TOPAL 2.0: improved detection of mosaic sequences within multiple alignments

Area of Science:

• Evolutionary biology
• Phylogenetics
• Bioinformatics

Background:

• The Dss statistic, proposed by McGuire et al. (1997), is used for detecting recombination in phylogenetic analyses.
• Limitations of the original Dss statistic include poor differentiation between recombination and among-site rate variation, and a lack of statistical significance testing.
• This study addresses these limitations to improve phylogenetic inference.

Purpose of the Study:

• To modify the Dss statistic to better distinguish between recombination and among-site rate variation.
• To introduce a statistical test for assessing the significance of the Dss statistic values.
• To enhance the reliability of recombination detection in phylogenetic analyses.

Main Methods:

• Modification of the Dss statistic to incorporate corrections for among-site rate variation.
• Development of a statistical significance test utilizing parametric bootstrapping.
• Application of the enhanced Dss statistic and test in phylogenetic data analysis.

Main Results:

• A modified Dss statistic is proposed that effectively accounts for among-site rate variation.
• A statistically sound method for testing the significance of the Dss statistic is presented.
• The enhanced statistic and test improve the accuracy of recombination detection.

Conclusions:

• The modified Dss statistic offers improved performance in identifying recombination compared to the original.
• The proposed parametric bootstrapping test provides a robust method for evaluating the statistical significance of recombination signals.
• These advancements contribute to more accurate phylogenetic analyses by refining recombination detection methods.