1. Introduction
1.1. Biological context and main result
Indices of phylogenetic balance—balance indices for short—are summary statistics that quantify the idea that some trees have more symmetries than others. They play a central role in theoretical evolutionary biology, and are also widely used in practical applications. There is a great diversity of balance indices, and their mathematical properties are for the most part well-understood; see [Reference Fischer, Herbst, Kersting, Kühn and Wicke11] for a comprehensive survey.
However, with the growing recognition of the importance of reticulate evolution, phylogenetic networks are increasingly used to describe phylogenies. Extending the definition and study of balance indices to networks is thus becoming an important topic in mathematical phylogenetics, and very recently some authors have started studying extensions of existing balance indices in networks [Reference Zhang30] and designing new balance indices specifically with networks in mind [Reference Knüver, Fischer, Hellmuth and Wicke20].
In that context, one balance index known as the
$B_2$
index stands out. Introduced in the context of trees in [Reference Shao and Sokal25], this balance index had gone largely unnoticed. However, as recently pointed out in [Reference Bienvenu, Cardona and Scornavacca3], where it was studied extensively, its formal definition and its interpretation as a balance index are unchanged in the context of networks; we come back to this in Subsection 1.2.
Although it has been studied for various models of random trees, the distribution of the
$B_2$
index has not been studied for random phylogenetic networks. In this paper, we do so for a natural and well-studied model: uniform leaf-labeled galled trees (note that there is some variation regarding the term galled tree—see [Reference Cardona, Llabrés, Rosselló and Valiente9] for a detailed discussion—and that our use of the term follows the prevalent usage [Reference Huson, Rupp and Scornavacca15] and refers to what are also known as level-1 networks).
We show that the
$B_2$
index of a galled tree
$G_n$
sampled uniformly at random among galled trees with n labeled leaves converges in distribution as n goes to infinity, and we give a characterization of the limiting distribution. We also show the convergence of all pth moments and that, in particular,
$\mathbb{E}[B_2(G_n)]$
converges to a constant
$c = 2.707911858984\ldots$
.
This is the first result of this type for the balance index of a random phylogenetic network: the only comparable result in the current literature is that the expected value of an extension of the Sackin index of a uniform simplex network with n labeled leaves is asymptotically
$\Theta(n^{7/4})$
, as proved in [Reference Zhang30]. However, beyond the fact that this result is less precise than ours, it is not clear that the extension of the Sackin index considered in that paper is a measure of phylogenetic balance. More results concerning the distribution of balance indices in phylogenetic networks are provided in [Reference Fuchs and Gittenberger13]. In this paper, the limiting distribution (after scaling) of various extensions of the Sackin index is studied for several models of phylogenetic networks—including the galled trees considered here—and is shown to be the Airy distribution.
A notable feature of this paper is that we use two very different—and completely independent—approaches to study the asymptotic behavior of
$B_2(G_n)$
:
-
• a combinatorial approach, based on analytic combinatorics;
-
• a probabilistic approach, based on modern tools from the study of branching processes: local limits of conditioned Galton–Watson trees.
The point of presenting these two approaches in the same paper, even though it means proving the main results twice, is that each approach has its advantages and disadvantages. The combinatorial approach is more direct, because it relies on a well-established framework (namely, the method of singularity analysis; see [Reference Flajolet and Sedgewick12]). However, it involves calculations that are very specific to the problem at hand, and while it is possible to characterize the limiting distribution of
$B_2(G_n)$
through its moments, this requires increasingly strenuous calculations as the moments get higher. The probabilistic approach, on the other hand, requires establishing a substantial number of technical preliminaries. This is because, although local limits have become a standard tool in probability theory, there are difficulties regarding the definition of
$B_2$
for infinite phylogenetic networks and its continuity for the local topology. This preliminary work is thus needed to justify the rigorousness of the approach, but the numerical calculations themselves are then fairly simple, and immediately yield a simple recursive characterization of the limiting distribution of
$B_2(G_n)$
. Moreover, now that the technicalities have been worked out, it is straightforward to apply this approach to any other random phylogenetic network with a suitable local limit.
