Genetic correlates of the evolving primate brain

Progress in Brain Research

Volumn 195, Issue , 2012, Pages 27-44

  Vallender, Eric J ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Catarrhine; Divergence; FOXP2; Gene regulation; Genetic evolution; Hominin; Hominoid; Microcephaly; Molecular evolution; Olfaction; Opsin; Pleiotropy; Polymorphism

Indexed keywords

GLUTAMATE DEHYDROGENASE; MYH16 PROTEIN; MYOSIN; OPSIN; UNCLASSIFIED DRUG;

ALOUATTA; ARTICLE; AUTOSOME; BRAIN; BRAIN REGION; CORRELATION ANALYSIS; GENE EXPRESSION; GENE LOSS; GENE MUTATION; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENETIC TRAIT; GENOMICS; HAPLORHINI; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; PHENOTYPE; PRIMATE; PRIORITY JOURNAL; PROSIMIAN; VULVA DISEASE; X CHROMOSOME;

EID: 84855485955     PISSN: 00796123     EISSN: 18757855     Source Type: Book Series    
DOI: 10.1016/B978-0-444-53860-4.00002-7     Document Type: Chapter

References (92)

1. Arbiza L., Dopazo J., Dopazo H. Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Computational Biology 2006, 2:e38.
2. Boissinot S., Tan Y., Shyue S.K., Schneider H., Sampaio I., Neiswanger K., et al. Origins and antiquity of X-linked triallelic color vision systems in New World monkeys. Proceedings of the National Academy of Sciences of the United States of America 1998, 95:13749-13754.
3. Burki F., Kaessmann H. Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nature Genetics 2004, 36:1061-1063.
4. Bustamante C.D., Fledel-Alon A., Williamson S., Nielsen R., Hubisz M.T., Glanowski S., et al. Natural selection on protein-coding genes in the human genome. Nature 2005, 437:1153-1157.
5. Carlson C.S., Thomas D.J., Eberle M.A., Swanson J.E., Livingston R.J., Rieder M.J., et al. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Research 2005, 15:1553-1565.
6. Carroll S.B. Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 2008, 134:25-36.
7. Caveney S., Cladman W., Verellen L., Donly C. Ancestry of neuronal monoamine transporters in the Metazoa. Journal of Experimental Biology 2006, 209:4858-4868.
8. Choi S.S., Lahn B.T. Adaptive evolution of MRG, a neuron-specific gene family implicated in nociception. Genome Research 2003, 13:2252-2259.
9. Clark A.G., Glanowski S., Nielsen R., Thomas P.D., Kejariwal A., Todd M.A., et al. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 2003, 302:1960-1963.
10. Cruz-Gordillo P., Fedrigo O., Wray G.A., Babbitt C.C. Extensive changes in the expression of the opioid genes between humans and chimpanzees. Brain, Behavior and Evolution 2010, 76:154-162.
11. Currat M., Excoffier L., Maddison W., Otto S.P., Ray N., Whitlock M.C., et al. Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens" and "Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans". Science 2006, 313:172.
12. Da Fonseca R.R., Kosiol C., Vinar T., Siepel A., Nielsen R. Positive selection on apoptosis related genes. FEBS Letters 2010, 584:469-476.
13. Dicicco-Bloom E., Lu N., Pintar J.E., Zhang J. The PACAP ligand/receptor system regulates cerebral cortical neurogenesis. Annals of the New York Academy of Sciences 1998, 865:274-289.
14. Dobson-Stone C., Gatt J.M., Kuan S.A., Grieve S.M., Gordon E., Williams L.M., et al. Investigation of MCPH1 G37995C and ASPM A44871G polymorphisms and brain size in a healthy cohort. NeuroImage 2007, 37:394-400.
15. Dobyns W.B. Primary microcephaly: New approaches for an old disorder. American Journal of Medical Genetics 2002, 112:315-317.
16. Dong D., He G., Zhang S., Zhang Z. Evolution of olfactory receptor genes in primates dominated by birth-and-death process. Genome Biology and Evolution 2009, 1:258-264.
17. Dorus S., Anderson J.R., Vallender E.J., Gilbert S.L., Zhang L., Chemnick L.G., et al. Sonic Hedgehog, a key development gene, experienced intensified molecular evolution in primates. Human Molecular Genetics 2006, 15:2031-2037.
18. Dorus S., Vallender E.J., Evans P.D., Anderson J.R., Gilbert S.L., Mahowald M., et al. Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell 2004, 119:1027-1040.
