Distinct genomic signatures of adaptation in pre- and postnatal environments during human evolution

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 9, 2008, Pages 3215-3220

  Uddin, Monica ^a   Goodman, Morris ^a   Erez, Offer ^b   Romero, Roberto ^b   Liu, Guozhen ^a   Islam, Munirul ^c   Opazo, Juan C ^a   Sherwood, Chet C ^d   Grossman, Lawrence I ^a   Wildman, Derek E ^a,b  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^c Wayne State University   (United States)

^d GEORGE WASHINGTON UNIVERSITY   (United States)

Author keywords

Fetal; Human disease; Mitochondria; Placenta; Thyroid

Indexed keywords

AEROBIC METABOLISM; APE; ARTICLE; BRAIN CORTEX; BRAIN DEVELOPMENT; ENERGY YIELD; EVOLUTIONARY ADAPTATION; FETUS; FETUS DEVELOPMENT; GENE EXPRESSION; GENE FUNCTION; GENE SEQUENCE; GENOMICS; GENOTYPE; HEART DEVELOPMENT; HUMAN; LAST COMMON ANCESTOR; MITOCHONDRION; PERINATAL PERIOD; PHENOTYPE; PRENATAL PERIOD; PRIORITY JOURNAL; RODENT; VERTEBRATE; ADAPTATION; EMBRYO (ANATOMY); ENVIRONMENT; EVOLUTION; GENETICS; GENOME; NEWBORN; PLACENTA;

PAN; RODENTIA; VERTEBRATA;

ADAPTATION, PHYSIOLOGICAL; EMBRYO, MAMMALIAN; ENVIRONMENT; EVOLUTION; GENOME, HUMAN; HUMANS; INFANT, NEWBORN; PHENOTYPE; PLACENTA;

EID: 42149146088     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0712400105     Document Type: Article

References (56)

