Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

Area of Science:

• Phylogenetics
• Bioinformatics
• Computational Biology

Background:

• Partial gene sequences are more common than full genomes, leading to gappy multiple sequence alignments.
• Staggered gaps in these alignments can impact phylogenetic analysis accuracy, an area needing further understanding.

Purpose of the Study:

• To assess the accuracy of phylogenetic trees generated from gappy alignments using common reconstruction methods.
• To investigate methods for improving phylogenetic accuracy from gappy datasets.

Main Methods:

• Simulation study using Neighbor Joining, Maximum Parsimony, and Maximum Likelihood methods.
• Evaluation of alignment masking (excluding columns/sequences) and alignment subdivision (modeling missing data).

Main Results:

• Gappy alignments substantially compromise phylogenetic accuracy beyond the expected impact of missing data.
• Alignment masking improved accuracy up to 100-fold but excluded 17% of sequences.
• Alignment subdivision offered modest accuracy improvements while retaining nearly all sequences.

Conclusions:

• Partial gene sequences and gappy alignments present significant challenges for phylogenetic inference, particularly in high-throughput phylogenomics.
• Both alignment masking and subdivision enhance phylogenetic accuracy.
• Alignment masking provides greater accuracy improvements but at the cost of data loss; subdivision retains more data with moderate gains.