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A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years

Hang Zhou, Sile Hu, Rostislav Matveev, Qianhui Yu, Jing Li, Philipp Khaitovich, Li Jin, Michael Lachmann, Mark Stoneking, Qiaomei Fu, Kun Tang
doi: https://doi.org/10.1101/018929
Hang Zhou
1Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China
2University of Chinese Academy of Sceiences, Beijing 100049, China
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Sile Hu
1Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China
2University of Chinese Academy of Sceiences, Beijing 100049, China
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Rostislav Matveev
3Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
4Max Planck Institute for Mathematics in the Sciences, D-04103 Leipzig, Germany
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Qianhui Yu
1Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China
2University of Chinese Academy of Sceiences, Beijing 100049, China
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Jing Li
1Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China
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Philipp Khaitovich
1Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China
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Li Jin
1Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China
5MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200433, China
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Michael Lachmann
3Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
6Santa Fe Institute, Santa Fe, New Mexico 87501, USA
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Mark Stoneking
3Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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Qiaomei Fu
7Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
8Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
9Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
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Kun Tang
1Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China
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Abstract

The spatiotemporal distribution of recent human adaptation is a long standing question. We developed a new coalescent-based method that collectively assigned human genome regions to modes of neutrality or to positive, negative, or balancing selection. Most importantly, the selection times were estimated for all positive selection signals, which ranged over the last half million years, penetrating the emergence of anatomically modern human (AMH). These selection time estimates were further supported by analyses of the genome sequences from three ancient AMHs and the Neanderthals. A series of brain function-related genes were found to carry signals of ancient selective sweeps, which may have defined the evolution of cognitive abilities either before Neanderthal divergence or during the emergence of AMH. Particularly, signals of brain evolution in AMH are strongly related to Alzheimer’s disease pathways. In conclusion, this study reports a chronological atlas of natural selection in Human.

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Posted May 26, 2015.
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A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years
Hang Zhou, Sile Hu, Rostislav Matveev, Qianhui Yu, Jing Li, Philipp Khaitovich, Li Jin, Michael Lachmann, Mark Stoneking, Qiaomei Fu, Kun Tang
bioRxiv 018929; doi: https://doi.org/10.1101/018929
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A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years
Hang Zhou, Sile Hu, Rostislav Matveev, Qianhui Yu, Jing Li, Philipp Khaitovich, Li Jin, Michael Lachmann, Mark Stoneking, Qiaomei Fu, Kun Tang
bioRxiv 018929; doi: https://doi.org/10.1101/018929

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