Bernardi G. The vertebrate genome: isochores and evolution. Mol Biol Evol. 1993;10(1):186–204.
CAS
PubMed
Google Scholar
Salinas J, Zerial M, Filipski J, Crepin M, Bernardi G. Nonrandom distribution of MMTV proviral sequences in the mouse genome. Nucleic Acids Res. 1987;15(7):3009–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Matassi G, Sharp PM, Gautier C. Chromosomal location effects on gene sequence evolution in mammals. Curr Biol. 1999;9(15):786–91.
Article
CAS
PubMed
Google Scholar
Wolfe KH, Sharp PM, Li WH. Mutation rates differ among regions of the mammalian genome. Nature. 1989;337(6204):283–5.
Article
CAS
PubMed
Google Scholar
Cuny G, Soriano P, Macaya G, Bernardi G. The major components of the mouse and human genomes. 1. Preparation, basic properties and compositional heterogeneity. Eur J Biochem. 1981;115(2):227–33.
Article
CAS
PubMed
Google Scholar
Duret L, Eyre-Walker A, Galtier N. A new perspective on isochore evolution. Gene. 2006;385:71–4.
Article
CAS
PubMed
Google Scholar
Holmquist GP. Chromosome bands, their chromatin flavors, and their functional features. Am J Hum Genet. 1992;51(1):17–37.
CAS
PubMed
PubMed Central
Google Scholar
Eyre-Walker A. Recombination and mammalian genome evolution. Proc Biol Sci. 1993;252(1335):237–43.
Article
CAS
PubMed
Google Scholar
Eyre-Walker A. Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics. 1999;152(2):675–83.
CAS
PubMed
PubMed Central
Google Scholar
Galtier N, Piganeau G, Mouchiroud D, Duret L. GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics. 2001;159(2):907–11.
CAS
PubMed
PubMed Central
Google Scholar
Galtier N, Duret L, Glemin S, Ranwez V. GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet. 2009;25(1):1–5.
Article
CAS
PubMed
Google Scholar
Blain JF, Aumont N, Theroux L, Dea D, Poirier J. A polymorphism in lipoprotein lipase affects the severity of Alzheimer's disease pathophysiology. Eur J Neurosci. 2006;24(5):1245–51.
Article
PubMed
Google Scholar
Surtees JA, Argueso JL, Alani E. Mismatch repair proteins: key regulators of genetic recombination. Cytogenet Genome Res. 2004;107(3–4):146–59.
Article
CAS
PubMed
Google Scholar
Lesecque Y, Mouchiroud D, Duret L. GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance. Mol Biol Evol. 2013;30(6):1409–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Meunier J, Duret L. Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol. 2004;21(6):984–90.
Article
CAS
PubMed
Google Scholar
Necsulea A, Popa A, Cooper DN, Stenson PD, Mouchiroud D, Gautier C, Duret L. Meiotic recombination favors the spreading of deleterious mutations in human populations. Hum Mutat. 2010;32(2):198–206.
Article
Google Scholar
Pessia E, Popa A, Mousset S, Rezvoy C, Duret L, Marais GA. Evidence for widespread GC-biased gene conversion in eukaryotes. Genome Biol Evol. 2012;4(7):675–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harrison RJ, Charlesworth B. Biased gene conversion affects patterns of codon usage and amino acid usage in the Saccharomyces sensu stricto group of yeasts. Mol Biol Evol. 2010;28(1):117–29.
Article
PubMed
Google Scholar
Yang S, Yuan Y, Wang L, Li J, Wang W, Liu H, Chen JQ, Hurst LD, Tian D. Great majority of recombination events in Arabidopsis are gene conversion events. Proc Natl Acad Sci U S A. 2012;109(51):20992–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kent CF, Minaei S, Harpur BA, Zayed A. Recombination is associated with the evolution of genome structure and worker behavior in honey bees. Proc Natl Acad Sci U S A. 2012;109(44):18012–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Doring Y, Zechner U, Roos C, Rosenkranz D, Zischler H, Herlyn H. Accelerated evolution of Fetuin-a (FETUA, also AHSG) is driven by positive Darwinian selection, not GC-biased gene conversion. Gene. 2010;463(1–2):49–55.
Article
PubMed
Google Scholar
Robinson MC, Stone EA, Singh ND. Population genomic analysis reveals no evidence for GC-biased gene conversion in Drosophila melanogaster. Mol Biol Evol. 2014;31(2):425–33. https://doi.org/10.1093/molbev/mst220. Epub 2013 Nov 9. PubMed PMID: 24214536.
Assis R, Kondrashov AS. Nonallelic gene conversion is not GC-biased in Drosophila or primates. Mol Biol Evol. 2011;29(5):1291–5.
Article
PubMed
Google Scholar
Mugal CF, Arndt PF, Ellegren H. Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable Karyotype. Mol Biol Evol. 2013;30(7):1700–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Katzman S, Capra JA, Haussler D, Pollard KS. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biol Evol. 2011;3:614–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, et al. Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2006;2(10):e168.
