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Compositional evolution of noncoding DNA in the human and chimpanzee genomes
Matthew T Webster1, Nick G C Smith, Hans Ellegren
1Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. matthew.webster@ebc.uu.se
Molecular Biology and Evolution
|February 25, 2003
Summary
Primate genome evolution shows a weak bias favoring AT to GC mutations, potentially due to selection or gene conversion. This fixation bias is subtle, as genomes homogenize GC content over time.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Noncoding DNA plays a crucial role in genome evolution.
- Understanding nucleotide substitution patterns is key to deciphering evolutionary processes.
- Primate genomes offer a valuable model for studying long-term evolutionary changes.
Purpose of the Study:
- To investigate the compositional evolution of noncoding DNA in the primate lineage.
- To compare nucleotide substitution patterns between fixed and polymorphic sites.
- To identify potential biases in mutation fixation and their underlying mechanisms.
Main Methods:
- Analysis of 1.8 Mb of genomic alignments from human, chimpanzee, and baboon.
- Utilizing 6542 human single-nucleotide polymorphisms (SNPs) rooted with chimpanzee sequence.
- Examining GC to AT and AT to GC changes at both fixed and polymorphic sites.
Main Results:
- A significant difference in compositional evolution between fixed and polymorphic sites was observed.
- Evidence suggests a bias toward fixation of AT to GC mutations, possibly from selection or biased gene conversion.
- While AT to GC polymorphisms show slightly higher frequencies in high GC regions, overall substitution data indicate genome-wide homogenization of GC content.
Conclusions:
- A weak fixation bias favoring higher GC content exists in primate noncoding DNA.
- This bias is counteracted by forces leading to compositional homogenization across human and chimpanzee genomes.
- Regional GC content does not significantly impact nucleotide substitution rates in Alu repeats, suggesting limited regional mutation bias variation.