Sequence divergence, functional constraint, and selection in protein evolution.

@article{Fay2003SequenceDF,
  title={Sequence divergence, functional constraint, and selection in protein evolution.},
  author={Justin C. Fay and Chung-I Wu},
  journal={Annual review of genomics and human genetics},
  year={2003},
  volume={4},
  pages={
          213-35
        }
}
  • J. Fay, Chung-I Wu
  • Published 2003
  • Biology, Medicine
  • Annual review of genomics and human genetics
The genome sequences of multiple species has enabled functional inferences from comparative genomics. A primary objective is to infer biological functions from the conservation of homologous DNA sequences between species. A second, more difficult, objective is to understand what functional DNA sequences have changed over time and are responsible for species' phenotypic differences. The neutral theory of molecular evolution provides a theoretical framework in which both objectives can be… Expand
Chromosomal rearrangements are associated with higher rates of molecular evolution in mammals.
TLDR
This work test the hypothesis of a relationship between chromosomal rearrangements and higher rates of molecular evolution by studying the genomic distribution of divergence between 12,000 human-mouse orthologous genes and shows that genes located in genomic regions that have been highly rearranged between the two species presentHigher rates of synonymous and non-synonymous substitution. Expand
Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees
TLDR
It is found that genes active in brain have accumulated more changes on the human than on the chimpanzee lineage, and patterns suggestive of positive selection on sequence changes as well as expression changes are seen. Expand
Functional Evolution of Proteins
TLDR
The first functional clustering and evolutionary analysis of the RCSB Protein Data Bank (RCSB PDB) based on similarities between active‐site structures identified a sequential, step‐wise evolution of protein active‐sites and provides novel insights into the emergence of protein function or changes in substrate specificity based on subtle changes in geometry and amino acid composition. Expand
Is gene duplication a viable explanation for the origination of biological information and complexity?
TLDR
Although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms. Expand
Weighing the evidence for adaptation at the molecular level.
  • J. Fay
  • Biology, Medicine
  • Trends in genetics : TIG
  • 2011
TLDR
It is argued that the common assumption of independence among sites must be relaxed before abandoning the neutral theory of molecular evolution. Expand
Evaluating the role of natural selection in the evolution of gene regulation
TLDR
The various methods that have been used to test for signs of selection in genomic expression data are reviewed and properties of regulatory systems relevant to neutral models of gene expression are discussed. Expand
Evolution of primate gene expression
TLDR
A neutral model where negative selection and divergence time are the major factors is a useful null hypothesis for both transcriptome and genome evolution. Expand
Population genomics of domestic and wild yeasts
TLDR
Rather than one or two domestication events leading to the extant baker’s yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations. Expand
Two decades of suspect evidence for adaptive DNA-sequence evolution – Less negative selection misconstrued as positive selection
TLDR
The two approaches suggest that the variation in the strength of negative selection may be responsible for the bulk of the reported adaptive genome evolution in the last two decades. Expand
Functional Bias and Demographic History Obscure Patterns of Selection among Single-Copy Genes in a Fungal Species Complex
TLDR
It is found that two species have strongly negatively skewed Tajima’s D, while three other have a positive skew, corresponding well with patterns of demographic expansion and contraction, and an attempt is made to mitigate Gene Ontology term overrepresentation. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 121 REFERENCES
Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.
TLDR
A knowledge-based framework in which the maximum likelihood rate of evolution is used to quantify the level of constraint on the identity of a site is proposed and it is shown that functionally divergent sites occur in a cluster of sites interacting with the catalytic residues. Expand
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
Rate variation of DNA sequence evolution in the Drosophila lineages.
TLDR
The higher codon bias in Drosophila yakuba as compared with D. melanogaster and D. simulans was observed in the four AS-C genes, which suggests change(s) in action of natural selection involved in codon usage on these genes. 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
The Adaptive Evolution Database (TAED)
TLDR
Placed in a phylogenetic perspective, candidate genes that are undergoing evolution at the same time in the same lineage can be viewed together and this framework based upon coding sequence evolution can be readily expanded to include other types of evolution. Expand
Adaptive protein evolution in Drosophila
TLDR
It is estimated that 45% of all amino-acid substitutions have been fixed by natural selection, and that on average one adaptive substitution occurs every 45 years in these species. Expand
Positive Darwinian selection after gene duplication in primate ribonuclease genes.
  • J. Zhang, H. Rosenberg, M. Nei
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
It was found that the number of arginine residues increased substantially in a short period of evolutionary time after gene duplication, and these amino acid changes probably produced the novel anti-pathogen function of ECP. Expand
Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover.
TLDR
An analysis of the evolutionary dynamics of transcription factor binding sites whose function had been experimentally verified in promoters of 51 human genes and their sequence to homologous sequences in other primate species and rodents shows extensive divergence. Expand
Episodic adaptive evolution of primate lysozymes
TLDR
This approach can detect adaptive and purifying episodes, and localize them to specific lineages during protein evolution, and detect a previously unsuspected adaptive episode on the lineage leading to the common ancestor of the modern hominoid lysozymes. Expand
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins
TLDR
Relative rates of protein evolution are remarkably constant for the three species groups analyzed here, and deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Expand
...
1
2
3
4
5
...