Adaptive protein evolution in Drosophila

@article{Smith2002AdaptivePE,
  title={Adaptive protein evolution in Drosophila},
  author={Nick G. C. Smith and Adam Eyre-Walker},
  journal={Nature},
  year={2002},
  volume={415},
  pages={1022-1024}
}
For over 30 years a central question in molecular evolution has been whether natural selection plays a substantial role in evolution at the DNA sequence level. Evidence has accumulated over the last decade that adaptive evolution does occur at the protein level, but it has remained unclear how prevalent adaptive evolution is. Here we present a simple method by which the number of adaptive substitutions can be estimated and apply it to data from Drosophila simulans and D. yakuba. We estimate… Expand
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References

SHOWING 1-10 OF 25 REFERENCES
Adaptive protein evolution at the Adh locus in Drosophila
TLDR
A simple statistical test of the neutral protein evolution hypothesis is proposed based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus, finding that there are more fixed replacement differences between species than expected. Expand
The neutral theory of molecular evolution
By the early 1960s amino acid sequences of hemoglobins and cytochrome c for many mammals had been determined. When the sequences were compared, investigators began to notice that the number of aminoExpand
Molecular Evidence for Natural Selection
TLDR
A survey of statistical methods for detecting positive selection, which includes tests for balancing selection, for sequence convergence, and for high rates of evolution that cannot be accounted for by neutral models are presented. Expand
Recent Selection on Synonymous Codon Usage in Drosophila
  • R. Kliman
  • Biology, Medicine
  • Journal of Molecular Evolution
  • 1999
TLDR
Polymorphisms were classified as ancestrally preferred or unpreferred for several genes of D. simulans and D. melanogaster to assess whether the two frequency distributions deviated from neutral expectations in the direction predicted by selection on codons. Expand
The genome sequence of Drosophila melanogaster.
TLDR
The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Expand
Positive and negative selection on the human genome.
TLDR
The A/S ratio of fixed differences is greater than that of common SNPs and suggests that a large fraction of protein divergence is adaptive and driven by positive Darwinian selection. Expand
Statistical methods for detecting molecular adaptation
TLDR
Recent statistical methods for detecting molecular adaptation are summarized, and their limitations and possible improvements are discussed. Expand
Drosophila Molecular Phylogenies and Their Uses
TLDR
In the latter part of the century, molecular biology and development have become premier research fields and once again Drosophila is playing a major role. Expand
Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster
TLDR
For 20 gene regions from across the genome, the amount of nucleotide diversity in natural populations of D. melanogaster is positively correlated with the regional rate of recombination, and it is suggested that the correlation may result from genetic hitch-hiking associated with the fixation of advantageous mutants. Expand
The frequency distribution of nucleotide variation in Drosophila simulans.
  • D. Begun
  • Biology, Medicine
  • Molecular biology and evolution
  • 2001
TLDR
This work found that D. simulans has fixed more unpreferred than preferred mutations, suggesting that this lineage has not been at mutation-selection-drift equilibrium at silent sites, and found that X-linked polymorphisms occur at a higher average frequency than polymorphisms on chromosome arm 3R, even though an average X- linked site is significantly less likely to be polymorphic than an average site on 3R. Expand
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2
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