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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Synteny and Evolution02:31

Synteny and Evolution

John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral chromosome underwent...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins.

Tae-Kun Seo1, Hirohisa Kishino

  • 1Professional Programme for Agricultural Bioinformatics, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan. seo@iu.a.u-tokyo.ac.jp

Systematic Biology
|June 24, 2008
PubMed
Summary

Codon models, which analyze DNA substitutions, are superior to amino acid models. Synonymous substitutions provide crucial evolutionary information, even in highly divergent sequences, improving evolutionary inference.

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Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Bioinformatics

Background:

  • Codon and amino acid substitution models are vital for analyzing protein-coding DNA evolution.
  • Codon models estimate both synonymous and nonsynonymous substitutions, while amino acid models focus only on nonsynonymous changes.
  • The arbitrary selection of amino acid models is common, especially for divergent sequences, due to concerns about synonymous substitution saturation.

Purpose of the Study:

  • To statistically compare codon and amino acid substitution models.
  • To develop a method for assessing the informativeness of synonymous substitutions in evolutionary analyses.
  • To determine when amino acid models are appropriate and when codon models offer superior insights.

Main Methods:

  • Proposed a novel procedure to transform 20-dimensional amino acid models into 61-dimensional codon models.
  • Utilized likelihood ratio tests to statistically compare the models.
  • Analyzed theoretical frameworks and real biological sequence data.

Main Results:

  • Demonstrated that amino acid models are a subset of codon models.
  • Showed that synonymous substitutions are highly informative and significantly enhance evolutionary inference.
  • Confirmed the value of synonymous substitutions even for distantly related protein-coding sequences.

Conclusions:

  • Synonymous substitutions carry substantial evolutionary information and should not be disregarded.
  • Amino acid models should only be used after rigorous evaluation, ensuring that synonymous substitutions do not offer critical insights.
  • Codon models provide a more comprehensive framework for evolutionary analysis of protein-coding DNA.