In the rest of this section, we formally define the
$B_2$
index and the class of galled trees. We then split the paper into two independent sections: Section 2 details the combinatorial approach, and Section 3 the probabilistic one. To emphasize the practicality of the latter as a tool to perform concrete computations, only the main ideas of the framework and its application to galled trees are presented in the main text; its technical justification is detailed in the appendices.
1.2. Setting and notation
Let us start by specifying what we mean by phylogenetic network. To prepare the ground for the local limit approach, we include infinite graphs in our definition.
Recall that a directed acyclic graph (DAG) is a directed graph with no directed cycles. It is:
-
• countable if its vertex set is finite or countably infinite;
-
• locally finite if every vertex has finite in-degree and out-degree;
-
• rooted if there is a unique vertex with in-degree 0, called the root, and every vertex v is reachable from the root (that is, there exists a directed path going from the root to v).
Definition 1. A phylogenetic network is a countable, locally finite rooted DAG. Its vertices with out-degree 0, if any, are called the leaves.
Next, we recall the definition of the
$B_2$
index of a finite phylogenetic network, as given in [Reference Bienvenu, Cardona and Scornavacca3]. Extending this definition to infinite phylogenetic networks will be one of the main challenges for the local limit approach.
Let G be a finite phylogenetic network, and let
$X = (X_t)_{t\geqslant 0}$
be the simple random walk on G, started from the root and constrained to follow the direction of the edges: at each step, one of the outgoing edges of the current vertex is chosen uniformly at random, until a leaf is reached. In the rest of this paper, we refer to X simply as the directed random walk on G. For each vertex
$v \in G$
, let
$p_v$
denote the probability that X visits v. In a finite phylogenetic network,
$(p_{\ell})_{\ell \in \mathcal{L}}$
is a probability distribution on
$\mathcal{L}$
, the leaf set of G.
Definition 2. Let G be a finite phylogenetic network. The
$B_2$
index ofG is the Shannon entropy of the probability distribution
$(p_{\ell})_{\ell \in \mathcal{L}}$
induced on the leaves of G by the directed random walk; that is,
We recall, without proof, an elementary but fundamental property of the
$B_2$
index that will be of constant use in this paper. We refer the reader to [Reference Bienvenu, Cardona and Scornavacca3] for a more detailed presentation.
Proposition 1. (Grafting property.) Let
$G_1$
and
$G_2$
be two finite phylogenetic networks, and let G be the phylogenetic network obtained by identifying a leaf
$\ell \in G_1$
with the root of
$G_2$
. Then
where
$p_{\ell}$
denotes the probability that the directed random walk on
$G_1$
ends in
$\ell$
.
We close this subsection by formally defining the class of galled trees that we consider. Since in this paper we work in the context of DAGs, we use the term connectivity to refer to the notion of weak connectivity (that is, connectivity of the underlying undirected graph): there is no risk of confusion with the notion of strong connectivity, as this notion makes little sense for DAGs (whose strongly connected components are reduced to single vertices).
Recall that v is a cut-vertex of G if removing v increases the number of connected components of G. A graph is said to be biconnected if it has no cut-vertices, and a biconnected component is a maximal biconnected subgraph. A biconnected component consisting of a single vertex is said to be trivial.
Finally, a phylogenetic network G is binary either if it is reduced to a single vertex, or if the root has out-degree 2, the leaves have in-degree 1, and every other vertex has either in-degree 1 and out-degree 2 (tree-vertices) or in-degree 2 and out-degree 1 (reticulations).
Definition 3. A galled tree, also known as a level-1 network, is a binary phylogenetic network with no multiedge where each biconnected component has at most one reticulation.
The non-trivial biconnected components of a galled tree are known as its galls. They correspond to undirected cycles made of two directed paths connecting a vertex, known as the root of the gall, to a reticulation. Note that the galls of a galled tree are, by definition, vertex-disjoint; see Figure 1.
