Skip Navigation



MBE Advance Access published online on March 21, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msk008
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Material
Right arrow All Versions of this Article:
23/6/1203    most recent
msk008v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Webster, M. T.
Right arrow Articles by Ellegren, H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Webster, M. T.
Right arrow Articles by Ellegren, H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted March 13, 2006

Research Article

Strong Regional Biases in Nucleotide Substitution in the Chicken Genome

Matthew T. Webster 1 *, Erik Axelsson 2, and Hans Ellegren 2

1 Department of Evolution, Genomics and Systematics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Present address: Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
2 Department of Evolution, Genomics and Systematics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden

* To whom correspondence should be addressed.
Matthew T. Webster, E-mail: websterm{at}tcd.ie


  Abstract

Interspersed repeats have emerged as a valuable tool for studying neutral patterns of molecular evolution. Here we analyse variation in the rate and pattern of nucleotide substitution across all autosomes in the chicken genome by comparing present-day CR1 repeat sequences with their ancestral copies and reconstructing nucleotide substitutions with a maximum-likelihood model. The results shed light on the origin and evolution of large-scale heterogeneity in GC content found in the genomes of birds and mammals - the isochore structure. In contrast to mammals, where GC content is becoming homogenised, heterogeneity in GC content is being reinforced in the chicken genome. This is also supported by patterns of substitution inferred from alignments of introns in chicken, turkey and quail. Analysis of individual substitution frequencies is consistent with the biased gene conversion (BGC) model of isochore evolution and it is likely that patterns of evolution in the chicken genome closely resemble those in the ancestral amniote genome, when it is inferred that isochores originated. Microchromosomes and distal regions of macrochromosomes are found to have elevated substitution rates and a more GC-biased pattern of nucleotide substitution. This can largely be accounted for by a strong correlation between GC content and the rate and pattern of substitution. The results suggest that an interaction between increased mutability at CpG motifs and fixation biases due to BGC could explain increased levels of divergence in GC-rich regions.

Keywords: Isochore; base composition; chicken; mutation; recombination.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J HeredHome page
D. E. Janes, T. Ezaz, J. A. Marshall Graves, and S. V. Edwards
Recombination and Nucleotide Diversity in the Sex Chromosomal Pseudoautosomal Region of the Emu, Dromaius novaehollandiae
J. Hered., March 1, 2009; 100(2): 125 - 136.
[Abstract] [Full Text] [PDF]

Home page
 Integr. Comp. Biol.Home page
C. L. Organ, R. G. Moreno, and S. V. Edwards
Three tiers of genome evolution in reptiles
Integr. Comp. Biol., October 1, 2008; 48(4): 494 - 504.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. Peifer, J. E. Karro, and H. H. von Grunberg
Is there an acceleration of the CpG transition rate during the mammalian radiation?
Bioinformatics, October 1, 2008; 24(19): 2157 - 2164.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. Nam and H. Ellegren
The Chicken (Gallus gallus) Z Chromosome Contains at Least Three Nonlinear Evolutionary Strata
Genetics, October 1, 2008; 180(2): 1131 - 1136.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. Brandstrom and H. Ellegren
Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
Genome Res., June 1, 2008; 18(6): 881 - 887.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
G. Abrusan, H.-J. Krambeck, T. Junier, J. Giordano, and P. E. Warburton
Biased Distributions and Decay of Long Interspersed Nuclear Elements in the Chicken Genome
Genetics, January 1, 2008; 178(1): 573 - 581.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. E. Mank, L. Hultin-Rosenberg, E. Axelsson, and H. Ellegren
Rapid Evolution of Female-Biased, but Not Male-Biased, Genes Expressed in the Avian Brain
Mol. Biol. Evol., December 1, 2007; 24(12): 2698 - 2706.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
L. Gordon, S. Yang, M. Tran-Gyamfi, D. Baggott, M. Christensen, A. Hamilton, R. Crooijmans, M. Groenen, S. Lucas, I. Ovcharenko, et al.
Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions
Genome Res., November 1, 2007; 17(11): 1603 - 1613.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. Brandstrom and H. Ellegren
The Genomic Landscape of Short Insertion and Deletion Polymorphisms in the Chicken (Gallus gallus) Genome: A High Frequency of Deletions in Tandem Duplicates
Genetics, July 1, 2007; 176(3): 1691 - 1701.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
J. E. Mank, E. Axelsson, and H. Ellegren
Fast-X on the Z: Rapid evolution of sex-linked genes in birds
Genome Res., May 1, 2007; 17(5): 618 - 624.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. M. Hoffman and E. Birney
Estimating the Neutral Rate of Nucleotide Substitution Using Introns
Mol. Biol. Evol., February 1, 2007; 24(2): 522 - 531.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.