DNA variability and divergence at the notch locus in Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergence

Genetics
Vanessa L Bauer DuMontCharles F Aquadro

Abstract

DNA diversity in two segments of the Notch locus was surveyed in four populations of Drosophila melanogaster and two of D. simulans. In both species we observed evidence of non-steady-state evolution. In D. simulans we observed a significant excess of intermediate frequency variants in a non-African population. In D. melanogaster we observed a disparity between levels of sequence polymorphism and divergence between one of the Notch regions sequenced and other neutral X chromosome loci. The striking feature of the data is the high level of synonymous site divergence at Notch, which is the highest reported to date. To more thoroughly investigate the pattern of synonymous site evolution between these species, we developed a method for calibrating preferred, unpreferred, and equal synonymous substitutions by the effective (potential) number of such changes. In D. simulans, we find that preferred changes per "site" are evolving significantly faster than unpreferred changes at Notch. In contrast we observe a significantly faster per site substitution rate of unpreferred changes in D. melanogaster at this locus. These results suggest that positive selection, and not simply relaxation of constraint on codon bias, has contributed to the...Continue Reading

References

Dec 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·F SangerA R Coulson
Jun 20, 1991·Nature·J H McDonald, M Kreitman
Sep 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·C W Birky, J B Walsh
Jan 1, 1996·Molecular Biology and Evolution·E N Moriyama, Jeffrey R Powell
Dec 24, 1997·Molecular Biology and Evolution·V L Bauer, Charles F Aquadro
Apr 29, 1998·Journal of Molecular Evolution·Ziheng Yang, Rasmus Nielsen
Jun 6, 1998·Journal of Molecular Evolution·R M Kliman, A Eyre-Walker
Oct 27, 1998·Journal of Neuroscience Research·P Beatus, U Lendahl
Jan 27, 1999·Seminars in Cell & Developmental Biology·R J Fleming
Feb 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·Dmitri A Petrov, D L Hartl
Apr 30, 1999·Science·S Artavanis-TsakonasR J Lake
Jun 16, 1999·Molecular Biology and Evolution·J A LabateW F Eanes
Sep 4, 1999·Journal of Molecular Evolution·R M Kliman
Feb 10, 2000·Molecular Biology and Evolution·Ziheng Yang, Rasmus Nielsen
Feb 10, 2000·Molecular Biology and Evolution·J D Wall
May 24, 2000·Proceedings of the National Academy of Sciences of the United States of America·David J Begun, P Whitley
Mar 27, 2001·Molecular Biology and Evolution·Toshiyuki Takano-Shimizu
May 24, 2001·Molecular Biology and Evolution·Agustí MuntéCarmen Segarra
Jun 23, 2001·Molecular Biology and Evolution·David J Begun
Aug 28, 2001·Journal of Molecular Evolution·N G Smith, A Eyre-Walker
Oct 30, 2001·Current Opinion in Genetics & Development·H Akashi
Mar 5, 2002·Nature·Nick G C Smith, A Eyre-Walker
Apr 5, 2002·Nature·Carlos D BustamanteD L Hartl
Jun 11, 2002·Biochemical and Biophysical Research Communications·Patricia CortazzoAtilio Deana
Nov 16, 2002·Current Opinion in Genetics & Development·Laurent Duret
Jan 10, 2003·Molecular Biology and Evolution·Willie J SwansonQiaofeng Yang
Mar 29, 2003·Journal of Molecular Evolution·Matej OresicDavid Shalloway

Citations

Nov 20, 2012·Genome Biology and Evolution·Yu-Ping PohDavid J Begun
Aug 30, 2008·Molecular Biology and Evolution·Shamoni MaheshwariDaniel A Barbash
Apr 9, 2009·Molecular Biology and Evolution·Nadia D SinghCharles F Aquadro
Jun 28, 2008·Genome Research·Alisha K HollowayKatherine S Pollard
Nov 6, 2008·Annual Review of Genetics·Ruth Hershberg, Dmitri A Petrov
Jul 21, 2007·BMC Evolutionary Biology·Daniel E Neafsey, James E Galagan
Jun 6, 2013·PLoS Genetics·David S LawrieDmitri A Petrov
Nov 28, 2007·Genetics·Andreas Heger, Chris P Ponting
Sep 7, 2014·Genome Biology and Evolution·Daniel GarriganDaven C Presgraves
Jul 17, 2008·Molecular Ecology·P PavlidisWolfgang Stephan
Oct 2, 2012·Journal of Evolutionary Biology·F Clemente, C Vogl
Nov 10, 2013·PLoS Genetics·Andrew T SchusterMichelle S Longworth
Oct 17, 2012·PLoS Genetics·Josep M ComeronSamuel Bailin
Aug 3, 2016·Journal of Molecular Evolution·Jae Young Choi, Charles F Aquadro
Jun 13, 2003·Trends in Genetics : TIG·Gabriel Marais
Nov 26, 2008·Trends in Genetics : TIG·Vera B Kaiser, Brian Charlesworth
Nov 13, 2007·Nature·Drosophila 12 Genomes ConsortiumIain MacCallum
Feb 12, 2015·G3 : Genes - Genomes - Genetics·Heather A FloresCharles F Aquadro
Aug 22, 2018·Heredity·Inês FragataClaudia Bank

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