Kimura M: Evolutionary rate at the molecular level. Nature. 1968, 217 (5129): 624-626.
Article
CAS
PubMed
Google Scholar
Charlesworth B, Morgan MT, Charlesworth D: The effect of deleterious mutations on neutral molecular variation. Genetics. 1993, 134 (4): 1289-1303.
PubMed Central
CAS
PubMed
Google Scholar
Smith JM, Haigh J: The hitch-hiking effect of a favourable gene. Genet Res. 1974, 23 (1): 23-35.
Article
CAS
PubMed
Google Scholar
Andolfatto P: Adaptive hitchhiking effects on genome variability. Curr Opin Genet Dev. 2001, 11 (6): 635-641.
Article
CAS
PubMed
Google Scholar
Berry AJ, Ajioka JW, Kreitman M: Lack of polymorphism on the drosophila fourth chromosome resulting from selection. Genetics. 1991, 129 (4): 1111-1117.
PubMed Central
CAS
PubMed
Google Scholar
Begun DJ, Aquadro CF: Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. Melanogaster. Nature. 1992, 356 (6369): 519-520.
Article
CAS
PubMed
Google Scholar
Nachman MW: Patterns of DNA variability at X-linked loci in Mus domesticus. Genetics. 1997, 147 (3): 1303-1316.
PubMed Central
CAS
PubMed
Google Scholar
Nachman MW, Bauer VL, Crowell SL, Aquadro CF: DNA variability and recombination rates at X-Linked loci in humans. Genetics. 1998, 150 (3): 1133-1141.
PubMed Central
CAS
PubMed
Google Scholar
Hellmann I, Prafer K, Ji H, Zody MC, Pääbo S, Ptak SE: Why do human diversity levels vary at a megabase scale?. Genome Res. 2005, 15 (9): 1222-1231.
Article
PubMed Central
CAS
PubMed
Google Scholar
Spencer CCA, Deloukas P, Hunt S, Mullikin J, Myers S, Silverman B, Donnelly P, Bentley D, McVean G: The influence of recombination on human genetic diversity. PLoS Genetics. 2006, 2 (9): e148-
Article
PubMed Central
PubMed
Google Scholar
Cutter AD, Payseur BA: Selection at linked sites in the partial selfer caenorhabditis elegans. Mol Biol Evol. 2003, 20 (5): 665-673.
Article
CAS
PubMed
Google Scholar
Cutter AD, Choi JY: Natural selection shapes nucleotide polymorphism across the genome of the nematode caenorhabditis briggsae. Genome Res. 2010, 20 (8): 1103-1111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kraft T, Säll T, Magnusson-Rading I, Nilsson N-O, Halldén C: Positive correlation between recombination rates and levels of genetic variation in natural populations of sea beet (Beta vulgaris subsp. maritima). Genetics. 1998, 150 (3): 1239-1244.
PubMed Central
CAS
PubMed
Google Scholar
Dvorák J, Luo M-C, Yang Z-L: Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing Aegilops species. Genetics. 1998, 148 (1): 423-434.
PubMed Central
PubMed
Google Scholar
Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS: Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. Mays L.). Proc Natl Acad Sci U S A. 2001, 98 (16): 9161-9166.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lercher MJ, Hurst LD: Human SNP variability and mutation rate are higher in regions of high recombination. Trends in Genetics. 2002, 18 (7): 337-340.
Article
CAS
PubMed
Google Scholar
Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh Y-P, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN: Population genomics: whole-genome analysis of polymorphism and divergence in drosophila simulans. PLoS Biology. 2007, 5 (11): e310-
Article
PubMed Central
PubMed
Google Scholar
Kulathinal RJ, Bennett SM, Fitzpatrick CL, Noor MAF: Fine-scale mapping of recombination rate in drosophila refines its correlation to diversity and divergence. Proc Natl Acad Sci U S A. 2008, 105 (29): 10051-10056.
Article
PubMed Central
CAS
PubMed
Google Scholar
Huang S-W, Friedman R, Yu N, Yu A, Li W-H: How strong is the mutagenicity of recombination in mammals?. Mol Biol Evol. 2005, 22 (3): 426-431.
