constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints

TL;DR

constNJ is a novel algorithm for reconstructing multiple phylogenetic trees that satisfy specified pairwise topological constraints, enabling better modeling of complex evolutionary processes like recombination and hybridization.

Contribution

It introduces constNJ, the first algorithm to estimate sets of trees with enforced rSPR distance constraints, generalizing neighbor-joining for constrained phylogenetic reconstruction.

Findings

Consistent and generalizes neighbor-joining.

Uses maximum agreement partitions to enforce constraints.

Effective in reconstructing trees fitting into recombination networks.

Abstract

This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which must fit into a recombination, hybridization, or similar network. Rather than first finding a set of trees which are optimal according to a phylogenetic criterion (e.g. likelihood or parsimony) and then attempting to fit them into a network, constNJ estimates the trees while enforcing specified rSPR distance constraints. The primary input for constNJ is a collection of distance matrices derived from sequence blocks which are assumed to have evolved in a tree-like manner, such as blocks of an alignment which do not contain any recombination breakpoints. The other input is a set of rSPR constraints for any set of pairs of trees. ConstNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of "maximum agreement partitions" to assure that the resulting trees satisfy the given rSPR distance constraints.