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Keywords:
Reticulate evolution
binary phylogenetic network
tree-based network
2010 MSC:
05C05 (Primary)
05C20
05C25
a b s t r a c t
A tree-based network on a set X of n leaves is said to be universal if any rooted binary phylogenetic tree
on X can be its base tree. Francis and Steel showed that there is a universal tree-based network on X in
the case of n 3, and asked whether such a network exists in general. We settle this problem by proving
that there are innitely many universal tree-based networks for any n 4 1.
& 2016 The Author. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND
license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
1. Introduction
Throughout this paper, n denotes a natural number that is
greater than 1 and X represents the set f1, 2, , ng. All graphs
considered here are directed acyclic graphs. A graph G0 is said to be
a subdivision of a graph G if G0 can be obtained from G by inserting
vertices into arcs of G zero or more times. Given a vertex v of a
graph with indegv outdegv 1, smoothing (or suppressing) v
refers to removing v and then adding an arc from the parent to the
child of v. Two graphs are said to be homeomorphic if they become
isomorphic after smoothing all vertices of in-degree one and outdegree one.
For the reader's convenience, we briey recall the relevant
background from Francis and Steel (2015) (see Semple and Steel,
2003 for the terminology in phylogenetics).
Denition 1.1. A rooted binary phylogenetic network on X is
dened to be a directed acyclic graph (V, A) with the following
properties:
2. Preliminaries
Here, we slightly generalise the concept of tree shapes. Given a
tree-based network N on X, ignoring the labels on the leaves of N
results in an unlabelled tree-based network N with n leaves. We
use the two different types of symbols, such as N and N , to mean
unlabelled and labelled tree-based networks, respectively. Two
0
tree-based networks N and N on X are said to be shape equivalent
0
if N and N are isomorphic. This equivalence relation partitions a
set of the tree-based networks on X into equivalence classes called
tree-based network shapes with n leaves.
http://dx.doi.org/10.1016/j.jtbi.2016.02.023
0022-5193/& 2016 The Author. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
205
Fig. 1. The rst part of the proof of Theorem 3.1. The left panel is an illustration of Un for n 8. The other panels show examples of T n 1 in U n 1 for n 1 8, and the right
panel describes the case of T n 1 T k T n k 1 with k 3.
Fig. 2. The second part of the proof of Theorem 3.1. Left: A crossover ij is dened to
be a pair of crossed additional arcs placed between arcs i and j (i a j) after subdividing both arcs twice. Right: When the two arcs in ij are selected as tree arcs, ij
represents the transposition i j.
rn
8
1
>
>
>
< Pk 1
i 1 ri rn i
>
r k r k 1 Pk 1
>
>
i 1 ri rn i
:
2
if n 2;
if n 2k 1;
if n 2k:
3. Results
Theorem 3.1. For any natural number n 41, there are innitely
many universal tree-based networks on a set X of n leaves.
Proof. First, we will show that there is a universal tree-based
network shape with n leaves. Let Un be a rooted binary phylogenetic network shape with n leaves as illustrated in the left panel of
Comments
We studied Problem 1.4 independently from Louxin Zhang
(Zhang, 2015).
206
Acknowledgements
The author thanks Kenji Fukumizu and the anonymous
reviewers for their careful reading and helpful comments.
References
Francis, A.R., Steel, M., 2015. Which phylogenetic networks are merely trees with
additional arcs? Syst. Biol. 64 (5), 768777, http://dx.doi.org/10.1093/sysbio/syv037.
Harding, E.F., 1971. The probabilities of rooted tree-shapes generated by random bifurcation. Adv. Appl. Probab. 3 (1), 4477, http://www.jstor.org/stable/1426329.
Huson, D.H., Rupp, R., Scornavacca, C., 2010. Phylogenetic Networks: Concepts,
Algorithms and Applications. Cambridge University Press, New York, NY, USA,
ISBN-10: 0521755964, ISBN-13; 9780521755962.
Semple, C., Steel, M., 2003. Phylogenetics, Oxford Lecture Series in Mathematics and
its Applications, vol. 24, Oxford University Press, Oxford.
Zhang, L., 2015. On tree based phylogenetic networks, http://arxiv.org/abs/1509.
01663.
Momoko Hayamizun
Department of Statistical Science, School of Multidisciplinary
Sciences, SOKENDAI (The Graduate University for Advanced Studies),
Tokyo 190-8562, Japan
The Institute of Statistical Mathematics, Tokyo 190-8562, Japan
E-mail address: hayamizu@ism.ac.jp
n
Correspondence address: The Institute of Statistical Mathematics, Tokyo 190-8562,
Japan.