19. Duret L., Mouchiroud D. Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate. Molecular Biology and Evolution 2000, 17:68-74.
20. Enard W., Fassbender A., Model F., Adorjan P., Paabo S., Olek A. Differences in DNA methylation patterns between humans and chimpanzees. Current Biology 2004, 14:R148-R149.
21. Enard W., Gehre S., Hammerschmidt K., Holter S.M., Blass T., Somel M., et al. A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice. Cell 2009, 137:961-971.
22. Enard W., Przeworski M., Fisher S.E., Lai C.S., Wiebe V., Kitano T., et al. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 2002, 418:869-872.
23. Evans P.D., Anderson J.R., Vallender E.J., Choi S.S., Lahn B.T. Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size. Human Molecular Genetics 2004, 13:1139-1145.
24. Evans P.D., Anderson J.R., Vallender E.J., Gilbert S.L., Malcom C.M., Dorus S., et al. Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans. Human Molecular Genetics 2004, 13:489-494.
25. Evans P.D., Gilbert S.L., Mekel-Bobrov N., Vallender E.J., Anderson J.R., Vaez-Azizi L.M., et al. Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science 2005, 309:1717-1720.
26. Evans P.D., Vallender E.J., Lahn B.T. Molecular evolution of the brain size regulator genes CDK5RAP2 and CENPJ. Gene 2006, 375:75-79.
27. Farcas R., Schneider E., Frauenknecht K., Kondova I., Bontrop R., Bohl J., et al. Differences in DNA methylation patterns and expression of the CCRK gene in human and nonhuman primate cortices. Molecular Biology and Evolution 2009, 26:1379-1389.
28. Finlay B.L., Darlington R.B. Linked regularities in the development and evolution of mammalian brains. Science 1995, 268:1578-1584.
29. Force A., Lynch M., Pickett F.B., Amores A., Yan Y.L., Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999, 151:1531-1545.
30. Gibbs R.A., Rogers J., Katze M.G., Bumgarner R., Weinstock G.M., Mardis E.R., et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 2007, 316:222-234.
31. Gilad Y., Bustamante C.D., Lancet D., Paabo S. Natural selection on the olfactory receptor gene family in humans and chimpanzees. American Journal of Human Genetics 2003, 73:489-501.
32. Gilad Y., Man O., Paabo S., Lancet D. Human specific loss of olfactory receptor genes. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:3324-3327.
33. Goldman N., Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 1994, 11:725-736.
34. Guernsey D.L., Jiang H., Hussin J., Arnold M., Bouyakdan K., Perry S., et al. Mutations in centrosomal protein CEP152 in primary microcephaly families linked to MCPH4. American Journal of Human Genetics 2010, 87:40-51.
35. Haesler S., Wada K., Nshdejan A., Morrisey E.E., Lints T., Jarvis E.D., et al. FoxP2 expression in avian vocal learners and non-learners. Journal of Neuroscience 2004, 24:3164-3175.
36. Haygood R., Fedrigo O., Hanson B., Yokoyama K.D., Wray G.A. Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nature Genetics 2007, 39:1140-1144.
37. Hoffman M.M., Birney E. An effective model for natural selection in promoters. Genome Research 2010, 20:685-692.
38. Hughes A.L. The evolution of functionally novel proteins after gene duplication. Proceedings. Biological Sciences 1994, 256:119-124.
39. A haplotype map of the human genome. Nature 2005, 437:1299-1320. International Hapmap Consortium.
40. Jerison J.H. Evolution of the brain and intelligence 1973, Academic Press, New York.
41. Johnson M.E., Viggiano L., Bailey J.A., Abdul-Rauf M., Goodwin G., Rocchi M., et al. Positive selection of a gene family during the emergence of humans and African apes. Nature 2001, 413:514-519.
42. Kaas J.H. From mice to men: The evolution of the large, complex human brain. Journal of Biosciences 2005, 30:155-165.
43. Kaindl A.M., Passemard S., Kumar P., Kraemer N., Issa L., Zwirner A., et al. Many roads lead to primary autosomal recessive microcephaly. Progress in Neurobiology 2010, 90:363-383.
44. Kelley J.L., Madeoy J., Calhoun J.C., Swanson W., Akey J.M. Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Research 2006, 16:980-989.
