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Purifying selection shapes the coincident SNP distribution of primate coding sequences
Chia-Ying Chen1, Li-Yuan Hung1, Chan-Shuo Wu1
1Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
Scientific Reports
|June 4, 2016
Summary
An excess of coincident single nucleotide polymorphisms (coSNPs) exists in human-chimpanzee coding regions, particularly at zero-fold degenerate sites. This pattern, influenced by purifying selection, suggests coSNPs are a signature of primate protein evolution.
Area of Science:
- Evolutionary genetics
- Comparative genomics
- Human-primate divergence
Background:
- Genome-wide studies reveal excess coincident single nucleotide polymorphisms (coSNPs) between humans and chimpanzees, attributed to mutation rate variation.
- The prevalence and characteristics of coSNPs within coding sequences remain largely unexplored.
Purpose of the Study:
- To investigate the presence and patterns of coSNPs in human-chimpanzee coding regions.
- To determine the factors influencing coSNP distribution, especially the difference between zero-fold and nonzero-fold degenerate sites.
Main Methods:
- Calculation of the observed-to-expected ratio of coSNPs (coSNPO/E) for human-chimpanzee orthologous positions.
- Analysis of coSNP distribution across different coding site types (zero-fold vs. nonzero-fold degenerate).
- Statistical assessment of factors including sequence context, ancestral polymorphisms, SNP density, recombination rate, and purifying selection.
Main Results:
- An excess of coSNPs is confirmed in human-chimpanzee coding regions.
- The coSNPO/E ratio is significantly higher at zero-fold than at nonzero-fold degenerate sites.
- Purifying selection strongly influences coSNP distribution in coding sequences, independent of mutation rate.
- coSNPs are less damaging and more associated with human diseases than non-coSNPs.
Conclusions:
- The excess of coSNPs in coding regions is a robust finding across primates, driven by selection.
- coSNPs may serve as evolutionary signatures reflecting constraints and outcomes of primate protein evolution.
- Understanding coSNP patterns offers insights into genetic disease correlations and evolutionary processes.
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