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Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over
Penelope R Haddrill, Daniel L Halligan, Dimitris Tomaras, Brian Charlesworth
Genome Biol. 2007; 8(2): R18. Published online 2007 February 6. doi: 10.1186/gb-2007-8-2-r18
PMCID:
PMC1852418
Abstract Full Text PDF–291K Supplementary Material
 Is Cited by the Following 26 Articles in this Archive:
Mutation Bias is the Driving Force of Codon Usage in the Gallus gallus genome
Yousheng Rao, Guozuo Wu, Zhangfeng Wang, Xuewen Chai, Qinghua Nie, Xiquan Zhang
DNA Res. 2011 December; 18(6): 499–512. Published online 2011 October 27. doi: 10.1093/dnares/dsr035
PMCID:
PMC3223081
Abstract Full Text PDF–431K Supplementary Material
Sequencing and Analysis of Plastid Genome in Mycoheterotrophic Orchid Neottia nidus-avis
Maria D. Logacheva, Mikhail I. Schelkunov, Aleksey A. Penin
Genome Biol Evol. 2011; 3: 1296–1303. Published online 2011 October 4. doi: 10.1093/gbe/evr102
PMCID:
PMC3228488
Abstract Full Text PDF–654K
Massive Changes in Genome Architecture Accompany the Transition to Self-Fertility in the Filamentous Fungus Neurospora tetrasperma
Christopher E. Ellison, Jason E. Stajich, David J. Jacobson, Donald O. Natvig, Alla Lapidus, Brian Foster, Andrea Aerts, Robert Riley, Erika A. Lindquist, Igor V. Grigoriev, John W. Taylor
Genetics. 2011 September; 189(1): 55–69. doi: 10.1534/genetics.111.130690
PMCID:
PMC3176108
Abstract Full Text PDF–1.3M
Signatures of selection in loci governing major colour patterns in Heliconius butterflies and related species
Grace C Wu, Mathieu Joron, Chris D Jiggins
BMC Evol Biol. 2010; 10: 368. Published online 2010 November 29. doi: 10.1186/1471-2148-10-368
PMCID:
PMC3001726
Abstract Full Text PDF–989K Supplementary Material
Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis
Wilson Leung, Christopher D. Shaffer, Taylor Cordonnier, Jeannette Wong, Michelle S. Itano, Elizabeth E. Slawson Tempel, Elmer Kellmann, David Michael Desruisseau, Carolyn Cain, Robert Carrasquillo, Tien M. Chusak, Katazyna Falkowska, Kelli D. Grim, Rui Guan, Jacquelyn Honeybourne, Sana Khan, Louis Lo, Rebecca McGaha, Jevon Plunkett, Justin M. Richner, Ryan Richt, Leah Sabin, Anita Shah, Anushree Sharma, Sonal Singhal, Fine Song, Christopher Swope, Craig B. Wilen, Jeremy Buhler, Elaine R. Mardis, Sarah C. R. Elgin
Genetics. 2010 August; 185(4): 1519–1534. doi: 10.1534/genetics.110.116129
PMCID:
PMC2927774
Abstract Full Text PDF–3.9M
Molecular evolution of genes in avian genomes
Kiwoong Nam, Carina Mugal, Benoit Nabholz, Holger Schielzeth, Jochen BW Wolf, Niclas Backström, Axel Künstner, Christopher N Balakrishnan, Andreas Heger, Chris P Ponting, David F Clayton, Hans Ellegren
Genome Biol. 2010; 11(6): R68. Published online 2010 June 23. doi: 10.1186/gb-2010-11-6-r68
PMCID:
PMC2911116
Abstract Full Text PDF–1.3M Supplementary Material
Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis)
Lynn Y. Huynh, Donna L. Maney, James W. Thomas
Heredity. Author manuscript; available in PMC 2011 October 1.
Published in final edited form as: Heredity. 2011 April; 106(4): 537–546. Published online 2010 June 23. doi: 10.1038/hdy.2010.85
PMCID:
PMC2950911
Abstract Full Text PDF–374K Supplementary Material
Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila
Josefa González, Talia L. Karasov, Philipp W. Messer, Dmitri A. Petrov
PLoS Genet. 2010 April; 6(4): e1000905. Published online 2010 April 8. doi: 10.1371/journal.pgen.1000905
PMCID:
PMC2851572
Abstract Full Text PDF–325K Supplementary Material
On the Utility of Short Intron Sequences as a Reference for the Detection of Positive and Negative Selection in Drosophila
John Parsch, Sergey Novozhilov, Sarah S. Saminadin-Peter, Karen M. Wong, Peter Andolfatto
Mol Biol Evol. 2010 June; 27(6): 1226–1234. Published online 2010 February 11. doi: 10.1093/molbev/msq046
PMCID:
PMC2877998
Abstract Full Text Supplementary Material
Recombination Yet Inefficient Selection along the Drosophila melanogaster Subgroup's Fourth Chromosome
J. Roman Arguello, Yue Zhang, Tomoyuki Kado, Chuanzhu Fan, Ruoping Zhao, Hideki Innan, Wen Wang, Manyuan Long
Mol Biol Evol. 2010 April; 27(4): 848–861. Published online 2009 December 14. doi: 10.1093/molbev/msp291
PMCID:
PMC2877538
Abstract Full Text PDF–478K Supplementary Material
Population Genomic Inferences from Sparse High-Throughput Sequencing of Two Populations of Drosophila melanogaster
Timothy B. Sackton, Rob J. Kulathinal, Casey M. Bergman, Aaron R. Quinlan, Erik B. Dopman, Mauricio Carneiro, Gabor T. Marth, Daniel L. Hartl, Andrew G. Clark
Genome Biol Evol. 2009; 1: 449–465. Published online 2009 November 18. doi: 10.1093/gbe/evp048
PMCID:
PMC2839279
Abstract Full Text PDF–762K Supplementary Material
The Evolutionary Biology of Poxviruses
Austin L. Hughes, Stephanie Irausquin, Robert Friedman
Infect Genet Evol. Author manuscript; available in PMC 2011 January 1.
