Contrasting genetic paths to morphological and physiological evolution

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

Volumn 107, Issue 16, 2010, Pages 7353-7358

  Liao, Ben Yang ^a   Weng, Meng Pin ^a   Zhang, Jianzhi ^b  

^a NATIONAL HEALTH RESEARCH INSTITUTES   (Taiwan)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Evolutionary rate; Gene expression; Molecular evolution; Phenotypic evolution

Indexed keywords

CARRIER PROTEIN; ENZYME; RECEPTOR;

AMINO ACID SEQUENCE; ARTICLE; GENE EXPRESSION PROFILING; GENE MUTATION; MEMBRANE CHANNEL; MOLECULAR EVOLUTION; MORPHOLOGY; MUTANT; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; TISSUE SPECIFICITY;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOMICS; HUMANS; MICE; MODELS, BIOLOGICAL; MODELS, GENETIC; MUTATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE;

EID: 77952208125     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0910339107     Document Type: Article

References (37)

1. King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188:107-116.
2. Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87. (Pubitemid 41613428)
3. Glazko G, Veeramachaneni V, Nei M, Makałowski W (2005) Eighty percent of proteins are different between humans and chimpanzees. Gene 346:215-219. (Pubitemid 40332639)
4. Carroll SB (2008) Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 134:25-36.
5. Wray GA (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8:206-216.
6. Stern DL, Orgogozo V (2009) Is genetic evolution predictable? Science 323:746-751.
7. Stern DL, Orgogozo V (2008) The loci of evolution: How predictable is genetic evolution? Evolution 62:2155-2177.
8. Hoekstra HE, Coyne JA (2007) The locus of evolution: Evo devo and the genetics of adaptation. Evolution 61:995-1016.
9. Carroll SB (2005) Evolution at two levels: On genes and form. PLoS Biol 3:e245.
10. Al-Shahrour F, et al. (2007) FatiGO +: A functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res 35:W91-W96.
11. Liao BY, Zhang J (2008) Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc Natl Acad Sci USA 105:6987-6992.
12. Liao BY, Scott NM, Zhang J (2006) Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol Biol Evol 23:2072-2080.
13. He X, Zhang J (2006) Toward a molecular understanding of pleiotropy. Genetics 173:1885-1891.
14. Liao BY, Zhang J (2006) Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol 23:1119-1128.
15. Zhang L, Li WH (2004) Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol 21:236-239. (Pubitemid 38314611)
16. Su AI, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101:6062-6067. (Pubitemid 38520528)
17. Xing Y, Ouyang Z, Kapur K, Scott MP, Wong WH (2007) Assessing the conservation of mammalian gene expression using high-density exon arrays. Mol Biol Evol 24:1283-1285. (Pubitemid 47343944)
18. Tirosh I, Barkai N (2008) Evolution of gene sequence and gene expression are not correlated in yeast. Trends Genet 24:109-113.
19. Stern DL (2000) Evolutionary developmental biology and the problem of variation. Evolution 54:1079-1091.
20. Robertson G, et al. (2006) cisRED: A database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res 34 (Database issue):D68-D73.
21. Liao BY, Zhang J (2008) Coexpression of linked genes in mammalian genomes is generally disadvantageous. Mol Biol Evol 25:1555-1565.
22. De S, Teichmann SA, Babu MM (2009) The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Res 19:785-794.
23. Zhang J (2003) Evolution by gene duplication - an update. Trends Ecol Evol 18:292-298.
24. Nei M (2007) The new mutation theory of phenotypic evolution. Proc Natl Acad Sci USA 104:12235-12242.
25. Demuth JP, Hahn MW (2009) The life and death of gene families. BioEssays 31:29-39.
26. Wang X, Grus WE, Zhang J (2006) Gene losses during human origins. PLoS Biol 4:e52.
27. Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N (2005) Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res 15:1153-1160. (Pubitemid 41126871)
28. Austin CP, et al. (2004) The knockout mouse project. Nat Genet 36:921-924.
29. Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309-1321.
30. Doebley J, Lukens L (1998) Transcriptional regulators and the evolution of plant form. Plant Cell 10:1075-1082. (Pubitemid 28539992)
31. Lettice LA, et al. (2003) A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet 12:1725-1735.
32. Tirosh I, Weinberger A, Bezalel D, Kaganovich M, Barkai N (2008) On the relation between promoter divergence and gene expression evolution. Mol Syst Biol 4:159.
33. Chan ET, et al. (2009) Conservation of core gene expression in vertebrate tissues. J Biol 8:33.
34. Tirosh I, Reikhav S, Levy AA, Barkai N (2009) A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324:659-662.
35. Monteiro A, Podlaha O (2009) Wings, horns, and butterfly eyespots: How do complex traits evolve? PLoS Biol 7:e37.
36. Murphy WJ, Pevzner PA, O'Brien SJ (2004) Mammalian phylogenomics comes of age. Trends Genet 20:631-639.
37. Liao BY, Zhang J (2006) Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 23:530-540. (Pubitemid 43278264)