Example of a galled network with
$n = 8$
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
$p_1$
that the directed random walk ends in leaf 1 is
$1/8$
; the probability
$p_3$
that it ends in leaf 3 is
$1/16 + 1/8$
.

Our definitions so far make no mention of labelings: they apply to unlabeled, vertex-labeled, and leaf-labeled networks alike. However, the labeling plays an important role in the definition of our model of a random phylogenetic network.
Let
$\mathscr{G}_n$
denote the combinatorial class of galled trees with n leaves labeled with the integers from 1 to n. Note that
$\mathscr{G}_n$
is finite: the sequence
$(\text{Card}\,{\mathscr{G}_n})_{n\geqslant 1}$
is registered as A328122 in the On-Line Encyclopedia of Integer Sequences [1], and was studied extensively in [Reference Bouvel, Gambette and Mansouri8], where an explicit formula was obtained with use of analytic combinatorics. Recently, Stufler [Reference Stufler27] studied
$\mathscr{G}_n$
(and, more generally, level-k networks) using branching processes; his method is the starting point of our probabilistic approach, and we will come back to it later.
Since
$\mathscr{G}_n$
is finite, we can endow it with the uniform distribution: we write
$G_n \sim \mathrm{Unif}(\mathscr{G}_n)$
to denote a phylogenetic network
$G_n$
sampled uniformly at random from
$\mathscr{G}_n$
, and we refer to
$G_n$
as a uniform galled tree with n labeled leaves. Our main object of study in the rest of this paper is the asymptotic behavior of the random variable
$B_2(G_n)$
.
2. Analytic combinatorics approach
In this section, we derive the asymptotic behavior of moments of
$B_2(G_n)$
. To do so, we use a generating function approach that is based on the recursive decomposition of galled trees according to whether the root is in a gall or not; see Figure 2. This decomposition yields explicit expressions for the generating functions of moments, which can then be analyzed with the method of singularity analysis from [Reference Flajolet and Sedgewick12, Chapter VI]. The latter is based on so-called transfer theorems that say, in a nutshell, that if a generating function f(z) is analytic in a suitable large domain
$\Delta$
with a singularity
$\xi\in{\mathbb R}^{+}$
at its boundary and
$f(z)\sim c(1-z/\xi)^{-\alpha}$
as
$z\rightarrow\xi$
in
$\Delta$
, then
$[z^n]\,f(z)\sim cn^{\alpha-1}\xi^{-n}/\Gamma(\alpha)$
as
$n\rightarrow\infty$
, where
$[z^n]\,f(z)$
denotes the nth Taylor coefficient of f(z) at
$z=0$
. More precisely, we use domains
$\Delta$
of the form
with
$r > \vert\xi\vert$
and
$0<\phi_0<\pi/2$
. A function that is analytic in
$\Delta$
(for some r and
$\phi_0$
) is subsequently called
$\Delta$
-analytic at
$\xi$
.
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
$G_1$
and
$G_2$
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.
$k+m\geqslant 1$
). 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.

We first need to recall some results from [Reference Bouvel, Gambette and Mansouri8]. Set
$\mathscr{G}\,:\!=\,\bigcup_{n\geqslant 0}\mathscr{G}_n$
, which is the set of all galled trees. Moreover, we set
which is the (exponential) generating function of the number of galled trees G with
$\vert G\vert \,=\!:\, n$
leaves. Then, from [Reference Bouvel, Gambette and Mansouri8],
\begin{equation}{\text {GT}}(z)=-\frac{\sqrt{2}\sqrt{-4\left(\sqrt{1-8z}-2\right)z+9\sqrt{1-8z}-1}}{4(1-8z)^{1/4}}-\frac{1}{4}\sqrt{1-8z}+\frac{5}{4}.\end{equation}
Thus, for a
$\Delta$
-domain at
$1/8$
,
${\text {GT}}(z)$
is
$\Delta$
-analytic with an expansion at
$z=1/8$
of the form
The above limit is inside the
$\Delta$
-domain and
From this, by the transfer theorems,
compare with Proposition 5.3 in [Reference Bouvel, Gambette and Mansouri8].
