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Extensive parallelism in protein evolution.

Georgii A Bazykin1, Fyodor A Kondrashov, Michael Brudno

  • 1Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-2216, USA.

Biology Direct
|August 21, 2007
PubMed
Summary
This summary is machine-generated.

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Parallel evolution in protein sequences occurs at high rates, several times faster than average but slower than neutral evolution. This suggests most amino acid changes are influenced by weak, non-trivial selection.

Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Genomics

Background:

  • Independent evolutionary lineages typically diverge through accumulating different genetic changes.
  • However, parallel accumulation of identical genetic changes is frequent, particularly for traits with limited states.

Purpose of the Study:

  • To investigate the rate and patterns of parallel evolution in protein-coding sequences across different species.
  • To assess the role of selection in driving these parallel amino acid replacements.

Main Methods:

  • Comparative genomic analysis of three four-species sets: mammals, Drosophila, and yeasts.
  • Quantification of parallel amino acid replacements across independent evolutionary paths within each set.
  • Comparison of observed parallelism rates with neutral evolution expectations.

Related Experiment Videos

Main Results:

  • Parallel amino acid replacements occurred at 50-80% of the rate expected under neutral evolution.
  • The per-site rate of parallel protein evolution was several times higher than the average rate of evolution.
  • This rate was lower than that of neutral sequences, indicating constraints or selection.

Conclusions:

  • High rates of parallel amino acid replacements, though below neutral, support the nearly neutral theory of molecular evolution.
  • A majority of evolutionary amino acid replacements are subject to weak, but significant, selection.
  • The findings suggest constraints on amino acid sites, limiting the number of possible replacements.