Biologically feasible gene trees, reconciliation maps and informative triples

Area of Science:

• Computational Biology
• Evolutionary Genomics
• Phylogenetics

Background:

• Gene family histories are reconstructed using event-labeled gene trees derived from orthologous, paralogous, or xenologous gene relationships.
• Biological feasibility of inferred gene trees is assessed by determining if a true evolutionary history can explain the observed gene tree topology.
• Reconciliation mapping, or DTL-scenario construction, is a standard method to reconcile gene trees with species trees, even when the species tree is unknown.

Purpose of the Study:

• To characterize the conditions for a valid reconciliation map between binary event-labeled gene trees and an unknown species tree.
• To develop methods for inferring the unknown species tree topology from gene tree properties.
• To investigate the limitations of informative triples and DTL-scenarios in establishing biological feasibility for gene trees.

Main Methods:

• Characterization of binary event-labeled gene trees using 'informative' triples that reveal species tree topology.
• Inference of unknown species trees based on informative triples present in gene trees.
• Development of a polynomial-time algorithm to determine the existence of a species tree for a given gene tree and construct it if possible.

Main Results:

• Informative triples can be used to infer the topology of an unknown species tree for binary gene trees.
• A polynomial-time algorithm is presented for species tree inference and reconciliation map construction.
• The study demonstrates that while reconciliation maps imply biological feasibility, the converse is not always true, and informative triples have limitations for relaxed DTL-scenarios and non-binary gene trees.

Conclusions:

• Informative triples provide a method for inferring species trees and assessing biological feasibility of gene trees.
• The developed algorithm efficiently determines species tree compatibility and constructs reconciliation maps.
• Limitations exist in using informative triples and standard DTL-scenarios for complex evolutionary scenarios, particularly with non-binary gene trees.