Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup.
Comparative genetic analysis between human and chimpanzee may detect genetic divergences responsible for human-specific characteristics. Previous studies have identified a series of genes that potentially underwent Darwinian positive selection during human evolution. However, without a closely related species as outgroup, it is difficult to identify human-lineage-specific changes, which is critical in delineating the biological uniqueness of humans. In this study, we conducted phylogeny-based analyses of 2633 human brain-expressed genes using rhesus macaque as the outgroup. We identified 47 candidate genes showing strong evidence of positive selection in the human lineage. Genes with maximal expression in the brain showed a higher evolutionary rate in human than in chimpanzee. We observed that many immune-defense-related genes were under strong positive selection, and this trend was more prominent in chimpanzee than in human. We also demonstrated that rhesus macaque performed much better than mouse as an outgroup in identifying lineage-specific selection in humans.
Yu
Xiao-Jing
XJ
Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Primate Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Graduate School, Chinese Academy of Sciences, Beijing, China.
Zheng
Hong-Kun
HK
Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China; The Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark.
Wang
Jun
J
Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China; The Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark; Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark.
Wang
Wen
W
Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
Su
Bing
B
Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Primate Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. Electronic address: sub@mail.kiz.ac.cn.
D000220:Adaptation, Biological; D000818:Animals; D001921:Brain / Q000378:metabolism*; D019143:Evolution, Molecular; D006801:Humans; D008253:Macaca mulatta; D051379:Mice; D008957:Models, Genetic; D009419:Nerve Tissue Proteins / Q000235:genetics* / Q000378:metabolism; D002679:Pan troglodytes; D010802:Phylogeny; D012641:Selection, Genetic; D013045:Species Specificity
D009419:Nerve Tissue Proteins