Published in final edited form as: Infect Genet Evol. 2010 January; 10(1): 50. Published online 2009 October 13. doi: 10.1016/j.meegid.2009.10.001
PMCID:
PMC2818276
Abstract Full Text PDF–636K Supplementary Material
Protein Rates of Evolution Are Predicted by Double-Strand Break Events, Independent of Crossing-over Rates
Claudia C. Weber, Laurence D. Hurst
Genome Biol Evol. 2009; 1: 340–349. Published online 2009 September 2. doi: 10.1093/gbe/evp033
PMCID:
PMC2817428
Abstract Full Text PDF–189K Supplementary Material
Progress and prospects toward our understanding of the evolution of dosage compensation
Beatriz Vicoso, Doris Bachtrog
Chromosome Res. 2009 July; 17(5): 585–602. Published online 2009 July 23. doi: 10.1007/s10577-009-9053-y
PMCID:
PMC2758192
Abstract Full Text PDF–574K
Effective population size and the rate and pattern of nucleotide substitutions
Megan Woolfit
Biol Lett. 2009 June 23; 5(3): 417–420. Published online 2009 April 8. doi: 10.1098/rsbl.2009.0155
PMCID:
PMC2679941
Abstract Full Text PDF–104K
The causes of mutation accumulation in mitochondrial genomes
Maurine Neiman, Douglas R. Taylor
Proc Biol Sci. 2009 April 7; 276(1660): 1201–1209. Published online 2009 January 20. doi: 10.1098/rspb.2008.1758
PMCID:
PMC2660971
Abstract Full Text PDF–233K
Similar rates of protein adaptation in Drosophila miranda and D. melanogaster, two species with different current effective population sizes
Doris Bachtrog
BMC Evol Biol. 2008; 8: 334. Published online 2008 December 18. doi: 10.1186/1471-2148-8-334
PMCID:
PMC2633301
Abstract Full Text PDF–345K Supplementary Material
A new theory of MHC evolution: beyond selection on the immune genes
Cock van Oosterhout
Proc Biol Sci. 2009 February 22; 276(1657): 657–665. Published online 2008 November 4. doi: 10.1098/rspb.2008.1299
PMCID:
PMC2660941
Abstract Full Text PDF–263K Supplementary Material
Reduced purifying selection prevails over positive selection in human copy number variant evolution
Duc-Quang Nguyen, Caleb Webber, Jayne Hehir-Kwa, Rolph Pfundt, Joris Veltman, Chris P. Ponting
Genome Res. 2008 November; 18(11): 1711–1723. doi: 10.1101/gr.077289.108
PMCID:
PMC2577867
Abstract Full Text PDF–672K
Elevated levels of expression associated with regions of the Drosophila genome that lack crossing over
Penelope R Haddrill, Fergal M Waldron, Brian Charlesworth
Biol Lett. 2008 December 23; 4(6): 758–761. Published online 2008 September 9. doi: 10.1098/rsbl.2008.0376
PMCID:
PMC2614156
Abstract Full Text PDF–107K
Positive and Negative Selection on Noncoding DNA in Drosophila simulans
Penelope R. Haddrill, Doris Bachtrog, Peter Andolfatto
Mol Biol Evol. 2008 September; 25(9): 1825–1834. Published online 2008 May 29. doi: 10.1093/molbev/msn125
PMCID:
PMC2734132
Abstract Full Text PDF–290K Supplementary Material
Effects of X-Linkage and Sex-Biased Gene Expression on the Rate of Adaptive Protein Evolution in Drosophila
John F. Baines, Stanley A. Sawyer, Daniel L. Hartl, John Parsch
Mol Biol Evol. 2008 August; 25(8): 1639–1650. Published online 2008 May 13. doi: 10.1093/molbev/msn111
PMCID:
PMC2727381
Abstract Full Text PDF–246K Supplementary Material
The Impact of Recombination on Nucleotide Substitutions in the Human Genome
Laurent Duret, Peter F. Arndt
PLoS Genet. 2008 May; 4(5): e1000071. Published online 2008 May 9. doi: 10.1371/journal.pgen.1000071
PMCID:
PMC2346554
Abstract Full Text PDF–856K Supplementary Material
No effect of recombination on the efficacy of natural selection in primates
Kevin Bullaughey, Molly Przeworski, Graham Coop
Genome Res. 2008 April; 18(4): 544–554. doi: 10.1101/gr.071548.107
PMCID:
PMC2279242
Abstract Full Text PDF–408K
Near-Neutrality: the Leading Edge of the Neutral Theory of Molecular Evolution
Austin L. Hughes
Ann N Y Acad Sci. Author manuscript; available in PMC 2009 July 9.
Published in final edited form as: Ann N Y Acad Sci. 2008; 1133: 162–179. doi: 10.1196/annals.1438.001
PMCID:
PMC2707937
Abstract Full Text PDF–165K
Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
Peter Andolfatto
Genome Res. 2007 December; 17(12): 1755–1762. doi: 10.1101/gr.6691007
Correction in:
Genome Res. 2008 January; 18(1): 197.
PMCID:
PMC2099584
Abstract Full Text PDF–423K Correction
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