Recent Adaptive Events in Human Brain Revealed by Meta-Analysis of Positively Selected Genes

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Huang, Yue ^a   Xie, Chen ^a   Ye, Adam Y ^a   Li, Chuan Yun ^a   Gao, Ge ^a   Wei, Liping ^a  

^a PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BRAIN REGION; COGNITION; CONTROLLED STUDY; DNA BASE COMPOSITION; EVOLUTIONARY ADAPTATION; GENE DENSITY; GENE EXPRESSION; GENE IDENTIFICATION; GENE LENGTH; GENETIC ASSOCIATION; GENETIC CODE; GENETIC PARAMETERS; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; MORPHOLOGICAL ADAPTATION; NEGATIVE SELECTION INTENSITY; PROMOTER REGION; SPECIES COMPARISON; SYNAPSE; UPREGULATION;

ADAPTATION, BIOLOGICAL; BRAIN; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOMICS; HUMANS; MOLECULAR SEQUENCE ANNOTATION; ORGAN SPECIFICITY; SELECTION, GENETIC;

EID: 84876051120     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0061280     Document Type: Article

References (48)

1. Carroll SB, (2003) Genetics and the making of Homo sapiens. Nature 422: 849-857.
2. Roth G, Dicke U, (2005) Evolution of the brain and intelligence. Trends Cogn Sci 9: 250-257.
3. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG, (2007) Recent and ongoing selection in the human genome. Nat Rev Genet 8: 857-868.
4. Biswas S, Akey JM, (2006) Genomic insights into positive selection. Trends Genet 22: 437-446.
5. Enard W, Przeworski M, Fisher SE, Lai CSL, Wiebe V, et al. (2002) Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418: 869-872.
6. Akey JM, (2009) Constructing genomic maps of positive selection in humans: Where do we go from here? Genome Res 19: 711-722.
7. Gilbert SL, Dobyns WB, Lahn BT, (2005) Genetic links between brain development and brain evolution. Nat Rev Genet 6: 581-590.
8. Zhang J, Webb DM, Podlaha O, (2002) Accelerated Protein Evolution and Origins of Human-Specific Features: FOXP2 as an Example. Genetics 162: 1825-1835.
9. Tang BL, (2006) Molecular genetic determinants of human brain size. Biochem Biophys Res Commun 345: 911-916.
10. Wang H-Y, Chien H-C, Osada N, Hashimoto K, Sugano S, et al. (2007) Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates. PLoS Biol 5: e13.
11. Wang ET, Kodama G, Baldi P, Moyzis RK, (2006) Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci U S A 103: 135-140.
12. Consortium TCSaA, (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
13. Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, et al. (2005) Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.
14. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, et al. (2005) A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees. PLoS Biol 3: e170.
15. Arbiza L, Dopazo J, Dopazo H, (2006) Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome. PLoS Comput Biol 2: e38.
16. Bakewell MA, Shi P, Zhang J, (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci U S A 104: 7489-7494.
17. Jensen JD, Wong A, Aquadro CF, (2007) Approaches for identifying targets of positive selection. Trends Genet 23: 568-577.
18. Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, et al. (2003) Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios. Science 302: 1960-1963.
19. Voight BF, Kudaravalli S, Wen X, Pritchard JK, (2006) A Map of Recent Positive Selection in the Human Genome. PLoS Biol 4: e72.
20. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD, (2002) Interrogating a High-Density SNP Map for Signatures of Natural Selection. Genome Res 12: 1805-1814.
21. Grossman SR, Shylakhter I, Karlsson EK, Byrne EH, Morales S, et al. (2010) A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection. Science 327: 883-886.
22. Zhai W, Nielsen R, Slatkin M, (2009) An Investigation of the Statistical Power of Neutrality Tests Based on Comparative and Population Genetic Data. Mol Biol Evol 26: 273-283.
23. Kosiol C, Vinar T, Fonseca RRd, Hubisz MJ, Bustamante CD, et al. (2008) Patterns of Positive Selection in Six Mammalian Genomes. PLoS Genet 4: e1000144.
24. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, et al. (2006) Positive Natural Selection in the Human Lineage. Science 312: 1614-1620.
25. Moreno-Estrada A, Tang K, Sikora M, Marques-Bonet T, Casals F, et al. (2009) Interrogating 11 Fast-Evolving Genes for Signatures of Recent Positive Selection in Worldwide Human Populations. Mol Biol Evol 26: 2285-2297.
26. Moher D, Liberati A, Tetzlaff J, Altman DG, (2009) Group TP (2009) Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement. PLoS Medicine 6: e1000097.
27. Lin K-T, Liu C-H, Chiou J-J, Tseng W-H, Lin K-L, et al. (2007) Gene name service: no-nonsense alias resolution service for Homo Sapiens genes. Silicon Valley,CA,USA.pp. 185-188.
28. Hurst LD, (2009) Genetics and the understanding of selection. Nat Rev Genet 10: 83-93.
29. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
30. Daszykowski M, Kaczmarek K, Heyden YV, Walczak B, (2007) Robust statistics in data analysis- A review: Basic concepts. Chemometrics and Intelligent Laboratory Systems 85: 203-219.
31. Chung N, Zhang XD, Kreamer A, Locco L, Kuan P-F, et al. (2008) Median Absolute Deviation to Improve Hit Selection for Genome-Scale RNAi Screens. J Biomol Screen 13: 149-158.
32. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
33. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, et al. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37: D885-890.
34. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
35. Wu C, Orozco C, Boyer J, Leglise M, Goodale J, et al. (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 10: R130.
36. Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, et al. (2012) The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res 2012: D918-D923.
37. Enard D, Depaulis F, Crollius HR, (2010) Human and Non-Human Primate Genomes Share Hotspots of Positive Selection. PLoS Genet 6: e1000840.
38. Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2012) Ensembl 2012. Nucleic Acids Res 40: D84-D90.
39. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J R Statist Soc 57: 289-300.
40. Falcon S, Gentleman R, (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23: 257-258.
41. Pertea M, Salzberg SL, (2010) Between a chicken and a grape: estimating the number of human genes. Genome Biol 11: 206.
42. Teshima KM, Coop G, Przeworski M, (2006) How reliable are empirical genomic scans for selective sweeps?. Genome Res Vol 16: 702-712.
43. Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, et al. (2008) Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome. PLoS Genet 4: e1000083.
44. Mallick S, Gnerre S, Muller P, Reich D, (2009) The difficulty of avoiding false positives in genome scans for natural selection. Genome Res Vol. 19: 922-933.
45. Fletcher W, Yang Z, (2010) The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection. Mol Biol Evol Vol. 27: 2257-2267.
46. Rakic P, (2009) Evolution of the neocortex: a perspective from developmental biology. Nat Rev Neurosci 10: 724-735.
47. Haygood R, Fedrigo O, Hanson B, Yokoyama K-D, Wray GA, (2007) Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nat Genet Vol pp. 39.
48. Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admettla A, Pattini L, et al. (2011) Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution. PLoS Genet 7: e1002355.