Formula (2.1) was also derived with the decomposition mentioned above. (Actually, Bouvel et al. [Reference Bouvel, Gambette and Mansouri8] divided the third case in Figure 2 into two subcases, as this allowed an easier translation into a generating function.) We now extend the analysis to the mean.
Set
where
$B_2(G)$
is the
$B_2$
index of the galled tree G, whose definition we recall:
where
$\mathcal{L}(G)$
denotes the leaf set of G, and
$p_{\ell}$
is the probability of reaching
$\ell$
.
First, consider the case where the root of G is not in a gall. Then it has two galled subtrees
$G_1,G_2$
, and we have
as directly follows from the grafting property.
Next consider the case where the root of G is inside a gall. Assume that
$G_1,\ldots,G_{k}$
and
$\tilde{G}_1,\ldots,\tilde{G}_{m}$
are the galled subtrees attached to the left and right of the cycle (in any order) and
$G_r$
is the galled subtree below the reticulation vertex at the bottom of the gall. Then, for
$k,m\geqslant 0$
with
$k+m\geqslant 1$
, we have
\begin{align*}B_2(G)&=-\sum_{s=1}^{k}\sum_{\ell\in\mathcal{L}(G_s)}\frac{p_{\ell}}{2^{s+1}}\log_2\left(\frac{p_{\ell}}{2^{s+1}}\right)-\sum_{t=1}^{m}\sum_{\ell\in \mathcal{L}(\tilde{G}_t)}\frac{p_{\ell}}{2^{t+1}}\log_2\left(\frac{p_{\ell}}{2^{t+1}}\right)\nonumber\\&\qquad-\sum_{\ell\in\mathcal{L}(G_r)}\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)p_{\ell}\log_2\left(\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)p_{\ell}\right)\nonumber\\&=\sum_{s=1}^{k}\frac{B_2(G_s)}{2^{s+1}}+\sum_{t=1}^{m}\frac{B_2(\tilde{G}_t)}{2^{t+1}}+\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)B_2(G_r)\nonumber\\&\qquad+\sum_{s=1}^{k}\frac{s+1}{2^{s+1}}+\sum_{t=1}^{m}\frac{t+1}{2^{t+1}}-\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)\log_2\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)\nonumber\\\\&=\sum_{s=1}^{k}\frac{B_2(G_s)}{2^{s+1}}+\sum_{t=1}^{m}\frac{B_2(\tilde{G}_t)}{2^{t+1}}+\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)B_2(G_r)\nonumber\\&\qquad+3-\frac{k+3}{2^{k+1}}-\frac{m+3}{2^{m+1}}-\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)\log_2\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right).\end{align*}
We now use the recursive decomposition, which gives
\begin{align}A(z)&=\frac{1}{2}\sum_{G_1,G_2}B_2(G)\frac{z^{\vert G_1\vert+\vert G_2\vert}}{\vert G_1\vert!\vert G_2\vert!}\nonumber\\&\qquad+\frac{1}{2}\sum_{\substack{k,m\geqslant 0\\ k+m\geqslant 1}}\sum_{\substack{G_1,\ldots,G_k \\ \tilde{G}_1,\ldots,\tilde{G}_m \\ G_r}} B_2(G)\frac{z^{\vert G_1\vert+\cdots+\vert G_k\vert+\vert\tilde{G}_1\vert+\cdots+\vert\tilde{G}_m\vert+\vert G_r\vert}}{\vert G_1\vert!\cdots\vert G_k\vert!\vert\tilde{G}_1\vert!\cdots\vert\tilde{G}_m\vert!\vert G_r\vert!},\end{align}