Article
CAS
PubMed
Google Scholar
1000 GC: A map of human genome variation from population-scale sequencing. Nature. 2010, 467 (7319): 1061-1073.
Article
Google Scholar
Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD: Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice. Mol Biol Evol. 2012, 29 (2): 675-687.
Article
CAS
PubMed
Google Scholar
Gossmann TI, Woolfit M, Eyre-Walker A: Quantifying the variation in the effective population size within a genome. Genetics. 2011, 189 (4): 1389-1402.
Article
PubMed Central
PubMed
Google Scholar
Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J: Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci U S A. 2002, 99 (15): 9650-9655.
Article
PubMed Central
CAS
PubMed
Google Scholar
Clark RM, Linton E, Messing J, Doebley JF: Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Acad Sci U S A. 2004, 101 (3): 700-707.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rubin CJ, Zody MC, Eriksson J, Meadows JR, Sherwood E, Webster MT, Jiang L, Ingman M, Sharpe T, Ka S: Whole-genome resequencing reveals loci under selection during chicken domestication. Nature. 2010, 464 (7288): 587-591.
Article
CAS
PubMed
Google Scholar
Innan H, Kim Y: Pattern of polymorphism after strong artificial selection in a domestication event. Proc Natl Acad Sci U S A. 2004, 101 (29): 10667-10672.
Article
PubMed Central
CAS
PubMed
Google Scholar
ICGSC: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004, 432 (7018): 695-716.
Article
Google Scholar
ICPMC: A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature. 2004, 432 (7018): 717-722.
Article
Google Scholar
Betancourt AJ, Welch JJ, Charlesworth B: Reduced effectiveness of selection caused by a lack of recombination. Curr Biol. 2009, 19 (8): 655-660.
Article
CAS
PubMed
Google Scholar
Hodgkinson A, Eyre-Walker A: Variation in the mutation rate across mammalian genomes. Nat Rev Genet. 2011, 12 (11): 756-766.
Article
CAS
PubMed
Google Scholar
Slotte T, Bataillon T, Hansen TT, St. Onge K, Wright SI, Schierup MH: Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biol Evol. 2011, 3: 1210-1219.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cutter AD, Moses AM: Polymorphism, divergence, and the role of recombination in saccharomyces cerevisiae genome evolution. Mol Biol Evol. 2011, 28 (5): 1745-1754.
Article
CAS
PubMed
Google Scholar
Payseur BA, Nachman MW: Gene density and human nucleotide polymorphism. Mol Biol Evol. 2002, 19 (3): 336-340.
Article
CAS
PubMed
Google Scholar
Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng HG, Bakker E, Calabrese P, Gladstone J, Goyal R: The pattern of polymorphism in arabidopsis thaliana. PLoS Biology. 2005, 3 (7): 1289-1299.
Article
CAS
Google Scholar
Kawabe A, Forrest A, Wright SI, Charlesworth D: High DNA sequence diversity in pericentromeric genes of the plant arabidopsis lyrata. Genetics. 2008, 179 (2): 985-995.
Article
PubMed Central
CAS
PubMed
Google Scholar
Groenen MAM, Wahlberg P, Foglio M, Cheng HH, Megens H-J, Crooijmans RPMA, Besnier F, Lathrop M, Muir WM, Wong GK-S: A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res. 2009, 19 (3): 510-519.
Article
PubMed Central
CAS
PubMed
Google Scholar
Groenen MAM, Cheng HH, Bumstead N, Benkel BF, Briles WE, Burke T, Burt DW, Crittenden LB, Dodgson J, Hillel J: A consensus linkage map of the chicken genome. Genome Res. 2000, 10 (1): 137-147.
PubMed Central
CAS
PubMed
Google Scholar
Huynh LY, Maney DL, Thomas JW: Contrasting population genetic patterns within the white-throated sparrow genome (zonotrichia albicollis). BMC Genet. 2010, 11: 96-
Article
PubMed Central
PubMed
Google Scholar
Megens HJ, Crooijmans RPMA, Bastiaansen JWM, Kerstens HHD, Coster A, Jalving R, Vereijken A, Silva P, Muir WM, Cheng HH: Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken. BMC Genet. 2009, 10:
Google Scholar
Roselius K, Stephan W, Städler T: The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species. Genetics. 2005, 171 (2): 753-763.
