Ongoing GC-Biased Evolution Is Widespread in the Human Genome and Enriched Near Recombination Hot Spots

1000 Genomes Project Consortium, 2010, A map of human genome variation from population-scale sequencing, Nature, 467, 1061, 10.1038/nature09534

Bamber, 1975, The area above the ordinal dominance graph and the area below the receiver operating characteristic graph, J Math Psychol, 12, 387, 10.1016/0022-2496(75)90001-2

Baudat, 2010, PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice, Science, 327, 836, 10.1126/science.1183439

Berg, 2010, Prdm9 variation strongly influences recombination hot-spot activity and meiotic instability in humans, Nat Genet., 42, 859, 10.1038/ng.658

Berglund, 2009, Hotspots of biased nucleotide substitutions in human genes, PLoS Biol, 7, e26, 10.1371/journal.pbio.1000026

Bernardi, 1985, The mosaic genome of warm-blooded vertebrates, Science, 228, 953, 10.1126/science.4001930

Capra, 2011, Substitution patterns are GC-biased in divergent sequences across the metazoans. Revision, Genome Biol Evol, 10.1093/gbe/evr051

Coop, 2007, An evolutionary view of human recombination, Nat Rev Genet., 8, 23, 10.1038/nrg1947

Coop, 2008, High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans, Science, 319, 1395, 10.1126/science.1151851

Dreszer, 2007, Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion, Genome Res., 17, 1420, 10.1101/gr.6395807

Duret, 2008, The impact of recombination on nucleotide substitutions in the human genome, PLoS Genet, 4, e1000071, 10.1371/journal.pgen.1000071

Duret, 2006, A new perspective on isochore evolution, Gene, 385, 71, 10.1016/j.gene.2006.04.030

Duret, 2009, Biased gene conversion and the evolution of mammalian genomic landscapes, Annu Rev Genome Hum G, 10, 285, 10.1146/annurev-genom-082908-150001

Duret, 2009, Comment on “human-specific gain of function in a developmental enhancer”, Science, 323, 714, 10.1126/science.1165848

Duret, 2002, Vanishing gc-rich isochores in mammalian genomes, Genetics, 162, 1837, 10.1093/genetics/162.4.1837

Eyre-Walker, 1999, Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA, Genetics, 152, 675, 10.1093/genetics/152.2.675

Eyre-Walker, 2001, The evolution of isochores, Nat Rev Genet., 2, 549, 10.1038/35080577

Fledel-Alon, 2009, Broad-scale recombination patterns underlying proper disjunction in humans, PLoS Genet, 5, e1000658, 10.1371/journal.pgen.1000658

Fullerton, 2001, Local rates of recombination are positively correlated with GC content in the human genome, Mol Biol Evol., 18, 1139, 10.1093/oxfordjournals.molbev.a003886

Galtier, 2007, Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution, Trends Genet., 23, 273, 10.1016/j.tig.2007.03.011

Gay, 2007, Estimating meiotic gene conversion rates from population genetic data, Genetics, 177, 881, 10.1534/genetics.107.078907

Hernandez, 2007, Context dependence, ancestral misidentification, and spurious signatures of natural selection, Mol Biol Evol, 24, 1792, 10.1093/molbev/msm108

Hernandez, 2007, Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans, Mol Biol Evol, 24, 2196, 10.1093/molbev/msm149

Hill, 1966, The effect of linkage on limits to artificial selection, Genet Res., 8, 269, 10.1017/S0016672300010156

Hillier, 2005, April. Generation and annotation of the DNA sequences of human chromosomes 2 and 4, Nature, 434, 724, 10.1038/nature03466

Holloway, 2006, Allelic recombination and de novo deletions in sperm in the human β-globin gene region, Hum Mol Genetics, 15, 1099, 10.1093/hmg/ddl025

International Chicken Genome Sequencing Consort, 2004, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution, Nature, 432, 695, 10.1038/nature03154

Kaback, 1992, Chromosome size-dependent control of meiotic recombination, Science, 256, 228, 10.1126/science.1566070

Kaback, 1999, Chromosome size-dependent control of meiotic reciprocal recombination in Saccharomyces cerevisiae: The role of crossover interference, Genetics, 152, 1475, 10.1093/genetics/152.4.1475