1. Lander ES, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921.
2. Venter JC, et al. (2001) The sequence of the human genome. Science 291:1304-1351.
3. McConkey EH, Goodman M (1997) A Human Genome Evolution Project is needed. Trends Genet 13:350-351.
4. Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87.
5. Bakewell MA, Shi P, Zhang J (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci USA 104:7489-7494.
6. Clark AG, et al. (2003) Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302:1960-1963.
7. Goodman M (1999) The genomic record of humankind's evolutionary roots. Am J Hum Genet 64:31-39.
8. Thorpe SK, Holder RL, Crompton RH (2007) Origin of human bipedalism as an adaptation for locomotion on flexible branches. Science 316:1328-1331.
9. Martin RD (2003) Human reproduction: A comparative background for medical hypotheses. J Reprod Immunol 59:111-135.
10. Wildman DE, et al. (2006) Evolution of the mammalian placenta revealed by phylogenetic analysis. Proc Natl Acad Sci USA 103:3203-3208.
11. Su AI, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101:6062-6067.
12. Dennis G, Jr, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4:P3.
13. 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.
14. Bustamante CD, et al. (2005) Natural selection on protein-coding genes in the human genome. Nature 437:1153-1157.
15. Gibbs RA, et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222-234.
16. Nielsen R, et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3:e170.
17. Sabeti PC, et al. (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913-918.
18. Nei M (2007) The new mutation theory of phenotypic evolution. Proc Natl Acad Sci USA 104:12235-12242.
19. Davidson EH, Erwin DH (2006) Gene regulatory networks and the evolution of animal body plans. Science 311:796-800.
20. Goodman M (1961) The role of immunochemical differences in the phyletic development of human behavior. Hum Biol 33:131-162.
21. Frank M, Kemler R (2002) Protocadherins. Curr Opin Cell Biol 14:557-562.
22. Huguenard JR (1996) Low-threshold calcium currents in central nervous system neurons. Annu Rev Physiol 58:329-348.
23. Paracchini S, et al. (2006) The chromosome 6p22 haplotype associated with dyslexia reduces the expression of KIAA0319, a novel gene involved in neuronal migration. Hum Mol Genet 15:1659-1666.
24. Rilling JK, Seligman RA (2002) A quantitative morphometric comparative analysis of the primate temporal lobe. J Hum Evol 42:505-533.
25. Schenker NM, Desgouttes AM, Semendeferi K (2005) Neural connectivity and cortical substrates of cognition in hominoids. J Hum Evol 49:547-569.
26. Sherwood CC, Hof PR (2007) The evolution of neuron types and cortical histology in apes and humans. The Evolution of Primate Nervous Systems, ed Preuss TM, Kaas JH (Academic, Oxford), pp 355-378.
27. Grossman LI, Wildman DE, Schmidt TR, Goodman M (2004) Accelerated evolution of the electron transport chain in anthropoid primates. Trends Genet 20:578-585.
28. Uddin M, et al. (2004) Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. Proc Natl Acad Sci USA 101:2957-2962.
29. Sherwood CC, et al. (2006) Evolution of increased glia-neuron ratios in the human frontal cortex. Proc Natl Acad Sci USA 103:13606-13611.
30. Aiello LC, Wheeler P (1995) The expensive-tissue hypothesis: The brain and the digestive system in human and primate evolution. Curr Anthropol 36:199-221.
31. Fleagle JG (1999) Primate Adaptation and Evolution (Academic, San Diego), Second Ed.
32. Bernal J (2005) Thyroid hormones and brain development. Vitam Horm 71:95-122.
33. de Escobar GM, Obregon MJ, del Rey FE (2004) Maternal thyroid hormones early in pregnancy and fetal brain development. Best Pract Res Clin Endocrinol Metab 18:225-248.
34. Kester MH, et al. (2004) Iodothyronine levels in the human developing brain: Major regulatory roles of iodothyronine deiodinases in different areas. J Clin Endocrinol Metab 89:3117-3128.
35. Morreale de Escobar G, Obregon MJ, Escobar del Rey F (2004) Role of thyroid hormone during early brain development. Eur J Endocrinol 151 Suppl 3:U25.
36. Arnold S, Goglia F, Kadenbach B (1998) 3,5-Diiodothyronine binds to subunit Va of cytochrome-c oxidase and abolishes the allosteric inhibition of respiration by ATP. Eur J Biochem 252:325-330.
37. Sheehan TE, Kumar PA, Hood DA (2004) Tissue-specific regulation of cytochrome c oxidase subunit expression by thyroid hormone. Am J Physiol 286:E968-E974.
38. Wrutniak-Cabello C, Casas F, Cabello G (2001) Thyroid hormone action in mitochondria. J Mol Endocrinol 26:67-77.
39. Fernandez V, et al. (2006) Thyroid hormone-induced oxidative stress in rodents and humans: A comparative view and relation to redox regulation of gene expression. Comp Biochem Physiol C Toxicol Pharmacol 142:231-239.
40. Rose RW, Kuswanti N (2004) Thyroid function and the development of endothermy in a marsupial, the Tasmanian bettong, Bettongia gaimardi (Demarest 1822). Gen Comp Endocrinol 136:17-22.
41. Rochard P, et al. (2000) Mitochondrial activity is involved in the regulation of myoblast differentiation through myogenin expression and activity of myogenic factors. J Biol Chem 275:2733-2744.
42. Jeschke U, et al. (2002) Expression of the Thomsen-Friedenreich antigen and of its putative carrier protein mucin 1 in the human placenta and in trophoblast cells in vitro. Histochem Cell Biol 117:219-226.
43. Shalom-Barak T, et al. (2004) Peroxisome proliferator-activated receptor gamma controls Muc1 transcription in trophoblasts. Mol Cell Biol 24:10661-10669.
44. Thirkill TL, et al. (2007) MUC1 is involved in trophoblast transendothelial migration. Biochim Biophys Acta 1773:1007-1014.
45. Sood R, Zehnder JL, Druzin ML, Brown PO (2006) Gene expression patterns in human placenta. Proc Natl Acad Sci USA 103:5478-5483.
46. Carter AM (2007) Animal models of human placentation - a review. Placenta 28 Suppl A:S41-S47.
47. Bado A, et al. (1998) The stomach is a source of leptin. Nature 394:790-793.
48. Mise H, et al. (2007) The relationship between maternal plasma leptin levels and fetal growth restriction. Endocr J 10.1507/endocrj. K06-225.
49. Mittal P, et al. (2007) Placental growth hormone is increased in the maternal and fetal serum of patients with preeclampsia. J Matern Fetal Neonatal Med 20:651-659.
50. Hallast P, Rull K, Laan M (2007) The evolution and genomic landscape of CGB1 and CGB2 genes. Mol Cell Endocrinol 260-262:2-11.
51. Varki A (2007) Glycan-based interactions involving vertebrate sialic-acid-recognizing proteins. Nature 446:1023-1029.
52. Koike C, et al. (2007) Functionally important glycosyltransferase gain and loss during catarrhine primate emergence. Proc Natl Acad Sci USA 104:559-564.
53. Lipovich L, et al. (2006) Primate-specific endogenous cis-antisense transcription in the human 5q31 protocadherin gene cluster. J Mol Evol 62:73-88.
54. Liu G, et al. (2007) OCPAT: An online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences. Source Code Biol Med 2:5.
55. Yang Z (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556.
56. Yang Z (2006) Computational Molecular Evolution. (Oxford Univ Press, Oxford).