Article
PubMed Central
CAS
PubMed
Google Scholar
Axelsson E, Webster MT, Smith NGC, Burt DW, Ellegren H: Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res. 2005, 15 (1): 120-125.
Article
PubMed Central
CAS
PubMed
Google Scholar
Webster MT, Axelsson E, Ellegren H: Strong regional biases in nucleotide substitution in the chicken genome. Mol Biol Evol. 2006, 23 (6): 1203-1216.
Article
CAS
PubMed
Google Scholar
Duret L, Galtier N: Biased gene conversion and the evolution of mammalian genomic landscapes. Annual Rev Genomics Human Genetics. 2009, 10 (1): 285-311.
Article
CAS
Google Scholar
Hermisson J, Pennings PS: Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics. 2005, 169 (4): 2335-2352.
Article
PubMed Central
CAS
PubMed
Google Scholar
Granevitze Z, Hillel J, Chen GH, Cuc NTK, Feldman M, Eding H, Weigend S: Genetic diversity within chicken populations from different continents and management histories. Anim Genet. 2007, 38 (6): 576-583.
Article
CAS
PubMed
Google Scholar
vonHoldt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A: Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature. 2010, 464 (7290): 898-902.
Article
PubMed Central
CAS
PubMed
Google Scholar
Amaral AJ, Ferretti L, Megens H-J, Crooijmans RPMA, Nie H, Ramos-Onsins SE, Perez-Enciso M, Schook LB, Groenen MAM: Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS One. 2011, 6 (4): e14782-
Article
PubMed Central
CAS
PubMed
Google Scholar
Haudry A, Cenci A, Ravel C, Bataillon T, Brunel D, Poncet C, Hochu I, Poirier S, Santoni S, Glémin S: Grinding up wheat: A massive loss of nucleotide diversity since domestication. Mol Biol Evol. 2007, 24 (7): 1506-1517.
Article
CAS
PubMed
Google Scholar
Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS: The effects of artificial selection on the maize genome. Science. 2005, 308 (5726): 1310-1314.
Article
CAS
PubMed
Google Scholar
Fang L, Ye J, Li N, Zhang Y, Li S, Wong G, Wang J: Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome. Chin Sci Bull. 2008, 53 (5): 746-750.
Article
CAS
Google Scholar
Rao Y, Sun L, Nie Q, Zhang X: The influence of recombination on SNP diversity in chickens. Hereditas. 2011, 148 (2): 63-69.
Article
PubMed
Google Scholar
Sundström H, Webster MT, Ellegren H: Reduced variation on the chicken Z chromosome. Genetics. 2004, 167: 377-385.
Article
PubMed Central
PubMed
Google Scholar
Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A: The UCSC genome browser database: update 2011. Nucleic Acids Res. 2011, 39 (suppl 1): D876-D882.
Article
PubMed Central
CAS
PubMed
Google Scholar
Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A: BioMart - biological queries made easy. BMC Genomics. 2009, 10 (1): 22-
Article
PubMed Central
PubMed
Google Scholar
Keightley PD, Gaffney DJ: Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc Natl Acad Sci U S A. 2003, 100 (23): 13402-13406.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dutheil J, Gaillard S, Bazin E, Glemin S, Ranwez V, Galtier N, Belkhir K: Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinforma. 2006, 7 (1): 188-
Article
Google Scholar
Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, 17 (4): 540-552.
Article
CAS
PubMed
Google Scholar
Abril JF, Castelo R, Guigó R: Comparison of splice sites in mammals and chicken. Genome Res. 2005, 15 (1): 111-119.
Article
PubMed Central
CAS
PubMed
Google Scholar
Naes T, Martens H: Multivariate calibration .2. Chemometric methods. Trac-Trend Anal Chem. 1984, 3 (10): 266-271.
Article
CAS
Google Scholar