Related Experiment Video
Updated: Aug 8, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Observations of amino acid gain and loss during protein evolution are explained by statistical bias
Richard A Goldstein1, David D Pollock
1Division of Mathematical Biology, National Institute of Medical Research, Mill Hill, London, United Kingdom. richard.goldstein@nimr.mrc.ac.uk
Abstract:
The authors of a recent manuscript in "Nature" claim to have discovered "universal trends" of amino acid gain and loss in protein evolution. Here, we show that this universal trend can be simply explained by a bias that is unavoidable with the 3-taxon trees used in the original analysis. We demonstrate that a rigorously reversible equilibrium model, when analyzed with the same methods as the "Nature" manuscript, yields identical (and in this case, clearly erroneous) conclusions. A main source of the bias is the division of the sequence data into "informative" and "noninformative" sites, which favors the observation of certain transitions.
Related Concept Videos
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Conservation of Protein Domains
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Genetic Drift