45. Khaitovich P., Hellmann I., Enard W., Nowick K., Leinweber M., Franz H., et al. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 2005, 309:1850-1854.
46. King M.C., Wilson A.C. Evolution at two levels in humans and chimpanzees. Science 1975, 188:107-116.
47. Konopka G., Bomar J.M., Winden K., Coppola G., Jonsson Z.O., Gao F., et al. Human-specific transcriptional regulation of CNS development genes by FOXP2. Nature 2009, 462:213-217.
48. Kouprina N., Pavlicek A., Mochida G.H., Solomon G., Gersch W., Yoon Y.H., et al. Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion. PLoS Biology 2004, 2:E126.
49. Lai C.S., Fisher S.E., Hurst J.A., Vargha-Khadem F., Monaco A.P. A forkhead-domain gene is mutated in a severe speech and language disorder. Nature 2001, 413:519-523.
50. Lambert N., Lambot M.A., Bilheu A., Albert V., Englert Y., Libert F., et al. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PloS One 2011, 6:e17753.
51. Li W.H., Wu C.I., Luo C.C. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Molecular Biology and Evolution 1985, 2:150-174.
52. Lin L., Shen S., Jiang P., Sato S., Davidson B.L., Xing Y. Evolution of alternative splicing in primate brain transcriptomes. Human Molecular Genetics 2010, 19:2958-2973.
53. Mekel-Bobrov N., Gilbert S.L., Evans P.D., Vallender E.J., Anderson J.R., Hudson R.R., et al. Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science 2005, 309:1720-1722.
54. Miyata T., Kuma K., Iwabe N., Nikoh N. A possible link between molecular evolution and tissue evolution demonstrated by tissue specific genes. Japanese Journal of Genetics 1994, 69:473-480.
55. Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 1986, 3:418-426.
56. Nielsen R., Bustamante C., Clark A.G., Glanowski S., Sackton T.B., Hubisz M.J., et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology 2005, 3:e170.
57. Nowick K., Hamilton A.T., Zhang H.M., Stubbs L. Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes. Molecular Biology and Evolution 2010, 27:2606-2617.
58. Ohno S. Evolution by gene duplication 1970, Springer-Verlag, New York.
59. Ohno S. Argument for genetic simplicity of man and other mammals. Journal of Human Evolution 1972, 1:651-662.
60. Perry G.H., Verrelli B.C., Stone A.C. Comparative analyses reveal a complex history of molecular evolution for human MYH16. Molecular Biology and Evolution 2005, 22:379-382.
61. Plaitakis A., Spanaki C., Mastorodemos V., Zaganas I. Study of structure-function relationships in human glutamate dehydrogenases reveals novel molecular mechanisms for the regulation of the nerve tissue-specific (GLUD2) isoenzyme. Neurochemistry International 2003, 43:401-410.
62. Pollard K.S., Salama S.R., Lambert N., Lambot M.A., Coppens S., Pedersen J.S., et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 2006, 443:167-172.
63. Popesco M.C., Maclaren E.J., Hopkins J., Dumas L., Cox M., Meltesen L., et al. Human lineage-specific amplification, selection, and neuronal expression of DUF1220 domains. Science 2006, 313:1304-1307.
64. Putcha G.V., Harris C.A., Moulder K.L., Easton R.M., Thompson C.B., Johnson E.M. Intrinsic and extrinsic pathway signaling during neuronal apoptosis: Lessons from the analysis of mutant mice. The Journal of Cell Biology 2002, 157:441-453.
65. Rockman M.V., Hahn M.W., Soranzo N., Zimprich F., Goldstein D.B., Wray G.A. Ancient and recent positive selection transformed opioid cis-regulation in humans. PLoS Biology 2005, 3:e387.
66. Sabeti P.C., Varilly P., Fry B., Lohmueller J., Hostetter E., Cotsapas C., et al. Genome-wide detection and characterization of positive selection in human populations. Nature 2007, 449:913-918.
67. Semendeferi K., Lu A., Schenker N., Damasio H. Humans and great apes share a large frontal cortex. Nature Neuroscience 2002, 5:272-276.
68. Shashidharan P., Michaelidis T.M., Robakis N.K., Kresovali A., Papamatheakis J., Plaitakis A. Novel human glutamate dehydrogenase expressed in neural and testicular tissues and encoded by an X-linked intronless gene. Journal of Biological Chemistry 1994, 269:16971-16976.
