Bayesian Analysis Suggests that Most Amino Acid Replacements in Drosophila Are Driven by Positive Selection

@article{Sawyer2003BayesianA,
  title={
Bayesian Analysis Suggests that Most Amino Acid Replacements in Drosophila Are Driven by Positive Selection
},
  author={S. Sawyer and R. Kulathinal and C. Bustamante and D. Hartl},
  journal={Journal of Molecular Evolution},
  year={2003},
  volume={57},
  pages={S154-S164}
}
One of the principal goals of population genetics is to understand the processes by which genetic variation within species (polymorphism) becomes converted into genetic differences between species (divergence). In this transformation, selective neutrality, near neutrality, and positive selection may each play a role, differing from one gene to the next. Synonymous nucleotide sites are often used as a uniform standard of comparison across genes on the grounds that synonymous sites are subject to… Expand
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References

SHOWING 1-10 OF 48 REFERENCES
Testing the neutral theory of molecular evolution with genomic data from Drosophila
TLDR
The difference between polymorphism and divergence is limited to only a fraction of the genes, which are also evolving more rapidly, and this implies that positive selection is responsible, which suggests a rate of adaptive evolution that is far higher than permitted by the neutral theory of molecular evolution. Expand
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
Population genetics of polymorphism and divergence.
TLDR
The approach provides a theoretical basis for the use of a 2 x 2 contingency table to compare fixed differences and polymorphic sites with silent sites and amino acid replacements and suggests the estimate that the number of amino acids in the enzyme that are susceptible to favorable mutation is in the range 2-23 at any one time. Expand
Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA.
TLDR
An excess of unpreferred fixations in 28 genes suggests a relaxation of selection on synonymous mutations in D. melanogaster, and patterns of codon usage and "silent" DNA divergence suggest that natural selection discriminates among synonymous codons in Drosophila. Expand
Multi-locus selection and the structure of variation at the white gene of Drosophila melanogaster.
TLDR
A multi-locus selection model that combines features from both hypotheses and takes the recent history of D. melanogaster into account may be the best explanation for these data. Expand
Population, evolutionary and genomic consequences of interference selection.
TLDR
It is shown that IS reduces levels of polymorphism and increases low-frequency variants and linkage disequilibrium, in both selected and adjacent neutral mutations, and reasonably small differences in the length of intermediate "neutral" sequences embedded in a region under selection increase the effectiveness of selection on the adjacent selected sequences. Expand
The cost of inbreeding in Arabidopsis
TLDR
In a comparison of amino-acid replacements amongspecies of the mustard weed Arabidopsis with those among species of the fruitfly Drosophila, it is found that there is evidence for predominantly beneficial gene substitutions but predominantly detrimental substitutions inArabidopsis, corroborating a prediction of population genetics theory that species with a high frequency of inbreeding are less efficient in eliminating deleterious mutations. Expand
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.
  • Z. Yang
  • Biology, Medicine
  • Molecular biology and evolution
  • 1998
TLDR
The likelihood analysis confirmed most, but not all, conclusions Messier and Stewart reached using reconstructed ancestral sequences to estimate synonymous and nonsynonymous rates for different lineages. Expand
A screen for fast evolving genes from Drosophila.
  • K. Schmid, D. Tautz
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1997
TLDR
It is concluded that the Drosophila genome harbors a substantial proportion of genes with a very high divergence rate, and an analysis of within-species polymorphisms for one of these sequences reveals an exceptionally high number of polymorphic amino acid positions, indicating that the protein is not under strong negative selection. Expand
A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents.
TLDR
A new likelihood method for detecting constrained evolution at synonymous sites and other forms of nonneutral evolution in putative pseudogenes is presented, finding that, for pseudogene deposited in GC regions similar to those of their paralogs, the assumption of equal rates of silent and replacement site evolution in the pseudogene is upheld. Expand
...
1
2
3
4
5
...