title: Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination.
abstract: BACKGROUND
  Polymorphism is key to the evolutionary potential of populations. Understanding which factors shape levels of genetic diversity within genomes forms a central question in evolutionary genomics and is of importance for the possibility to infer episodes of adaptive evolution from signs of reduced diversity. There is an on-going debate on the relative role of mutation and selection in governing diversity levels. This question is also related to the role of recombination because recombination is expected to indirectly affect polymorphism via the efficacy of selection. Moreover, recombination might itself be mutagenic and thereby assert a direct effect on diversity levels.
  
  
  RESULTS
  We used whole-genome re-sequencing data from domestic chicken (broiler and layer breeds) and its wild ancestor (the red jungle fowl) to study the relationship between genetic diversity and several genomic parameters. We found that recombination rate had the largest effect on local levels of nucleotide diversity. The fact that divergence (a proxy for mutation rate) and recombination rate were negatively correlated argues against a mutagenic role of recombination. Furthermore, divergence had limited influence on polymorphism.
  
  
  CONCLUSIONS
  Overall, our results are consistent with a selection model, in which regions within a short distance from loci under selection show reduced polymorphism levels. This conclusion lends further support from the observations of strong correlations between intergenic levels of diversity and diversity at synonymous as well as non-synonymous sites. Our results also demonstrate differences between the two domestic breeds and red jungle fowl, where the domestic breeds show a stronger relationship between intergenic diversity levels and diversity at synonymous and non-synonymous sites. This finding, together with overall lower diversity levels in domesticates compared to red jungle fowl, seem attributable to artificial selection during domestication.
authors: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-752 36, Uppsala, Sweden.
authors: Carina F
authors: CF
authors: Mugal
authors: Benoit
authors: B
authors: Nabholz
authors: Hans
authors: H
authors: Ellegren
mesh_terms: D000818:Animals; D001482:Base Composition; D001947:Breeding; D002645:Chickens / Q000235:genetics*; D005260:Female; D014644:Genetic Variation / Q000235:genetics*; D023281:Genomics; D008297:Male; D011995:Recombination, Genetic / Q000235:genetics*; D012044:Regression Analysis
references: Nature. 2010 Oct 28;467(7319):1061-73
references: 20981092
references: Proc Natl Acad Sci U S A. 2004 Jul 20;101(29):10667-72
references: 15249682
references: Annu Rev Genomics Hum Genet. 2009;10:285-311
references: 19630562
references: Mol Biol Evol. 2005 Mar;22(3):426-31
references: 15496551
references: Genome Res. 2009 Mar;19(3):510-9
references: 19088305
references: BMC Genet. 2010 Oct 28;11:96
references: 21029465
references: Genetics. 2008 Jun;179(2):985-95
references: 18505875
references: Genetics. 1993 Aug;134(4):1289-303
references: 8375663
references: Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):700-7
references: 14701910
references: Genetics. 1997 Nov;147(3):1303-16
references: 9383072
references: Genome Res. 2010 Aug;20(8):1103-11
references: 20508143
references: Mol Biol Evol. 2000 Apr;17(4):540-52
references: 10742046
references: Anim Genet. 2007 Dec;38(6):576-83
references: 17931400
references: Mol Biol Evol. 2007 Jul;24(7):1506-17
references: 17443011
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82
references: 20959295
references: PLoS One. 2011 Apr 04;6(4):e14782
references: 21483733
references: Science. 2005 May 27;308(5726):1310-4
references: 15919994
references: Genetics. 2005 Oct;171(2):753-63
references: 16085701
references: Genetics. 1998 Nov;150(3):1133-41
references: 9799265
references: Genome Biol Evol. 2011;3:1210-9
references: 21926095
references: PLoS Biol. 2007 Nov 6;5(11):e310
references: 17988176
references: Nature. 2004 Dec 9;432(7018):695-716
references: 15592404
references: Nature. 1968 Feb 17;217(5129):624-6
references: 5637732
references: Mol Biol Evol. 2011 May;28(5):1745-54
references: 21199893
references: Mol Biol Evol. 2002 Mar;19(3):336-40
references: 11861892
references: Mol Biol Evol. 2006 Jun;23(6):1203-16
references: 16551647
references: Nature. 1992 Apr 9;356(6369):519-20
references: 1560824
references: Nature. 2010 Apr 8;464(7290):898-902
references: 20237475
references: Genetics. 2004 May;167(1):377-85
references: 15166162
references: Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):10051-6
references: 18621713
references: Nature. 2010 Mar 25;464(7288):587-91
references: 20220755
references: Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9650-5
references: 12105270
references: Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13402-6
references: 14597721
references: Genetics. 1998 Nov;150(3):1239-44
references: 9799275
references: Genome Res. 2005 Jan;15(1):120-5
references: 15590944
references: Curr Opin Genet Dev. 2001 Dec;11(6):635-41
references: 11682306
references: Genetics. 2005 Apr;169(4):2335-52
references: 15716498
references: Genetics. 2011 Dec;189(4):1389-402
references: 21954163
references: Nat Rev Genet. 2011 Oct 04;12(11):756-66
references: 21969038
references: BMC Genomics. 2009 Jan 14;10:22
references: 19144180
references: Genetics. 1991 Dec;129(4):1111-7
references: 1686006
references: Hereditas. 2011 Apr;148(2):63-9
references: 21561450
references: PLoS Genet. 2006 Sep 22;2(9):e148
references: 17044736
references: Nature. 2004 Dec 9;432(7018):717-22
references: 15592405
references: Mol Biol Evol. 2012 Feb;29(2):675-87
references: 21917724
references: PLoS Biol. 2005 Jul;3(7):e196
references: 15907155
references: Genome Res. 2005 Jan;15(1):111-9
references: 15590946
references: Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9161-6
references: 11470895
references: BMC Bioinformatics. 2006 Apr 04;7:188
references: 16594991
references: Mol Biol Evol. 2003 May;20(5):665-73
references: 12679551
references: BMC Genet. 2009 Dec 20;10:86
references: 20021697
references: Genet Res. 1974 Feb;23(1):23-35
references: 4407212
references: Genome Res. 2005 Sep;15(9):1222-31
references: 16140990
references: Curr Biol. 2009 Apr 28;19(8):655-60
references: 19285399
references: Genetics. 1998 Jan;148(1):423-34
references: 9475752
references: Trends Genet. 2002 Jul;18(7):337-40
references: 12127766
references: Genome Res. 2000 Jan;10(1):137-47
references: 10645958