69. Shyue S.K., Hewett-Emmett D., Sperling H.G., Hunt D.M., Bowmaker J.K., Mollon J.D., et al. Adaptive evolution of color vision genes in higher primates. Science 1995, 269:1265-1267.
70. Soranzo N., Bufe B., Sabeti P.C., Wilson J.F., Weale M.E., Marguerie R., et al. Positive selection on a high-sensitivity allele of the human bitter-taste receptor TAS2R16. Current Biology 2005, 15:1257-1265.
71. Stedman H.H., Kozyak B.W., Nelson A., Thesier D.M., Su L.T., Low D.W., et al. Myosin gene mutation correlates with anatomical changes in the human lineage. Nature 2004, 428:415-418.
72. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005, 437:69-87. The Chimpanzee Sequencing and Analysis Consortium.
73. Tuller T., Kupiec M., Ruppin E. Evolutionary rate and gene expression across different brain regions. Genome Biology 2008, 9:R142.
74. Vallender E.J., Lahn B.T. A primate-specific acceleration in the evolution of the caspase-dependent apoptosis pathway. Human Molecular Genetics 2006, 15:3034-3040.
75. Vincent J.D., Cardinaud B., Vernier P. Evolution of monoamine receptors and the origin of motivational and emotional systems in vertebrates. Bulletin of the National Academy of Medicine 1998, 182:1505-1514. discussion 1515-1516.
76. Voight B.F., Kudaravalli S., Wen X., Pritchard J.K. A map of recent positive selection in the human genome. PLoS Biology 2006, 4:e72.
77. Wang Y.Q., Qian Y.P., Yang S., Shi H., Liao C.H., Zheng H.K., et al. Accelerated evolution of the pituitary adenylate cyclase-activating polypeptide precursor gene during human origin. Genetics 2005, 170:801-806.
78. Wang Y.Q., Su B. Molecular evolution of microcephalin, a gene determining human brain size. Human Molecular Genetics 2004, 13:1131-1137.
79. Williamson S.H., Hubisz M.J., Clark A.G., Payseur B.A., Bustamante C.D., Nielsen R. Localizing recent adaptive evolution in the human genome. PLoS Genetics 2007, 3:e90.
80. Wong W.S., Nielsen R. Detecting selection in noncoding regions of nucleotide sequences. Genetics 2004, 167:949-958.
81. Wooding S., Bufe B., Grassi C., Howard M.T., Stone A.C., Vazquez M., et al. Independent evolution of bitter-taste sensitivity in humans and chimpanzees. Nature 2006, 440:930-934.
82. Wooding S., Kim U.K., Bamshad M.J., Larsen J., Jorde L.B., Drayna D. Natural selection and molecular evolution in PTC, a bitter-taste receptor gene. American Journal of Human Genetics 2004, 74:637-646.
83. Woods C.G., Bond J., Enard W. Autosomal recessive primary microcephaly (MCPH): A review of clinical, molecular, and evolutionary findings. American Journal of Human Genetics 2005, 76:717-728.
84. Woods R.P., Freimer N.B., De Young J.A., Sicotte N.L., Service S.K., et al. Normal variants of Microcephalin and ASPM do not account for brain size variability. Human Molecular Genetics 2006, 15:2025-2029.
85. Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 2007, 24:1586-1591.
86. Yang Z., Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution 2000, 17:32-43.
87. Young J.M., Friedman C., Williams E.M., Ross J.A., Tonnes-Priddy L., Trask B.J. Different evolutionary processes shaped the mouse and human olfactory receptor gene families. Human Molecular Genetics 2002, 11:535-546.
88. Yu F., Hill R.S., Schaffner S.F., Sabeti P.C., Wang E.T., Mignault A.A., et al. Comment on " Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens." Science 2007, 316:370.
89. Zhang J. Evolution of the human ASPM gene, a major determinant of brain size. Genetics 2003, 165:2063-2070.
90. Zhang J.Z. Evolution by gene duplication: An update. Trends in Ecology & Evolution 2003, 18:292-298.
91. Zhang J., Webb D.M., Podlaha O. Accelerated protein evolution and origins of human-specific features: Foxp2 as an example. Genetics 2002, 162:1825-1835.
92. Zhou Y.H., Li W.H. Gene conversion and natural selection in the evolution of X-linked color vision genes in higher primates. Molecular Biology and Evolution 1996, 13:780-783.