Phylogenomics using Compression Distances: Incorporating Rate Heterogeneity and Amino Acid Properties
Article No.: 46, Pages 1 - 6
Abstract
Efforts to reconstruct the tree of life have a long history, but the field has changed fundamentally in the genomic era. Phylogenomics examines evolutionary relationships using very large datasets, so a major problem in the field is the development of unbiased computational methods for tree inference. Sources of bias include sequence alignment errors, discordance among gene trees, and long branch attraction. Distances based on data compression can address sequence alignment errors and analyses of distances may be robust to a major source of discordance among gene trees (incomplete lineage sorting). However, compression distances appear to be susceptible to long branch attraction. This study tested the hypothesis that compression distances can be modified to be more resistant to long branch attraction and found that correcting compression distances for multiple substitutions improved their behavior. Calculating distances after grouping amino acids based on their physicochemical properties incorporated more biological information. The modified compression distances used in this study also made it possible to estimate tree support using a method that closely resembles the bootstrap, the most popular support metric in phylogenomics.
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Index Terms
- Phylogenomics using Compression Distances: Incorporating Rate Heterogeneity and Amino Acid Properties
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