Strong region-specific heterogeneity in base composition evolution on the Drosophila X chromosome.

@article{citeulike:572007, abstract = {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.}, address = {Penn State University.}, author = {Ko, Wen-Ya Y. and Piao, Shengfu and Akashi, Hiroshi }, citeulike-article-id = {572007}, doi = {10.1534/genetics.105.054346}, issn = {0016-6731}, journal = {Genetics}, keywords = {base, composition, drosophila, evolution, gene, nonstationary, rate, reconstruction, tree, variation}, month = {March}, posted-at = {2006-03-31 23:50:30}, priority = {5}, title = {Strong region-specific heterogeneity in base composition evolution on the Drosophila X chromosome.}, url = {http://dx.doi.org/10.1534/genetics.105.054346}, year = {2006} }

TY - JOUR ID - citeulike:572007 L3 - citeulike-article-id:572007 TI - Strong region-specific heterogeneity in base composition evolution on the Drosophila X chromosome. JF - Genetics AD - Penn State University. SN - 0016-6731 N2 - 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. KW - base KW - composition KW - drosophila KW - evolution KW - gene KW - nonstationary KW - rate KW - reconstruction KW - tree KW - variation AU - Ko, Wen-Ya AU - Piao, Shengfu AU - Akashi, Hiroshi PY - 2006/03/17/ UR - http://dx.doi.org/10.1534/genetics.105.054346 ER -