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Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination.

Mugal CF, Nabholz B, Ellegren H.

BMC Genomics. 2013 Feb 8;14:86. doi: 10.1186/1471-2164-14-86.


Reduced variation on the chicken Z chromosome.

Sundström H, Webster MT, Ellegren H.

Genetics. 2004 May;167(1):377-85.


A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate.

Groenen MA, Wahlberg P, Foglio M, Cheng HH, Megens HJ, Crooijmans RP, Besnier F, Lathrop M, Muir WM, Wong GK, Gut I, Andersson L.

Genome Res. 2009 Mar;19(3):510-9. doi: 10.1101/gr.086538.108. Epub 2008 Dec 16.


Genome-wide patterns of genetic variation in two domestic chickens.

Fan WL, Ng CS, Chen CF, Lu MY, Chen YH, Liu CJ, Wu SM, Chen CK, Chen JJ, Mao CT, Lai YT, Lo WS, Chang WH, Li WH.

Genome Biol Evol. 2013;5(7):1376-92. doi: 10.1093/gbe/evt097.


The influence of recombination on SNP diversity in chickens.

Rao Y, Sun L, Nie Q, Zhang X.

Hereditas. 2011 Apr;148(2):63-9. doi: 10.1111/j.1601-5223.2010.02210.x. Epub 2011 Apr 15.


Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken.

Megens HJ, Crooijmans RP, Bastiaansen JW, Kerstens HH, Coster A, Jalving R, Vereijken A, Silva P, Muir WM, Cheng HH, Hanotte O, Groenen MA.

BMC Genet. 2009 Dec 20;10:86. doi: 10.1186/1471-2156-10-86.


Whole-genome resequencing reveals loci under selection during chicken domestication.

Rubin CJ, Zody MC, Eriksson J, Meadows JR, Sherwood E, Webster MT, Jiang L, Ingman M, Sharpe T, Ka S, Hallböök F, Besnier F, Carlborg O, Bed'hom B, Tixier-Boichard M, Jensen P, Siegel P, Lindblad-Toh K, Andersson L.

Nature. 2010 Mar 25;464(7288):587-91. doi: 10.1038/nature08832. Epub 2010 Mar 10.


A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier LW, Yang SP, Warren WC, Wilson RK, Brandström M, Ellegren H, Crooijmans RP, van der Poel JJ, Bovenhuis H, Groenen MA, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young JR, Rogers S, Walker BA, van Hateren A, Kaufman J, Bumstead N, Lamont SJ, Zhou H, Hocking PM, Morrice D, de Koning DJ, Law A, Bartley N, Burt DW, Hunt H, Cheng HH, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi MT, Andersson B, Webber C, Ponting CP, Overton IM, Boardman PE, Tang H, Hubbard SJ, Wilson SA, Yu J, Wang J, Yang H; International Chicken Polymorphism Map Consortium.

Nature. 2004 Dec 9;432(7018):717-22.


Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls.

Bao W, Chen G, Li B, Wu X, Shu J, Wu S, Xu Q, Weigend S.

Sci China C Life Sci. 2008 Jun;51(6):560-8. doi: 10.1007/s11427-008-0076-y. Epub 2008 May 17.


Molecular evolution of the Bovini tribe (Bovidae, Bovinae): is there evidence of rapid evolution or reduced selective constraint in Domestic cattle?

MacEachern S, McEwan J, McCulloch A, Mather A, Savin K, Goddard M.

BMC Genomics. 2009 Apr 24;10:179. doi: 10.1186/1471-2164-10-179.


Indel segregating within introns in the chicken genome are positively correlated with the recombination rates.

Rao YS, Wang ZF, Chai XW, Wu GZ, Nie QH, Zhang XQ.

Hereditas. 2010 Apr;147(2):53-7. doi: 10.1111/j.1601-5223.2009.02141.x.


Chicken domestication: from archeology to genomics.

Tixier-Boichard M, Bed'hom B, Rognon X.

C R Biol. 2011 Mar;334(3):197-204. doi: 10.1016/j.crvi.2010.12.012. Review.


Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes.

Axelsson E, Webster MT, Smith NG, Burt DW, Ellegren H.

Genome Res. 2005 Jan;15(1):120-5. Epub 2004 Dec 8.


Gastrocnemius transcriptome analysis reveals domestication induced gene expression changes between wild and domestic chickens.

Li Q, Wang N, Du Z, Hu X, Chen L, Fei J, Wang Y, Li N.

Genomics. 2012 Nov;100(5):314-9. doi: 10.1016/j.ygeno.2012.07.008. Epub 2012 Jul 21.


[Comparative analysis of morphologic traits in Mediterranean and Chinese chicken breeds. The problem of the origin of the domestic chicken].

Moiseeva IG, Chzhan IuG, Zakharov IA, Nikiforov AA.

Genetika. 1996 Nov;32(11):1553-61. Russian.


Why do human diversity levels vary at a megabase scale?

Hellmann I, Prüfer K, Ji H, Zody MC, Pääbo S, Ptak SE.

Genome Res. 2005 Sep;15(9):1222-31.


Molecular evolutionary genomics of birds.

Ellegren H.

Cytogenet Genome Res. 2007;117(1-4):120-30. Review.


High genetic divergence in miniature breeds of Japanese native chickens compared to Red Junglefowl, as revealed by microsatellite analysis.

Tadano R, Nishibori M, Imamura Y, Matsuzaki M, Kinoshita K, Mizutani M, Namikawa T, Tsudzuki M.

Anim Genet. 2008 Feb;39(1):71-8. doi: 10.1111/j.1365-2052.2007.01690.x.


Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice.

Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD.

Mol Biol Evol. 2012 Feb;29(2):675-87. doi: 10.1093/molbev/msr225. Epub 2011 Sep 13.


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