L. Pagani | K. Harvati | J. Krause | G. Clark | C. Wissing | J. van der Plicht | K. Wehrberger | N. Conard | C. Posth | R. Schmitz | S. Talamo | A. Khokhlov | W. Haak | S. Benazzi | H. Bocherens | C. Scheib | M. Lari | D. Caramelli | Kathrin Nägele | Rita Radzevičiūtė | Harald Ringbauer | V. Moiseyev | K. Mannermaa | F. Valentin | E. Bortolini | R. Jankauskas | T. Terberger | M. G. González Morales | L. Straus | C. Thevenet | D. Grigorescu | H. Rougier | I. Crevecoeur | P. Semal | Christophe Cupillard | D. Drucker | J. Svoboda | A. Gómez‐Olivencia | G. Merceron | A. Zazzo | A. Rohrlach | M. Julien | S. Vai | B. López | A. Stoessel | M. Rué | B. Maureille | Pierre Bodu | S. Villotte | Laurent Klaric | A. Buzhilova | R. Schulting | F. Boschin | A. B. Marín‐Arroyo | L. Sìneo | G. Catalano | Olivier Bignon-Lau | He Yu | C. Polet | V. Sparacello | P. Bayle | Gregorio Oxilia | M. Romandini | Friedrich Lüth | Yilei Huang | Sandra Sázelová | Henny Piezonka | E. Starnini | R. Tukhbatova | A. Chizhevsky | S. Madelaine | Vanessa Villalba-Mouco | Isaac Rufí | J. Soler | H. Fewlass | Justina Kozakaitė | S. Shnaider | D. Bobak | M. Połtowicz-Bobak | E. Bocaege | Laure Pecqueur | Richard Cottiaux | S. Feine | Jean-Guillaume Bordes | E. Altena | T. Schüler | Tiago P. Ferraz | G. Garcia | AB Rohrlach | Michel Orliac | Franz Schopper | Borja González-Rabanal | Natalia Berezina | A. Morala | P. Storm | Neus Coromina | Laurent Crépin | L. Amkreutz | Bettina Jungklaus | Mona Le Luyer | A. Suvorov | Silvia Renhart | Dorothea Talaa | Magdalena Gómez-Puche | J. F. de Pablo | J. Kabaciński | S. Ricci | I. Jadin | Jean-Baptiste Caverne | Tina Saupe | Carmen Alonso-Llamazares | Grégory Debout | Nicolas Cauwe | Ayshin Ghalichi | A. Ronchitelli | A. Kotula | C. Hoffmann | Alessandra Modi | H. Piezonka | Bénédicte Souffi | M. A. Esquembre-Bebia | Foni Le Brun-Ricalens | Jean-Michel Leuvrey | Coralie Bay Garcia | T. Filimonova | Javier Fernández-López de Pablo | L. Smits | Hartmut Benthien | C. Wissing | Tiago Ferraz | Priscilla Bayle | Luca Pagani | Helen Fewlass | Belén López | Joaquim Soler | Martina Lari | Svetlana Shnaider | Svetlana V. Shnaider

[1]  C. Lalueza-Fox,et al.  A 23,000-year-old southern Iberian individual links human groups that lived in Western Europe before and after the Last Glacial Maximum , 2023, Nature Ecology & Evolution.

[2]  Thomas J. Booth,et al.  Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain , 2022, Nature Ecology & Evolution.

[3]  Choongwon Jeong,et al.  Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily , 2022, iScience.

[4]  W. Davies,et al.  Mid and Late Upper Palaeolithic in the Adriatic Basin: Chronology, transitions and human adaptations to a changing landscape , 2022, Quaternary Science Reviews.

[5]  Harald Ringbauer,et al.  hapCon: estimating contamination of ancient genomes by copying from reference haplotypes , 2021, bioRxiv.

[6]  L. Pagani,et al.  Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa , 2021, bioRxiv.

[7]  J. Novembre,et al.  Parental relatedness through time revealed by runs of homozygosity in ancient DNA , 2021, Nature Communications.

[8]  A. Hoischen,et al.  Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe , 2021, Current Biology.

[9]  Kay Prüfer,et al.  A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia , 2021, Nature Ecology & Evolution.

[10]  Qiaomei Fu,et al.  Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry , 2021, Nature.

[11]  C. Hillaire‐Marcel,et al.  Temperature and precipitation regime in LGM human refugia of southwestern Europe inferred from δ13C and δ18O of large mammal remains , 2021 .

[12]  Domingo C. Salazar-García,et al.  Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe , 2021, Scientific Reports.

[13]  M. D'Esposito,et al.  Early Alpine occupation backdates westward human migration in Late Glacial Europe , 2020, Current Biology.

