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06:03
Procedure for Adaptive Laboratory Evolution of Microorganisms Using a Chemostat
Published on: September 20, 2016
The adaptive evolution database (TAED)
D A Liberles1, D R Schreiber, S Govindarajan
1Departments of Chemistry, University of Florida, Gainesville, FL 32611, USA. liberles@sbc.su.se
Genome Biology
|September 5, 2001
Summary
The Adaptive Evolution Database (TAED) identifies potential positive selection in protein families using evolutionary trees and KA/KS values. This resource aids researchers in finding adaptive evolution examples for further study.
Area of Science:
- Evolutionary Biology
- Genomics
- Bioinformatics
Background:
- The Master Catalog houses evolutionary data for GenBank genes, including alignments and phylogenetic trees.
- This catalog supports large-scale genomic surveys, leading to the development of The Adaptive Evolution Database (TAED).
Purpose of the Study:
- To identify and catalog instances of potential positive adaptation in protein families.
- To provide a resource for researchers studying evolutionary processes and functional changes in proteins.
Main Methods:
- Extracted evolutionary trees and ancestral sequences from the Master Catalog for Chordata and Embryophyta.
- Identified branches with high normalized nonsynonymous to synonymous nucleotide substitution rates (KA/KS values) as indicators of positive selection.
Main Results:
- A significant proportion (10-20%) of examined protein families showed branches with high KA/KS values, suggesting positive selection.
- Most identified candidate adaptive evolution episodes passed a robustness test and were included in TAED.
Conclusions:
- TAED serves as a valuable resource for bioinformaticians and experimental evolutionists.
- The database can be expanded to incorporate additional evolutionary data, such as gene regulation and splicing changes, within a phylogenetic context.
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