title: Evolution of primate gene expression: drift and corrective sweeps?
abstract: Changes in gene expression play an important role in species' evolution. Earlier studies uncovered evidence that the effect of mutations on expression levels within the primate order is skewed, with many small downregulations balanced by fewer but larger upregulations. In addition, brain-expressed genes appeared to show an increased rate of evolution on the branch leading to human. However, the lack of a mathematical model adequately describing the evolution of gene expression precluded the rigorous establishment of these observations. Here, we develop mathematical tools that allow us to revisit these earlier observations in a model-testing and inference framework. We introduce a model for skewed gene-expression evolution within a phylogenetic tree and use a separate model to account for biological or experimental outliers. A Bayesian Markov chain Monte Carlo inference procedure allows us to infer the phylogeny and other evolutionary parameters, while quantifying the confidence in these inferences. Our results support previous observations; in particular, we find strong evidence for a sustained positive skew in the distribution of gene-expression changes in primate evolution. We propose a "corrective sweep" scenario to explain this phenomenon.
authors.affiliation: Department of Statistics, University of Oxford, Oxford, United Kingdom.
authors.forename: R
authors.initials: R
authors.lastname: Chaix
authors.forename: M
authors.initials: M
authors.lastname: Somel
authors.forename: D P
authors.initials: DP
authors.lastname: Kreil
authors.forename: P
authors.initials: P
authors.lastname: Khaitovich
authors.forename: G A
authors.initials: GA
authors.lastname: Lunter
mesh_terms: D000818:Animals; D001921:Brain / Q000502:physiology*; D003198:Computer Simulation; D019143:Evolution, Molecular; D015870:Gene Expression; D020869:Gene Expression Profiling; D016678:Genome; D006801:Humans; D008954:Models, Biological; D015233:Models, Statistical; D009010:Monte Carlo Method; D010802:Phylogeny; D011323:Primates / Q000235:genetics*; D013045:Species Specificity
references.citation: Mol Biol Evol. 2002 Jul;19(7):1114-21
references.pmid: 12082130
references.citation: J Mol Evol. 1981;17(6):368-76
references.pmid: 7288891
references.citation: Curr Opin Genet Dev. 2004 Dec;14(6):667-74
references.pmid: 15531162
references.citation: Bioinformatics. 2002;18 Suppl 1:S96-104
references.pmid: 12169536
references.citation: Science. 2002 Apr 12;296(5566):340-3
references.pmid: 11951044
references.citation: Mol Biol Evol. 2005 Jan;22(1):40-50
references.pmid: 15356281
references.citation: Science. 2005 Sep 16;309(5742):1850-4
references.pmid: 16141373
references.citation: Plant Cell. 2005 Mar;17(3):676-90
references.pmid: 15705952
references.citation: Genetics. 2003 Oct;165(2):747-57
references.pmid: 14573485
references.citation: Evolution. 1988 Sep;42(5):1085-1089
references.pmid: 28581161
references.citation: Nature. 2006 Mar 9;440(7081):242-5
references.pmid: 16525476
references.citation: Evolution. 2005 Jan;59(1):126-37
references.pmid: 15792233
references.citation: Curr Biol. 2006 May 23;16(10):R356-8
references.pmid: 16618540
references.citation: Evolution. 1986 Sep;40(5):915-935
references.pmid: 28556213
references.citation: Science. 1975 Apr 11;188(4184):107-16
references.pmid: 1090005
references.citation: Bioinformatics. 2007 May 15;23(10):1235-42
references.pmid: 17384014
references.citation: Nucleic Acids Res. 2005 Nov 10;33(20):e175
references.pmid: 16284200
references.citation: Nat Genet. 2005 Jun;37(6):601-6
references.pmid: 15880103
references.citation: Genetics. 2005 Jun;170(2):929-39
references.pmid: 15834146
references.citation: Am J Hum Genet. 1973 Sep;25(5):471-92
references.pmid: 4741844
references.citation: PLoS Biol. 2004 May;2(5):E132
references.pmid: 15138501
references.citation: Mol Biol Evol. 2004 Jul;21(7):1308-17
references.pmid: 15034135
references.citation: Evolution. 1976 Jun;30(2):314-334
references.pmid: 28563044
references.citation: Nature. 2002 Aug 22;418(6900):869-72
references.pmid: 12192408
references.citation: Genome Res. 2007 Jan;17(1):42-9
references.pmid: 17038563
references.citation: Nat Genet. 2003 Feb;33(2):138-44
references.pmid: 12548287
references.citation: Nature. 1973 Nov 9;246(5428):96-8
references.pmid: 4585855
references.citation: Genome Res. 2005 May;15(5):674-80
references.pmid: 15867429
references.citation: PLoS Biol. 2005 Feb;3(2):e42
references.pmid: 15678168
references.citation: PLoS Comput Biol. 2006 Oct;2(10):e130
references.pmid: 17040121
references.citation: Nat Genet. 2005 May;37(5):544-8
references.pmid: 15852004
references.citation: Bioinformatics. 2004 Aug 4;20 Suppl 1:i216-23
references.pmid: 15262802