Katzman, 2010, GC-biased evolution near human accelerated regions, PLoS Genet, 6, e1000960, 10.1371/journal.pgen.1000960

Kent, 2002, The human genome browser at UCSC, Genome Res., 12, 996, 10.1101/gr.229102

Khelifi, 2006, GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates, J Mol Evol, 62, 745, 10.1007/s00239-005-0186-0

Kimura, 1983, The neutral theory of molecular evolution, 10.1017/CBO9780511623486

Kong, 2002, A high-resolution recombination map of the human genome, Nat Genet., 31, 241, 10.1038/ng917

Kong, 2010, Fine-scale recombination rate differences between sexes, populations and individuals, Nature, 467, 1099, 10.1038/nature09525

Kudla, 2006, High guanine and cytosine content increases mRNA levels in mammalian cells, PLoS Biol, 4, e180, 10.1371/journal.pbio.0040180

Lercher, 2002, Can mutation or fixation biases explain the allele frequency distribution of human single nucleotide polymorphisms (SNPs)?, Gene, 300, 53, 10.1016/S0378-1119(02)01040-5

Lercher, 2002, The evolution of isochores: evidence from SNP frequency distributions, Genetics, 162, 1805, 10.1093/genetics/162.4.1805

Marais, 2003, Jun. Biased gene conversion: implications for genome and sex evolution, Trends Genet., 19, 330, 10.1016/S0168-9525(03)00116-1

Meunier, 2004, Recombination drives the evolution of GC-content in the human genome, Mol Biol Evol., 21, 984, 10.1093/molbev/msh070

Myers, 2005, A fine-scale map of recombination rates and hotspots across the human genome, Science, 310, 321, 10.1126/science.1117196

Myers, 2010, Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination, Science, 327, 876, 10.1126/science.1182363

Myers, 2008, A common sequence motif associated with recombination hot spots and genome instability in humans, Nat Genet., 40, 1124, 10.1038/ng.213

Nagylaki, 1983, Evolution of a finite population under gene conversion, Proc Natl Acad Sci U S A, 80, 6278, 10.1073/pnas.80.20.6278

Necşulea, 2011, Meiotic recombination favors the spreading of deleterious mutations in human populations, Hum Mutat, 32, 198, 10.1002/humu.21407

Parvanov, 2010, Prdm9 controls activation of mammalian recombination hotspots, Science, 327, 835, 10.1126/science.1181495

Paten, 2008, Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs, Genome Res., 18, 1814, 10.1101/gr.076554.108

Paten, 2008, Genome-wide nucleotide-level mammalian ancestor reconstruction, Genome Res., 18, 1829, 10.1101/gr.076521.108

Pollard, 2006, Forces shaping the fastest evolving regions in the human genome, PLoS Genet, 2, e168, 10.1371/journal.pgen.0020168

R Development Core Team, 2009, R: a language and environment for statistical computing

Ratnakumar, 2010, Detecting positive selection within genomes: the problem of biased gene conversion, Philos Trans R Soc B Biol Sci, 365, 2571, 10.1098/rstb.2010.0007

Romiguier, 2010, Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes, Genome Res., 20, 1001, 10.1101/gr.104372.109

Spencer, 2006, The influence of recombination on human genetic diversity, PLoS Genet, 2, e148, 10.1371/journal.pgen.0020148

Strathern, 1995, DNA synthesis errors associated with double-strand-break repair, Genetics, 140, 965, 10.1093/genetics/140.3.965

The International Hapmap Consortium, 2007, A second generation human haplotype map of over 3.1 million SNPs, Nature, 449, 851, 10.1038/nature06258

Turney, 2004, Does chromosome size affect map distance and genetic interference in budding yeast?, Genetics, 168, 2421, 10.1534/genetics.104.033555

Webster, 2004, Fixation biases affecting human SNPs, Trends Genet., 20, 122, 10.1016/j.tig.2004.01.005

Webster, 2003, Compositional evolution of noncoding DNA in the human and chimpanzee genomes, Mol Biol Evol, 20, 278, 10.1093/molbev/msg037

Webster, 2005, Male-driven biased gene conversion governs the evolution of base composition in human alu repeats, Mol Biol Evol, 22, 1468, 10.1093/molbev/msi136