where inside the first and second sums we have to replace
$B_2(G)$
by (2.3) and (2.4), respectively. For the first sum, this gives
\begin{align*}\sum_{G_1,G_2}B_2(G)\frac{z^{\vert G_1\vert+\vert G_2\vert}}{\vert G_1\vert!\vert G_2\vert!}=A(z){\text {GT}}(z)+{\text {GT}}(z)^2.\end{align*}
For the second sum, we have
\begin{align*}&\sum_{\substack{k,m\geqslant 0\\ k+m\geqslant 1}}\sum_{\substack{G_1,\ldots,G_k \\ \tilde{G}_1,\ldots,\tilde{G}_m \\ G_r}} B_2(G)\frac{z^{\vert G_1\vert+\cdots+\vert G_k\vert+\vert\tilde{G}_1\vert+\cdots+\vert\tilde{G}_m\vert+\vert G_r\vert}}{\vert G_1\vert!\cdots\vert G_k\vert!\vert\tilde{G}_1\vert!\cdots\vert\tilde{G}_m\vert!\vert G_r\vert!}\\ &\qquad=A(z)\sum_{\substack{k,m\geqslant 0\\ k+m\geqslant 1}}\left(\sum_{s=1}^{k}\frac{1}{2^{s+1}}+\sum_{t=1}^{m}\frac{1}{2^{t+1}}+\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)\right){\text {GT}}(z)^{k+m}\\ &\qquad\quad+\sum_{\substack{k,m\geqslant 0\\ k+m\geqslant 1}}\left(3-\frac{k+3}{2^{k+1}}-\frac{m+3}{2^{m+1}}\right){\text {GT}}(z)^{k+m+1}\\ &\qquad\quad-\sum_{\substack{k,m\geqslant 0\\ k+m\geqslant 1}}\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)\log_2\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right){\text {GT}}(z)^{k+m+1}\\ &\qquad=A(z)\sum_{\substack{k,m\geqslant 0\\ k+m\geqslant 1}}{\text {GT}}(z)^{k+m}+\sum_{k,m\geqslant 0}\left(3-\frac{k+3}{2^{k+1}}-\frac{m+3}{2^{m+1}}\right){\text {GT}}(z)^{k+m+1}\\ &\qquad\quad-\sum_{k,m\geqslant 0}\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)\log_2\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right){\text {GT}}(z)^{k+m+1}\\ &\qquad=A(z)\left(\frac{1}{({\text {GT}}(z)-1)^2}-1\right)-\frac{{\text {GT}}(z)^2({\text {GT}}(z)-4)}{({\text {GT}}(z)-1)^2({\text {GT}}(z)-2)^2}-h({\text {GT}}(z)),\end{align*}
where
Plugging everything into (2.5) and solving for A(z), we obtain
where
and
We next show that A(z) is
$\Delta$
-analytic (with a
$\Delta$
-domain at
$1/8$
) and derive its expansion as
$z\rightarrow 1/8$
. First note that
$f(\omega)/g(\omega)$
is analytic in
$\vert\omega\vert<1$
. Expanding at
$\rho\approx 0.219$
, we obtain
By plugging into this (2.2), we get
Thus, by the transfer theorems,
which implies for the mean of the
$B_2$
index of a random galled tree
$G_n \sim \mathrm{Unif}(\mathscr{G}_n)$
:
where the numerical evaluation was done with MAPLE. We summarize this in our first result of this section.
Theorem 1. The mean value of the
$B_2$
index of a uniform galled tree with n labeled leaves converges to
$2.707911858984\ldots$
.
