Rapid divergence and diversification of mammalian duplicate gene functions

BMC Evolutionary Biology

Volumn 15, Issue 1, 2015, Pages

  Assis, Raquel ^a   Bachtrog, Doris ^b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Duplicate genes; Gene duplication; Neofunctionalization; Specialization; Subfunctionalization

Indexed keywords

CLASSIFICATION; CONSERVATION GENETICS; DIVERGENCE; EFFECTIVE POPULATION SIZE; EVOLUTIONARY BIOLOGY; FLY; GENE EXPRESSION; GENOME; MAMMAL; NATURAL SELECTION; PHENOTYPE; PHYLOGENETICS; SPECIALIZATION; CELLS AND CELL COMPONENTS; CONSPECIFIC; GENETIC VARIATION; POPULATION SIZE;

MAMMALIA;

ANIMAL; ANTIBODY SPECIFICITY; CLASSIFICATION; DUPLICATE GENE; EVOLUTION; FEMALE; GENE DUPLICATION; GENETICS; GENOME; HUMAN; MALE; MAMMAL; MOLECULAR EVOLUTION; PHYLOGENY; SYNTENY;

ANIMALS; BIOLOGICAL EVOLUTION; EVOLUTION, MOLECULAR; FEMALE; GENE DUPLICATION; GENES, DUPLICATE; GENOME; HUMANS; MALE; MAMMALS; ORGAN SPECIFICITY; PHYLOGENY; SYNTENY;

EID: 84937027093     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/s12862-015-0426-x     Document Type: Article

References (44)

1. Li WH, Gu Z, Wang H, Nekrutenko A. Evolutionary analyses of the human genome. Nature. 2001;409:847-9.
2. Ryvkin P, Jun J, Hemphill E, Nelson C. Duplication mechanisms and disruptions in flanking regions influence the fate of mammalian gene duplicates. J Comput Biol. 2009;16:1253-66.
3. Holland PW, Garcia-Fernández J, Williams NA, Sidow A. Gene duplications and the origins of vertebrate development. Dev Suppl. 1994;125-133.
4. Taylor JS, Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet. 2004;38:615-43.
5. Ohno S. Evolution by gene duplication. Berlin: Springer-Verlag; 1970.
6. Hughes AL. The evolution of functionally novel proteins after gene duplication. Proc Royal Soc B. 1994;256:119-24.
7. Force A, Lynch M, Pickett FB, Amores A, Yan Y, Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics. 1999;151:1531-45.
8. Stoltzfus A. On the possibility of constructive neutral evolution. J Mol Evol. 1999;49:169-81.
9. He X, Zhang J. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics. 2005;169:1157-64.
10. Assis R, Bachtrog D. Neofunctionalization of young duplicate genes in Drosophila. Proc Natl Acad Sci U S A. 2013;110:17409-14.
11. Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, Harrigan P, et al. The evolution of gene expression levels in mammalian organs. Nature. 2011;478:343-8.
12. Gu Z, Nicolae D, Lu HH, Li WH. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 2002;18:609-13.
13. Wagner A. Asymmetric functional divergence of duplicate genes in yeast. Mol Biol Evol. 2002;19:1760-8.
14. Makova KD, Li WH. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 2003;13:1638-45.
15. Gu Z, Rifkin SA, White KP, Li WH. Duplicate genes increase gene expression diversity within and between species. Nat Genet. 2004;36:577-9.
16. Gu X, Zhang Z, Huang W. Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc Natl Acad Sci U S A. 2005;102:707-12.
17. Li WH, Yang J, Gu X. Expression divergence between duplicate genes. Trends Genet. 2005;21:602-7.
18. Casneuf T, Bodt SD, Raes J, Maere S, Van de Peer Y. Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol. 2006;7:R13.
19. Chung WY, Albert R, Albert I, Nekrutenko A, Makova KD. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. BMC Bioinformatics. 2006;7:46.
20. Ganko EW, Meyers BC, Vision TJ. Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol. 2007;24:2298-309.
21. Farrè D, Albà MM. Heterogeneous patterns of gene-expression diversification in mammalian gene duplicates. Mol Biol Evol. 2010;27(2):325-35.
22. Huminiecki L, Wolfe KH. Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res. 2004;14:1870-9.
23. Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Briefings in Bioinformatics. 2011; doi: 10.1093/bib/bbr022
24. Lazzaro B. Elevated polymorphism and divergence in the class c scavenger receptors of Drosophila melanogaster and D. simulans. Genetics. 2005;169:2023-34.
25. Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 2005;15:1-18.
26. Chen FC, Li WH. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am J Hum Genet. 2001;68:444-56.
27. Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008;453:175-83.
28. Beckenbach AT, Wei YW, Liu H. Relationships in the Drosophila obscura species group inferred from mitochondrial cytochrome oxidase II sequences. Mol Biol Evol. 1993;10:619-34.
29. Lynch M, Conery S. The origins of genome complexity. Science. 2003;302:1401-4.
30. Jensen JD, Bachtrog D. Characterizing the influence of effective population size on the rate of adaptation, Gillespie's Darwin domain. Genome Biol Evol. 2011;3:687-701.
31. Britten RJ. Rates of DNA sequence evolution differ between taxonomic groups. Science. 1986;231:1393-8.
32. Moriyama EN. Higher rates of nucleotide substitution in Drosophila than in mammals. Jpn J Genetics. 1987;62:139-47.
33. Carroll SB. Evolution at two levels, on genes and form. PLoS Biol. 2005;3:e245.
34. Lynch M, O'hely M, Walsch B, Force A. The probability of preservation of a newly arisen gene duplicate. Genetics. 2001;159:1789-804.
35. Fares MA, Keane OM, Toft C, Carretero-Paulet L, Jones GW. The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes. PLoS Genet. 2013;9:e1003176.
36. Lynch M, Conery JS. The evolutionary fate and consequence of duplicate genes. Science. 2000;290:1151-5.
37. Chang AY, Liao BY. DNA methylation rebalances gene dosage after mammalian gene duplications. Mol Biol Evol. 2012;29:133-44.
38. Keller TE, Yi SV. DNA methylation and evolution of duplicate genes. Proc Natl Acad Sci U S A. 2014;111:5932-7.
39. Kaessmann H. Origins, evolution, and phenotypic impact of new genes. Genome Res. 2010;20:1313-26.
40. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-10.
41. Ranwez V, Harispe S, Delsuc F, Douzery EJP. MACSE, Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS One. 2011;6:e22594.
42. Yang Z. PAML 4, Phylogenetic Analysis by Maximum Likelihood. Mol Biol Evol. 2007;24:1586-91.
43. Pereira V, Waxman D, Eyre-Walker A. A problem with the correlation coefficient as a measure of gene expression divergence. Genetics. 2009;183:1597-600.
44. R, A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2009.