Using Gene Trees with Lineage-Specific Duplicates for Phylogenetic Inference Mitigates the Effects of Long-Branch...

Area of Science:

• Evolutionary biology
• Phylogenetics
• Genomics

Background:

• Traditional species tree inference relies on orthologs, excluding paralogs.
• This focus on single-copy genes limits data availability.
• Recent studies show paralog-based inference is accurate and data-rich.

Purpose of the Study:

• Investigate if larger gene families increase phylogenetic accuracy.
• Propose using gene families with multiple copies to mitigate long-branch attraction.
• Assess the utility of larger gene families for resolving Chelicerate relationships.

Main Methods:

• Simulated phylogenetic datasets to test accuracy with varying gene family sizes.
• Employed maximum parsimony and maximum likelihood inference methods.
• Analyzed Chelicerate genomic data, focusing on scorpion and pseudoscorpion relationships.

Main Results:

• Larger gene families mitigate long-branch attraction, particularly with parsimony or misspecified models.
• Using larger gene families increased support for the scorpion-pseudoscorpion clade in Chelicerates.
• Phylogenetic accuracy improved when utilizing data from larger gene families.

Conclusions:

• Larger gene families offer a valuable alternative to single-copy genes for phylogenetic inference.
• This approach can improve species tree accuracy and resolve challenging evolutionary relationships.
• The use of paralogs in larger gene families presents a promising avenue for future phylogenetic studies.