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The $B_2$ index of galled trees

Published online by Cambridge University Press:  10 August 2026

François Bienvenu*
Affiliation:
Université Marie et Louis Pasteur and ETH Zürich
Jean-jil Duchamps*
Affiliation:
Université Marie et Louis Pasteur
Michael Fuchs*
Affiliation:
National Chengchi University
Tsan-cheng Yu*
Affiliation:
Fu Jen Catholic University
*
*Postal address: Laboratoire de mathématiques de Besançon (UMR 6623), Université Marie et Louis Pasteur, Besançon, France. Email: francois.bienvenu@umlp.fr
***Postal address: Laboratoire de mathématiques de Besançon (UMR 6623), Université Marie et Louis Pasteur, Besançon, France. Email: jean-jil.duchamps@umlp.fr
****Postal address: Department of Mathematical Sciences, National Chengchi University, Taipei, Taiwan. Email: mfuchs@nccu.edu.tw
*****Postal address: Department of Mathematics, Fu Jen Catholic University, New Taipei City, Taiwan. Email: tsancheng@mail.fju.edu.tw
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Abstract

In recent years, there has been effort to extend the classical notion of phylogenetic balance, originally defined in the context of trees, to networks. One of the most natural ways to do this is with the so-called $B_2$ index. In this paper, we study the $B_2$ index for a prominent class of phylogenetic networks: galled trees. We show that the $B_2$ index of a uniform leaf-labeled galled tree converges in distribution as the network becomes large. We characterize the corresponding limiting distribution, and provide a way to compute its moments. This is the first time that a balance index has been studied to this level of detail for a random phylogenetic network. One specificity of this work is that we use two different and independent approaches, each with its advantages: analytic combinatorics, and local limits. The analytic combinatorics approach is more direct, as it relies on standard tools, but it involves slightly more complex calculations. Because it has not previously been used to study such questions, the local limit approach requires the development of an extensive framework beforehand; however, this framework is interesting in itself, and can be used to tackle other, similar problems.

Information

Type
Original Article
Copyright
© The Author(s), 2026. Published by Cambridge University Press on behalf of Applied Probability Trust
Figure 0

Figure 1. Example of a galled network with n=8$n = 8$ labeled leaves and two galls. The root is the black circle at the top, and each point where three lines meet is an internal vertex. The direction of the edges is not indicated: they are always pointing downwards. The two galls are highlighted in blue, and the corresponding reticulations are denoted by white squares. The probability p1$p_1$ that the directed random walk ends in leaf 1 is 1/8$1/8$; the probability p3$p_3$ that it ends in leaf 3 is 1/16+1/8$1/16 + 1/8$.

Figure 1

Figure 2. Recursive decomposition of a galled tree G. G is either a leaf (first case after the equality sign) or a root that is not contained in a gall, with two galled trees G1$G_1$ and G2$G_2$ attached to it (second case); or the root itself is in a gall (third case; both sides of the gall are not allowed to be empty at the same time, i.e. k+m⩾1$k+m\geqslant 1$). Note that in the second and third cases, there is a symmetry: it does not matter which side of the gall is drawn to the left versus to the right.

Figure 2

Figure 3. A phylogenetic network G illustrating why Definition 1.4 from [3] may fail. The root is the vertex highlighted in blue on the right, and the white squares denote reticulations. Here B2([G]k)=𝟙{k is odd}$B_2([G]_k) = \unicode{x1D7D9}_{\{k \text{ is odd}\}}$ does not converge.

Figure 3

Figure 4. Examples of infinite DAGs with various numbers of ends. The root is highlighted in blue, and the direction of the edges is not indicated, as they are always oriented away from the root. A$\mathsf{A}$: The infinite star graph, an infinite DAG with no ends. This DAG is not locally finite, and therefore is not a phylogenetic network. B$\mathsf{B}$: The semi-infinite path, a DAG with one end. C$\mathsf{C}$: The DAG obtained by grafting infinite paths to the leaves of the infinite caterpillar. This DAG has ℵ0=Card(N)$\aleph_0 = \text{Card}(\mathbb{N})$ ends. D$\mathsf{D}$: The infinite complete binary tree, a DAG with 2ℵ0=Card(R)$2^{\aleph_0} = \text{Card}(\mathbb{R})$ ends.

Figure 4

Figure 5. Let G be an infinite phylogenetic network, and let v1→v2→⋯$v_1 \to v_2 \to \cdots$ be a ray of G (being infinite and locally finite, G always has at least one ray). Pick a sequence (Gn′)$(G'_n)$ of phylogenetic networks, and let Gn$G_n$ be the phylogenetic network obtained by grafting Gn′$G'_n$ on vn$v_n$. Thus, Gn→G$G_n \to G$. However, by the grafting property, B2(Gn)=B2(G)+pvnB2(Gn′)$B_2(G_n) = B_2(G) + p_{v_n} B_2(G'_n)$ can be arbitrarily large.

Figure 5

Figure 6. The blowup: left, an ordered tree T with its Ulam–Harris labeling; center, the random networks associated with the internal vertices of T; right, the network G resulting from the blowup (with the Ulam–Harris labeling of the vertices of T indicated on the corresponding vertices of G, to make the link between T and G more apparent). Each vertex v∈T$v \in T$ has been ‘replaced’ by the network Γv$\Gamma_{\!v}$; for instance, vertex 3 corresponds to the subgraph of G highlighted in blue, which is isomorphic to Γ3$\Gamma_{\!3}$.

Figure 6

Figure 7. Recursive structure of G (on the left) and of G∗$G_*$ (on the right). The network G is either reduced to a single vertex or obtained by grafting ξ$\xi$ independent copies of itself on the leaves of a network Γ∼νξ$\Gamma \sim \nu_{\xi}$. By contrast, G∗$G_*$ is never reduced to a single vertex: it is obtained by grafting ξ^−1$\hat{\xi}-1$ independent copies of G and an independent copy of itself on the leaves of a network Γ∗∼νξ^$\Gamma_{\!*} \sim \nu_{\hat{\xi}}$.

Figure 7

Figure 8. The heads of size k used in the blowup construction of galled trees, for k=2$k =2$ (left) and k=3$k = 3$ (right). The blue dots are the roots, and the white squares are reticulations. Note that the heads are leaf-labeled.

Figure 8

Figure 9. As previously, the root is highlighted in blue and the edges are pointing downwards. In this example, the sequence (ℓn)$(\ell_n)$ has a limit m∈K∖∂G$m \in \mathcal{K} \setminus \partial G$. Note that this limit corresponds to the union of two ends: although we do not detail this here, it is not too hard to show that the limit in K$\mathcal{K}$ of a sequence of points of ∂G$\partial G$ is always either a leaf or a union of ends.

Figure 9

Figure 10. Two phylogenetic networks for which the Martin boundary differs from K$\mathcal{K}$. Again, the root is highlighted in blue and the edges are pointing downwards. Provided that the weights of the edges going out of a vertex are rational probabilities, by replacing that vertex by a network as in Subsection 3.3, we can assume that the probability that the directed random walk follows an edge is equal to its weight.