[14]  M. Metspalu,et al.  Genetic ancestry changes in Stone to Bronze Age transition in the East European plain , 2020, Science Advances.

[15]  R. Durbin,et al.  Placing Ancient DNA Sequences into Reference Phylogenies , 2020, bioRxiv.

[16]  T. Terberger,et al.  THE MESOLITHIC CEMETERY OF GROß FREDENWALDE (NORTH-EASTERN GERMANY) AND ITS CULTURAL AFFILIATIONS , 2020 .

[17]  S. Vasilyev,et al.  Gravettian cranial morphology and human group affinities during the European Upper Palaeolithic , 2020, Scientific Reports.

[18]  C. Posth,et al.  Hunter-gatherers across the great Adriatic-Po region during the Last Glacial Maximum: Environmental and cultural dynamics , 2020 .

[19]  M. Meyer,et al.  Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA , 2020, Nature Protocols.

[20]  C. Posth,et al.  Latest trends in archaeogenetic research of west Eurasians. , 2020, Current opinion in genetics & development.

[21]  E. Jones,et al.  A dynastic elite in monumental Neolithic society , 2020, Nature.

[22]  M. Pruvost,et al.  Ancient genomes from present-day France unveil 7,000 years of its demographic history , 2020, Proceedings of the National Academy of Sciences.

[23]  Choongwon Jeong,et al.  Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers , 2020, Science Advances.

[24]  T. Terberger,et al.  The emergence of hunter-gatherer pottery in the Urals and West Siberia: New dating and stable isotope evidence , 2020 .

[25]  D. Reich,et al.  ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium , 2020, bioRxiv.

[26]  M. Meyer,et al.  Emergence of human-adapted Salmonella enterica is linked to the Neolithization process , 2020, Nature Ecology & Evolution.

[27]  S. Rasmussen,et al.  A 5700 year-old human genome and oral microbiome from chewed birch pitch , 2019, Nature Communications.

[28]  Margaret L. Antonio,et al.  Ancient Rome: A genetic crossroads of Europe and the Mediterranean , 2019, Science.

[29]  Michael D. Frachetti,et al.  The formation of human populations in South and Central Asia , 2019, Science.

[30]  D. Reich,et al.  Late Upper Palaeolithic hunter-gatherers in the Central Mediterranean: new archaeological and genetic data from the Late Epigravettian burial Oriente C (Favignana, Sicily) , 2019, bioRxiv.

[31]  A. Burke,et al.  Habitat suitability and the genetic structure of human populations during the Last Glacial Maximum (LGM) in Western Europe , 2019, PloS one.

[32]  Thomas J. Booth,et al.  Ancient genomes indicate population replacement in Early Neolithic Britain , 2019, Nature Ecology & Evolution.

[33]  Domingo C. Salazar-García,et al.  Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula , 2019, Current Biology.

[34]  Domingo C. Salazar-García,et al.  The genomic history of the Iberian Peninsula over the past 8000 years , 2019 .

[35]  S. Pääbo,et al.  Limits of long-term selection against Neandertal introgression , 2019, Proceedings of the National Academy of Sciences.

[36]  R. Durbin,et al.  The population history of northeastern Siberia since the Pleistocene , 2018 .

[37]  M. Meyer,et al.  Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing , 2018, Nature Protocols.

[38]  Choongwon Jeong,et al.  Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia , 2018, bioRxiv.

[39]  Sudhir Kumar,et al.  MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.

[40]  R. Durbin,et al.  The first horse herders and the impact of early Bronze Age steppe expansions into Asia , 2018, Science.

[41]  B. Nickel,et al.  Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations , 2018, Science.

[42]  Chuan-Chao Wang,et al.  The genetic prehistory of the Baltic Sea region , 2018, Nature Communications.

[43]  Mattias Jakobsson,et al.  Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation , 2018, PLoS biology.

[44]  Ivor Karavanić,et al.  The Genomic History of Southeastern Europe , 2017, Nature.

[45]  L. Excoffier,et al.  Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers , 2017, Science.

[46]  M. Slatkin,et al.  40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia , 2017, Current Biology.

[47]  Andrea Manica,et al.  Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin , 2017, Current Biology.

[48]  A. Zimmermann,et al.  Populations headed south? The Gravettian from a palaeodemographic point of view , 2017, Antiquity.

[49]  Swapan Mallick,et al.  Parallel paleogenomic transects reveal complex genetic history of early European farmers , 2017, Nature.

[50]  L. Pagani,et al.  Extensive Farming in Estonia Started through a Sex-Biased Migration from the Steppe , 2017, Current Biology.

