The link between orthology relations and gene trees: a correction perspective

Area of Science:

• Computational Biology
• Phylogenetics
• Evolutionary Genomics

Background:

• Traditional gene orthology inference uses gene trees reconciled with species trees.
• Tree-free methods often rely on sequence similarity.
• The formal link between orthology relations and gene trees is an emerging area.

Purpose of the Study:

• To investigate the computational complexity of correcting infeasible gene relation sets.
• To determine the difficulty of minimally correcting gene trees to fit given relations.
• To explore algorithmic perspectives arising from hardness results.

Main Methods:

• Analysis of four variants of relation and gene tree correction problems.
• Application of computational complexity theory, including NP-Hardness proofs.
• Investigation of approximation hardness for related problems.

Main Results:

• Proved that minimally editing a set of gene relations for species tree consistency is NP-Hard.
• Demonstrated that finding a maximum subset of genes with consistent relations is hard to approximate.
• Established the NP-Hardness of minimally editing a gene tree to satisfy given relations.

Conclusions:

• Significant computational challenges exist in correcting gene relations and gene trees.
• The findings imply that exact solutions for these correction problems are likely intractable for large datasets.
• Algorithmic approaches need to consider these hardness results for practical applications in phylogenetics.