Article
PubMed
PubMed Central
Google Scholar
Williams AL, Genovese G, Dyer T, Altemose N, Truax K, Jun G, Patterson N, Myers SR, Curran JE, Duggirala R, et al. Non-crossover gene conversions show strong GC bias and unexpected clustering in humans. elife. 2015;4.
Halldorsson BV, Hardarson MT, Kehr B, Styrkarsdottir U, Gylfason A, Thorleifsson G, Zink F, Jonasdottir A, Jonasdottir A, Sulem P, et al. The rate of meiotic gene conversion varies by sex and age. Nat Genet. 2016;48(11):1377–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Durand EY, Eriksson N, McLean CY. Reducing pervasive false-positive identical-by-descent segments detected by large-scale pedigree analysis. Mol Biol Evol. 2014;31(8):2212–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Glusman G, Hu H, Shankaracharya, Caballero J, Hubley R, Witherspoon D, Guthery SL, Mauldin DE, Jorde LB, et al. Relationship estimation from whole-genome sequence data. PLoS Genet. 2014;10(1):e1004144.
Article
PubMed
PubMed Central
Google Scholar
Huff CD, Witherspoon DJ, Simonson TS, Xing J, Watkins WS, Zhang Y, Tuohy TM, Neklason DW, Burt RW, Guthery SL, et al. Maximum-likelihood estimation of recent shared ancestry (ERSA). Genome Res. 2011;21(5):768–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Glemin S, Arndt PF, Messer PW, Petrov D, Galtier N, Duret L. Quantification of GC-biased gene conversion in the human genome. Genome Res. 2015;25(8):1215–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
NCBI trace FTP site [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/]. Accessed 4 Mar 2018.
Genomes Project C, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422):56–65.
Article
Google Scholar
Dutta R, Mainsah J, Yatskiv Y, Chakrabortty S, Brennan P, Khuder B, Qiu S, Fedorova L, Fedorov A. Intricacies in arrangement of SNP haplotypes suggest “great admixture” that created modern humans. BMC Genomics. 2017;18(1):433.
Article
PubMed
PubMed Central
Google Scholar
R Development Core Team: R: a language and environment for statistical computing. In. Vienna, Austria: R foundation for statistical computing; 2010.
Google Scholar
Downloading web site for 1000 Human Genomes carry widespread signatures of GC biased gene conversion [http://bpg.utoledo.edu/~afedorov/lab/BGC.html ]. Accessed 4 Mar 2018.
Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, et al. The structure of haplotype blocks in the human genome. Science. 2002;296(5576):2225–9.
Article
CAS
PubMed
Google Scholar
Bechtel JM, Wittenschlaeger T, Dwyer T, Song J, Arunachalam S, Ramakrishnan SK, Shepard S, Fedorov A. Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures. BMC Genomics. 2008;9:284.
Article
PubMed
PubMed Central
Google Scholar
Prakash A, Shepard SS, He J, Hart B, Chen M, Amarachintha SP, Mileyeva-Biebesheimer O, Bechtel J, Fedorov A. Evolution of genomic sequence inhomogeneity at mid-range scales. BMC Genomics. 2009;10:513.
Article
PubMed
PubMed Central
Google Scholar
Odenthal-Hesse L, Berg IL, Veselis A, Jeffreys AJ, May CA. Transmission distortion affecting human noncrossover but not crossover recombination: a hidden source of meiotic drive. PLoS Genet. 2014;10(2):e1004106.
Article
PubMed
PubMed Central
Google Scholar
Ardlie K, Liu-Cordero SN, Eberle MA, Daly M, Barrett J, Winchester E, Lander ES, Kruglyak L. Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion. Am J Hum Genet. 2001;69(3):582–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Frisse L, Hudson RR, Bartoszewicz A, Wall JD, Donfack J, Di Rienzo A. Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am J Hum Genet. 2001;69(4):831–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jeffreys AJ, May CA. Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nat Genet. 2004;36(2):151–6.
Article
CAS
PubMed
Google Scholar
Gay J, Myers S, McVean G. Estimating meiotic gene conversion rates from population genetic data. Genetics. 2007;177(2):881–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cole F, Baudat F, Grey C, Keeney S, de Massy B, Jasin M. Mouse tetrad analysis provides insights into recombination mechanisms and hotspot evolutionary dynamics. Nat Genet. 2014;46(10):1072–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, et al. Variation in genome-wide mutation rates within and between human families. Nat Genet. 2011;43(7):712–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. 2011;475(7357):493–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kondrashov AS, Shabalina SA. Classification of common conserved sequences in mammalian intergenic regions. Hum Mol Genet. 2002;11(6):669–74.
Article
CAS
PubMed
Google Scholar
Fledel-Alon A, Leffler EM, Guan Y, Stephens M, Coop G, Przeworski M. Variation in human recombination rates and its genetic determinants. PLoS One. 2011;6(6):e20321.
Article
CAS
PubMed
PubMed Central
Google Scholar
Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genet. 2013;9(8):e1003684.
Article
CAS
PubMed
PubMed Central
Google Scholar