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Comparative analysis of protein coding sequences from human, mouse and the domesticated pig
Frank Grønlund Jørgensen1, Asger Hobolth, Henrik Hornshøj
1Department of Ecology and Genetics, University of Aarhus, Aarhus C, Denmark. frank@birc.au.dk
BMC Biology
|February 1, 2005
Summary
Comparative analysis of mammalian genes reveals rapid evolutionary splits and varying rates of molecular evolution. Codon models detected positive selection in human, pig, and mouse lineages, highlighting the value of cross-species genomic studies.
Area of Science:
- Genomics
- Molecular Evolution
- Comparative Genomics
Background:
- Leveraging abundant sequence data from model organisms for large-scale molecular evolution studies.
- Utilizing full-length cDNA alignments from human, mouse, pig, and Fugu rubripes (700,000+ nucleotides).
Purpose of the Study:
- Investigate evolutionary relationships among rodents, artiodactyls, and primates.
- Analyze evolutionary rates and detect positive Darwinian selection using codon-based models.
Main Methods:
- Comparative analysis of protein-coding genes across mammalian lineages.
- Application of codon-based models for sequence evolution analysis.
- Phylogenetic analysis using gene trees and unrooted topologies.
Main Results:
- Evidence for rapid evolutionary splits among primates, rodents, and artiodactyls, with rodents often as an outgroup.
- Pig and mouse lineages show higher synonymous substitution rates than humans; non-synonymous rates are more similar.
- Positive Darwinian selection detected in ~5-6% of genes across human, pig, and mouse lineages.
- A significant fraction of unannotated genes may be recently defunct or still functional.
Conclusions:
- Comparative analysis of protein-coding genes across major mammalian lineages.
- Demonstrates the efficacy of codon-based likelihood models in detecting selection.
- Highlights the value of sequencing organisms at diverse phylogenetic distances for comparative studies.