The above computations can be generalized to higher moments. More precisely, define
so that
$A^{[0]}(z)={\text {GT}}(z)$
and
$A^{[1]}(z)=A(z)$
. Then, by raising (2.3) and (2.4) to the
$\ell$
th power, plugging them into (2.5), and expanding, we obtain
where
\begin{align*} g_{\ell}(\omega) \,:\!=\, 1-\frac{\omega}{2^{\ell}}&-\sum_{k\geqslant 1}\left(\sum_{s=1}^{k}\frac{1}{2^{(s+1)\ell}}+\left(\frac{1}{2}+\frac{1}{2^{k+1}}\right)^{\ell}\right)\omega^k\\&-\frac{1}{2}\sum_{k,m\geqslant 1}\left(\sum_{s=1}^{k}\frac{1}{2^{(s+1)\ell}}+\sum_{t=1}^{m}\frac{1}{2^{(t+1)\ell}}+\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)^{\ell}\right)\omega^{k+m}\end{align*}
and
\begin{align} f_{\ell}(z) \,:\!=\, &\frac{1}{2}\sum_{\substack{\ell_1+\ell_2+\ell_3=\ell\\\ell_1,\ell_2<\ell}}\binom{\ell}{\ell_1,\ell_2,\ell_3}\frac{1}{2^{\ell_1+\ell_2}}A^{[\ell_1]}(z)A^{[\ell_2]}(z)\nonumber\\&+\frac{1}{2}\sum_{\substack{k,m\geqslant 0\\k+m\geqslant 1}}\sum_{\substack{\ell_1+\cdots+\ell_{k+m+2}=\ell\\\ell_j<\ell,1\leqslant \,j\leqslant k+m+1}}\binom{\ell}{\ell_1,\ldots,\ell_{k+m+2}}\prod_{s=1}^{k}\frac{1}{2^{(s+1)\ell_s}}\prod_{t=1}^{m}\frac{1}{2^{(t+1)\ell_{k+t}}}\nonumber\\&\qquad\qquad\times\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)^{\ell_{k+m+1}}\mu_{k,m}^{\ell_{k+m+2}}\prod_{s=1}^{k}A^{[\ell_s]}(z)\prod_{t=1}^{m+1}A^{[\ell_{k+t}]}(z),\end{align}
where
Now define two sequences
$c_{\ell}$
and
$d_{\ell}$
by
Then we have
$c_{0}=\rho$
and
$d_{0}=1$
, and for
$\ell\geqslant 1$
,
and
where
$f_{\ell}(A^{[j]}(z)\leftrightarrow c_j)$
means that in
$f_{\ell}(z)$
we replace
$A^{[j]}(z)$
with
$j<\ell$
by
$c_j$
and similarly for the numerator of the first fraction on the right-hand side of (2.7).
Finally, by applying singularity analysis as above, we obtain
The above recurrence for
$d_{\ell}$
can be used, for example, to compute
$d_2=7.965561677362\ldots$
(again, e.g., with MAPLE). Thus, we have the following result for the variance.
Theorem 2. The variance of the
$B_2$
index of a uniform galled tree with n labeled leaves converges to
$0.632774946963\ldots$
.
In addition, from (2.8) and the method of moments, we can identify the limit law.
Theorem 3. There exists a random variable B with
$\mathbb{E}[{B^{\ell}}]=d_{\ell}$
whose distribution is the limit distribution of the
$B_2$
index of a uniform galled tree with n labeled leaves, i.e.
where the convergence also holds for all moments.
Remark 1. An explicit construction of the random variable B from Theorem 3 is given in Section 3, where it is obtained as the
$B_2$
index of the infinite phylogenetic network
$G_*$
corresponding to the local limit of uniform leaf-labeled galled trees.
Proof. According to classical results from probability theory (see [Reference Billingsley6, Section 30]), we only have to show that the exponential generating function of
$\sum_{\ell\geqslant 0}d_{\ell}z^{\ell}/\ell!$
has a non-zero radius of convergence. This follows from an estimate of the form
where
$K>0$
is a suitable constant. Such an estimate is derived from the recurrence for
$d_{\ell}$
and induction; see Appendix A.
3. Local limit approach
3.1. General principle
Local limits make it possible to capture certain aspects of the structure of large graphs. Typically, one considers a sequence
$(G_n)$
of finite graphs of increasing size. The idea is then to define a (potentially infinite) rooted graph
$G_{\infty} = \lim_n G_n$
whose structure around the root tends to match the local structure of
$G_n$
‘as seen from a focal vertex’ when n goes to infinity. This focal vertex can be fixed or random, depending on the application.
Let us be more specific and briefly recall the definition of local convergence. First, we need to introduce a notion of restriction of a phylogenetic network.
Definition 4. Let G be a phylogenetic network and let v be a vertex of G. The height of v, which we denote by h(v), is the number of edges of a shortest path going from the root of G to v. The restriction of height k of G, which we denote by
$[G]_k$
, is the subgraph of G induced by its vertices of height at most k.
