#40 · Systems biology

Parsimony and consistency algorithms for phylogenetic networks and ancestral genomes

The common thread is computing or testing ancestral structure under parsimony and consistency criteria on phylogenetic networks and ancestral genomes. One preprint gives polynomial-time algorithms for checking ancestor-based consistency of rooted and anchored triples through least common ancestors, with and without forbidden triples. A second addresses the parental parsimony score problem on binary, tree-child phylogenetic networks, reporting a first constant-factor approximation together with a new exact result. A third preprint, on bioRxiv, develops an exact small parsimony solver for ancestral genome reconstruction under the DCJ-indel model, using an ILP with indel costs and theoretical bounds to shrink the search space. What is new across these is algorithmic tractability: explicit polynomial-time or approximation guarantees for network-level problems, and exact optimization for genome-level reconstruction under a rearrangement model.