[51]  A. Manica,et al.  The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers , 2017, Current Biology.

[52]  F. Djindjian Territories and economies of hunter–gatherer groups during the last glacial maximum in Europe , 2016 .

[53]  Swapan Mallick,et al.  Genomic insights into the origin of farming in the ancient Near East , 2016, Nature.

[54]  D. Reich,et al.  The genetic history of Ice Age Europe , 2016, Nature.

[55]  Hans-Jürgen Bandelt,et al.  HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing , 2016, Nucleic Acids Res..

[56]  J. Krause,et al.  EAGER: efficient ancient genome reconstruction , 2016, Genome Biology.

[57]  G. Renaud,et al.  Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe , 2016, Current Biology.

[58]  L. Orlando,et al.  AdapterRemoval v2: rapid adapter trimming, identification, and read merging , 2016, BMC Research Notes.

[59]  R. Nielsen,et al.  The Genetic Cost of Neanderthal Introgression , 2015, Genetics.

[60]  L. Straus The Human Occupation of Southwestern Europe during the Last Glacial Maximum , 2015, Journal of Anthropological Research.

[61]  D. Reich,et al.  Genome-wide patterns of selection in 230 ancient Eurasians , 2015, Nature.

[62]  Anders Eriksson,et al.  Upper Palaeolithic genomes reveal deep roots of modern Eurasians , 2015, Nature Communications.

[63]  G. Renaud,et al.  Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA , 2015, Genome Biology.

[64]  M. Meyer,et al.  Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. , 2015, BioTechniques.

[65]  Swapan Mallick,et al.  An early modern human from Romania with a recent Neanderthal ancestor , 2015, Nature.

[66]  Michael C. Westaway,et al.  A recent bottleneck of Y chromosome diversity coincides with a global change in culture , 2015, Genome research.

[67]  J. Kozłowski The origin of the Gravettian , 2015 .

[68]  Swapan Mallick,et al.  Partial uracil–DNA–glycosylase treatment for screening of ancient DNA , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

[69]  Michael C. Westaway,et al.  Genomic structure in Europeans dating back at least 36,200 years , 2014, Science.

[70]  Anders Albrechtsen,et al.  ANGSD: Analysis of Next Generation Sequencing Data , 2014, BMC Bioinformatics.

[71]  Heng Li,et al.  Genome sequence of a 45,000-year-old modern human from western Siberia , 2014, Nature.

[72]  Mattias Jakobsson,et al.  Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers , 2014, Science.

[73]  M. Jakobsson,et al.  Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal , 2014, Proceedings of the National Academy of Sciences.

[74]  Bonnie Berger,et al.  Ancient human genomes suggest three ancestral populations for present-day Europeans , 2013, Nature.

[75]  R. Mägi,et al.  Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans , 2013, Nature.

[76]  Cristina E. Valdiosera,et al.  Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments , 2013, Proceedings of the National Academy of Sciences.

[77]  Philip L. F. Johnson,et al.  mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters , 2013, Bioinform..

[78]  T. Higham,et al.  Freshwater Radiocarbon Reservoir Effects at the Burial Ground of Minino, Northwest Russia , 2013, Radiocarbon.

[79]  Qiaomei Fu,et al.  DNA analysis of an early modern human from Tianyuan Cave, China , 2013, Proceedings of the National Academy of Sciences.

[80]  Swapan Mallick,et al.  Ancient Admixture in Human History , 2012, Genetics.

[81]  Adrian W. Briggs,et al.  A High-Coverage Genome Sequence from an Archaic Denisovan Individual , 2012, Science.

[82]  Marcel Otte,et al.  Appearance, expansion and dilution of the Magdalenian civilization , 2012 .

[83]  T. Terberger,et al.  New information from Maszycka Cave and the Late Glacial recolonisation of Central Europe , 2012 .

[84]  Martin Kircher,et al.  Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform , 2011, Nucleic acids research.

[85]  Matthias Meyer,et al.  Illumina sequencing library preparation for highly multiplexed target capture and sequencing. , 2010, Cold Spring Harbor protocols.

[86]  Philip L. F. Johnson,et al.  A Draft Sequence of the Neandertal Genome , 2010, Science.

[87]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[88]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[89]  Michael Hofreiter,et al.  Ancient DNA extraction from bones and teeth , 2007, Nature Protocols.

[90]  T. Schmitt Molecular biogeography of Europe: Pleistocene cycles and postglacial trends , 2007, Frontiers in Zoology.

[91]  D. Reich,et al.  Population Structure and Eigenanalysis , 2006, PLoS genetics.

[92]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[93]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..