Note that, because phylogenetic networks are locally finite,
$[G]_k$
is finite for every phylogenetic network G and every
$k\geqslant 0$
. Therefore, it is natural to endow the set of finite phylogenetic networks with the discrete topology and thus say that
$[G_n]_k \to [G]_k$
when there exists N such that for all
$n \geqslant N$
,
$[G_n]_k = [G]_k$
.
Definition 5. A sequence
$(G_n)$
of phylogenetic networks converges locally to the phylogenetic network G if, for all fixed
$k \geqslant 0$
, as n goes to infinity,
$[G_n]_k$
converges to
$[G]_k$
in the discrete topology.
Remark 2. Note that local convergence is metrizable: the metric d defined by
$d(G,G') = \exp(\!-\min\{k \geqslant 0 \,:\, [G]_k \neq [G']_k\})$
, with the convention
$\min\emptyset = +\infty$
, generates the so-called local topology, and
$G_n$
converges locally to G if and only if
$d(G_n, G)\to 0$
. Furthermore, the space
$\mathbb{G}$
of a phylogenetic network equipped with the metric d is separable and complete.
Local convergence has now become a standard tool in probability theory, and we refer the reader to [Reference van der Hofstad28, Chapter 2] for a detailed introduction. Its usefulness comes in great part from the fact that the local limit
$G_{\infty}$
of a sequence
$(G_n)$
of graphs is often more tractable than the finite graphs
$G_n$
. In particular, regions of
$G_n$
that are only ‘asymptotically independent’ can become truly independent in
$G_{\infty}$
. As a result, given a functional f of interest, it is sometimes much easier to compute
$f(G_{\infty})$
than
$f(G_n)$
, and this can yield a simple way to compute
$\lim_n f(G_n)$
. However, for this one must
-
• identify the limit
$G_{\infty}$
as a tractable graph; -
• ensure that f is well-defined for infinite graphs, and that it is continuous for the local topology (or at least along the sequence of interest).
In the case of galled trees, the local limit was identified in [Reference Stufler27] and is indeed highly tractable; see Subsection 3.3. However, the extension of the
$B_2$
index to infinite phylogenetic networks and its continuity are challenging.
3.2. The
$B_2$
index of infinite phylogenetic networks
The definition (Definition 2) of the
$B_2$
index of a finite phylogenetic network as the Shannon entropy of the probability distribution induced on its leaves by the directed random walk X does not immediately extend to infinite networks. This is because the random walk can escape to infinity, without ever ending in a leaf (note that an infinite phylogenetic network may not even have leaves).
In [Reference Bienvenu, Cardona and Scornavacca3, Definition 1.4], it was claimed that a simple way to circumvent this problem is to define the
$B_2$
index of an infinite phylogenetic network G as
$\lim_k B_2([G]_k)$
. However, while this works for trees (Proposition 11 in Appendix D), this is not the case for general phylogenetic networks, because the sequence
$B_2([G]_k)$
may not converge, as the simple example given in Figure 3 shows.
A phylogenetic network G illustrating why Definition 1.4 from [Reference Bienvenu, Cardona and Scornavacca3] may fail. The root is the vertex highlighted in blue on the right, and the white squares denote reticulations. Here
$B_2([G]_k) = \unicode{x1D7D9}_{\{k \text{ is odd}\}}$
does not converge.

To get a general definition, we define a suitable notion of a ‘boundary’ of DAGs on which the random walk X induces a probability distribution. In the finite case, this boundary is simply the leaf set, but in the infinite case it consists of the leaf set and of all ‘directions’ in which X can escape. While there already exist several notions of boundaries to quantify the asymptotic behavior of random walks, such as the Martin boundary [Reference Kemeny, Snell and Knapp18, Chapter 10], we are unaware of a notion of boundary that matches ours. Moreover, here we give an explicit construction that is useful to understand the properties of the
$B_2$
index.
We now give the formal definition of the
$B_2$
index of an arbitrary phylogenetic network, and list some of its most important properties. First, we recall the notion of ends of an infinite graph. Note that here we are working with directed graphs, and therefore that the notion of end that we use differs from the more common notion of end of an undirected graph.
