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doi:10.1534/genetics.105.054346
A more recent version of this article appeared on September 1, 2006.
REGULAR RESEARCH PAPERS |
Strong region-specific heterogeneity in base composition evolution on the Drosophila X chromosome
Wen-Ya Ko 1, Shengfu Piao 1 and Hiroshi Akashi 1*
1 Penn State University
* To whom correspondence should be addressed. E-mail: akashi{at}psu.edu.
Submitted on December 5, 2005
Revised on January 13, 2006
Accepted on 10 March 2006
Fluctuations in base composition appear to be prevalent in Drosophila and mammal genome evolution, but their time-scale, genomic breadth, and causes remain obscure. Here, we study base composition evolution within the X chromosomes of Drosophila melanogaster and five of its close relatives. Substitutions were inferred for 14 telomeric and nine non-telomeric X chromosome loci on six extant and two ancestral lineages using a maximum likelihood method. Heterogeneity in GC content evolution is highly localized both within the genome and within the phylogenetic tree. In the lineages leading to D. yakuba and D. orena, GC content at silent sites is increasing rapidly near telomeres, but is decreasing in more proximal (non-telomeric) regions. D. orena shows a 17-fold excess of GC-increasing synonymous changes within a small (~130kb) telomeric region. Intron GC content increases are consistent with fluctuations in mutational processes, but greater GC elevation at synonymous sites suggest contributions of biased gene conversion and/or natural selection. The D. yakuba lineage shows a less extreme elevation of GC content distributed over a wider genetic region (~1.2Mb). A lack of change in GC content for most introns within this region suggests a role of natural selection in regional base composition evolution.
Key Words: Drosophila melanogaster subgroup, X chromosome, base composition evolution, codon bias, telomeric
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