Genomic Heterogeneity of Background Substitutional Patterns in Drosophila melanogaster
- 1 February 2005
- journal article
- Published by Oxford University Press (OUP) in Genetics
- Vol. 169 (2), 709-722
- https://doi.org/10.1534/genetics.104.032250
Abstract
Mutation is the underlying force that provides the variation upon which evolutionary forces can act. It is important to understand how mutation rates vary within genomes and how the probabilities of fixation of new mutations vary as well. If substitutional processes across the genome are heterogeneous, then examining patterns of coding sequence evolution without taking these underlying variations into account may be misleading. Here we present the first rigorous test of substitution rate heterogeneity in the Drosophila melanogaster genome using almost 1500 nonfunctional fragments of the transposable element DNAREP1_DM. Not only do our analyses suggest that substitutional patterns in heterochromatic and euchromatic sequences are different, but also they provide support in favor of a recombination-associated substitutional bias toward G and C in this species. The magnitude of this bias is entirely sufficient to explain recombination-associated patterns of codon usage on the autosomes of the D. melanogaster genome. We also document a bias toward lower GC content in the pattern of small insertions and deletions (indels). In addition, the GC content of noncoding DNA in Drosophila is higher than would be predicted on the basis of the pattern of nucleotide substitutions and small indels. However, we argue that the fast turnover of noncoding sequences in Drosophila makes it difficult to assess the importance of the GC biases in nucleotide substitutions and small indels in shaping the base composition of noncoding sequences.Keywords
This publication has 37 references indexed in Scilit:
- DNA Variability and Divergence at the Notch Locus in Drosophila melanogaster and D. simulans: A Case of Accelerated Synonymous Site DivergenceGenetics, 2004
- Rapid Sequence Turnover at an Intergenic Locus in DrosophilaMolecular Biology and Evolution, 2004
- DNA Sequence Evolution with Neighbor-Dependent MutationJournal of Computational Biology, 2003
- A Neutral Explanation for the Correlation of Diversity with Recombination Rates in HumansAmerican Journal of Human Genetics, 2003
- Retroelement Distributions in the Human Genome: Variations Associated With Age and Proximity to GenesGenome Research, 2002
- DNA Repair in DrosophilaThe Journal of cell biology, 2000
- Intron size and natural selectionNature, 1999
- The repair of UV-induced cyclobutane pyrimidine dimers in the individual genes Gart, Notch and white from isolated brain tissue of Drosophila melanogasterMutation Research/DNA Repair, 1997
- High intrinsic rate of DNA loss in DrosophilaNature, 1996
- Neither enhanced removal of cyclobutane pyrimidine dimers nor strand-specific repair is found after transcription induction of the β3-tubulin gene in a Drosophila embryonic cell line KcMutation Research/DNA Repair, 1992