Jane: a new tool for the cophylogeny reconstruction problem

Abstract

Background: This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools.

Results: The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program.

Conclusions: Jane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.

Figure 1

Top: A simple tanglegram with host tree in black at left and parasite tree in gray on right. The associations φ between tips is shown in dotted lines. Bottom: Two possible reconstructions that explain the relationship between H and P with events labeled.

Figure 2

(a) Strongly incompatible host switching events. Parasite a on edge (u, w) switches to child b on edge (t, v) implying that v occurs after u. Similarly, parasite c on edge (v, y) switches to child d on edge (t, u) implying that u occurs before v. This results in an irreconcilable timing conflict. (b) Weakly incompatible host switching events. Parasite a on edge (t, v) switches to child b on edge (u, w) implying that a occurs after u and thus after c. Similarly, parasite c on edge (t, u) switches to child d on edge (v, z) implying that c occurs after v and thus after a. (c) This conflict can be resolved, for example, by moving one of the landing sites of a host switch earlier in time, incurring an additional loss event at u.

Figure 3

(a) A host tree with three different timings shown in (b), (c), and (d). The numbers underneath each timing indicate the relative time of each vertex in that timing. The timings in (c) and (d) differ only in the relative times of nodes b and c, two nodes that occur at consecutive relative times but such that neither is the parent of the other. Thus, these two timings are said to be neighbors.

Figure 4

The host tree with a randomly selected subtree.

Figure 5

At left, two selected timings, τ₁ and τ₂. The subtree T is removed from τ₁ while only T is kept in τ₂, as indicated by grayed edges and vertices. The new timing τ_new is shown on the right.

Figure 6

The Jane graphical user interface with a selected solution shown in the inset window.