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Relationship between amino acid usage and amino acid evolution in primates
Haoxuan Liu1, Zhengqing Xie1, Shengjun Tan1
1State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China.
Gene
|December 21, 2014
Summary
Amino acid usage influences evolutionary patterns across species. This study in primates suggests that amino acid gain and loss trends are linked to usage and compatible with neutral evolution.
Area of Science:
- Evolutionary Biology
- Genomics
- Molecular Evolution
Background:
- Amino acid usage varies across species, with a previously proposed universal trend of amino acid gain and loss.
- This pattern has been suggested to be compatible with neutral evolutionary theory.
Purpose of the Study:
- To investigate the evolutionary patterns of amino acids in primates.
- To analyze the relationship between amino acid usage, mutation, and fixation trends.
- To evaluate the influence of time on amino acid evolution rates and selection.
Main Methods:
- Analysis of nucleotide and protein alignments from 8 primate species.
- Calculation of amino acid gain and loss numbers and inference of evolutionary trends.
- Examination of human single nucleotide polymorphisms (SNPs) to analyze mutational and fixation trends.
- Evaluation of amino acid evolution on different time scales, including dS/dN ratio analysis.
Main Results:
- Amino acid gain/loss values correlate with their usage.
- Human mutational trends for amino acid substitution are highly correlated with fixation trends.
- The rate of increase for significantly increasing amino acids decreases over evolutionary time.
- The dS/dN ratio increases with time elapsed since divergence, indicating purifying selection's role.
Conclusions:
- Amino acid usage is a significant factor shaping observed amino acid evolution patterns.
- The universal trend of amino acid gain and loss is consistent with neutral evolution.
- Both mutation and purifying selection influence amino acid substitution patterns.
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