Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution
Kevin E. Langergraber,Kay Prüfer,Carolyn Rowney,Christophe Boesch,Catherine Crockford,Katie A. Fawcett,Eiji Inoue,Miho Inoue-Muruyama,John C. Mitani,Martin N. Muller,Martha M. Robbins,Grit Schubert,Tara S. Stoinski,Bence Viola,David P. Watts,Roman M. Wittig,Richard W. Wrangham,Klaus Zuberbühler,Svante Pääbo,Linda Vigilant +19 more
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TLDR
The human–chimpanzee split is dated to at least 7–8 million years and the population split between Neanderthals and modern humans to 400,000–800,000 y ago, which suggests that molecular divergence dates may not be in conflict with the attribution of 6- to 7-million-y-old fossils to the human lineage and 400,,000-Y-old bones to the Neanderthal lineage.Abstract:
Fossils and molecular data are two independent sources of information that should in principle provide consistent inferences of when evolutionary lineages diverged. Here we use an alternative approach to genetic inference of species split times in recent human and ape evolution that is independent of the fossil record. We first use genetic parentage information on a large number of wild chimpanzees and mountain gorillas to directly infer their average generation times. We then compare these generation time estimates with those of humans and apply recent estimates of the human mutation rate per generation to derive estimates of split times of great apes and humans that are independent of fossil calibration. We date the human–chimpanzee split to at least 7–8 million years and the population split between Neanderthals and modern humans to 400,000–800,000 y ago. This suggests that molecular divergence dates may not be in conflict with the attribution of 6- to 7-million-y-old fossils to the human lineage and 400,000-y-old fossils to the Neanderthal lineage.read more
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The complete genome sequence of a Neanderthal from the Altai Mountains
Kay Prüfer,Fernando Racimo,Nick Patterson,Flora Jay,Sriram Sankararaman,Susanna Sawyer,Anja Heinze,Gabriel Renaud,Peter H. Sudmant,Cesare de Filippo,Heng Li,Swapan Mallick,Michael Dannemann,Qiaomei Fu,Martin Kircher,Martin Kuhlwilm,Michael Lachmann,Matthias Meyer,Matthias Ongyerth,Michael Siebauer,Christoph Theunert,Arti Tandon,Priya Moorjani,Joseph K. Pickrell,James C. Mullikin,Samuel H. Vohr,Richard E. Green,Ines Hellmann,Philip L. F. Johnson,Hélène Blanché,Howard M. Cann,Jacob O. Kitzman,Jay Shendure,Evan E. Eichler,Ed S. Lein,Trygve E. Bakken,Liubov V. Golovanova,Vladimir B. Doronichev,Michael V. Shunkov,A.P. Derevianko,Bence Viola,Montgomery Slatkin,David Reich,Janet Kelso,Svante Pääbo +44 more
TL;DR: It is shown that interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene and a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans is established.
Journal ArticleDOI
Genome sequence of a 45,000-year-old modern human from western Siberia
Qiaomei Fu,Heng Li,Priya Moorjani,Flora Jay,Sergey Mikhailovich Slepchenko,Aleksei A. Bondarev,Philip L. F. Johnson,Ayinuer Aximu-Petri,Kay Prüfer,Cesare de Filippo,Matthias Meyer,Nicolas Zwyns,Domingo C. Salazar-García,Yaroslav V. Kuzmin,Susan G. Keates,Pavel A. Kosintsev,Dmitry Razhev,Michael P. Richards,Nikolai V. Peristov,Michael Lachmann,Katerina Douka,Thomas Higham,Montgomery Slatkin,Jean-Jacques Hublin,David Reich,Janet Kelso,T. Bence Viola,Svante Pääbo +27 more
TL;DR: The high-quality genome sequence of a ∼45,000-year-old modern human male from Siberia derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians.
Journal ArticleDOI
Robust and scalable inference of population history from hundreds of unphased whole genomes
TL;DR: SMC++ is presented, a new statistical tool capable of analyzing orders of magnitude more samples than existing methods while requiring only unphased genomes and employing a novel spline regularization scheme that greatly reduces estimation error.
Journal ArticleDOI
A high-coverage Neandertal genome from Vindija Cave in Croatia
Kay Prüfer,Cesare de Filippo,Steffi Grote,Fabrizio Mafessoni,Petra Korlević,Mateja Hajdinjak,Benjamin Vernot,Laurits Skov,PingHsun Hsieh,Stéphane Peyrégne,David Reher,Charlotte Hopfe,Sarah Nagel,Tomislav Maricic,Qiaomei Fu,Christoph Theunert,Christoph Theunert,Rebekah L. Rogers,Pontus Skoglund,Manjusha Chintalapati,Michael Dannemann,Bradley J. Nelson,Felix M. Key,Pavao Rudan,Željko Kućan,Ivan Gušić,Liubov V. Golovanova,Vladimir B. Doronichev,Nick Patterson,David Reich,David Reich,David Reich,Evan E. Eichler,Montgomery Slatkin,Mikkel H. Schierup,Aida M. Andrés,Janet Kelso,Matthias Meyer,Svante Pääbo +38 more
TL;DR: The genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, is sequenced to ~30-fold genomic coverage, allowing 10 to 20% more Ne andertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
Journal ArticleDOI
Cospeciation of gut microbiota with hominids
Andrew H. Moeller,Andrew H. Moeller,Alejandro Caro-Quintero,Deus Mjungu,Alexander V. Georgiev,Alexander V. Georgiev,Elizabeth V. Lonsdorf,Martin N. Muller,Anne E. Pusey,Martine Peeters,Beatrice H. Hahn,Howard Ochman +11 more
TL;DR: This study identifies human gut bacteria descended from ancient symbionts that speciated simultaneously with humans and the African apes.
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Initial sequence of the chimpanzee genome and comparison with the human genome
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TL;DR: It is found that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.
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TL;DR: The genome sequence of an Indian-origin Macaca mulatta female is determined and compared with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families.
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