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Detection of lineage-specific evolutionary changes among primate species
Mihaela Pertea1, Geo M Pertea, Steven L Salzberg
1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA. mpertea@umiacs.umd.edu
BMC Bioinformatics
|July 6, 2011
Summary
A new method, DivE, identifies evolutionary selection in primate genomes, including noncoding DNA. It detected thousands of regions with accelerated or constrained evolution, revealing lineage-specific changes.
Area of Science:
- Evolutionary biology
- Genomics
- Comparative genomics
Background:
- Primate genome comparison reveals evolutionary events shaping phenotypes.
- High similarity in primate genomes challenges traditional evolutionary selection detection methods.
Purpose of the Study:
- Develop a novel method to detect evolutionary selection in closely related species.
- Identify regions with rapid or slow evolution, including noncoding DNA.
Main Methods:
- Introduced DivE (Divergence Evolution) method for analyzing evolutionary rates.
- Applied DivE to ENCODE regions across 14 primate species.
- Validated DivE using simulated data and comparison with alternative methods.
Main Results:
- DivE successfully identified thousands of constrained or accelerated evolutionary regions in primate genomes.
- Detected 4942 regions potentially under positive selection, mostly in noncoding DNA.
- Identified 20 proteins that have undergone positive selection.
Conclusions:
- DivE is an effective tool for predicting positive and negative selection in noncoding DNA.
- The method is particularly suited for detecting lineage-specific selection in large genomes.
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