A ray is a one-way infinite directed path
$v_0 \to v_1 \to \cdots$
. Two rays r and r
′ are said to be co-directional, which we denote by
$r$
$r'$
, if there exists a ray r
″, which could be one of r or r
′, that intersects r and r
′ an infinite number of times. It is readily checked that is an equivalence relation.
Definition 6. Let G be a DAG with at least one ray. The equivalence classes of the co-directional relation are called the ends of G.
An infinite DAG that is not locally finite may or may not have ends. However, an infinite phylogenetic network, being locally finite, must have at least one end (since it has at least one ray). Moreover, for any
$\kappa \in \mathbb{N} \cup \{\aleph_0, 2^{\aleph_0}\}$
, there exist phylogenetic networks with
$\kappa$
ends, as illustrated in 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.
$\mathsf{A}$
: The infinite star graph, an infinite DAG with no ends. This DAG is not locally finite, and therefore is not a phylogenetic network.
$\mathsf{B}$
: The semi-infinite path, a DAG with one end.
$\mathsf{C}$
: The DAG obtained by grafting infinite paths to the leaves of the infinite caterpillar. This DAG has
$\aleph_0 = \text{Card}(\mathbb{N})$
ends.
$\mathsf{D}$
: The infinite complete binary tree, a DAG with
$2^{\aleph_0} = \text{Card}(\mathbb{R})$
ends.

Definition 7. Let G be phylogenetic network with leaf set
$\mathcal{L}$
and end set
$\mathcal{E}$
. The boundaryof G is the set
$\partial G = \mathcal{L} \cup \mathcal{E}$
.
In Appendix B, we prove that the limit of the random walk
$(X_t)_{t\geqslant 0}$
is a well-defined random variable
$X_{\infty}$
taking values in
$\partial G$
. We denote its distribution by
$\mu$
. With the usual definition of the Shannon entropy H of an arbitrary probability distribution (see Appendix C), this makes it possible to extend Definition 2 to infinite phylogenetic networks.
Definition 8. Let G be a phylogenetic network. The
$B_2$
indexof G is the Shannon entropy of the probability distribution
$\mu$
induced on the boundary of G by the directed random walk:
$B_2(G) = H(\mu)$
.
The properties of the
$B_2$
index of infinite phylogenetic networks are essentially the same as in the finite case, except that
$B_2$
can now equal
$+\infty$
. In particular, the grafting property still holds for infinite phylogenetic networks. This is proved in Appendix D, where other basic properties of the
$B_2$
index of general phylogenetic networks are provided.
There is, however, one major difficulty with our approach: the
$B_2$
index is not continuous for the local topology. In fact,
$B_2$
is nowhere continuous on the set of infinite phylogenetic networks—in the sense that for every infinite phylogenetic network G there exists a sequence
$(G_n)$
such that
$G_n \to G$
for the local topology but
$B_2(G_n) \not\to B_2(G)$
; see Figure 5. This is because the
$B_2$
index reflects the structure of the boundary of a network, and parts of the boundary can be located infinitely far away from the root, whereas functions that are continuous for the local topology must, by definition, depend on the local structure of the network around the root.
Let G be an infinite phylogenetic network, and let
$v_1 \to v_2 \to \cdots$
be a ray of G (being infinite and locally finite, G always has at least one ray). Pick a sequence
$(G'_n)$
of phylogenetic networks, and let
$G_n$
be the phylogenetic network obtained by grafting
$G'_n$
on
$v_n$
. Thus,
$G_n \to G$
. However, by the grafting property,
$B_2(G_n) = B_2(G) + p_{v_n} B_2(G'_n)$
can be arbitrarily large.

Nevertheless, it is still possible to use local limits to study the
$B_2$
index: indeed,
$B_2$
can be continuous along sequences
$(G_n)$
of interest—in fact, we expect that this should be the case for many biologically relevant models of phylogenetic networks. In Appendix D, we provide general results to study the continuity of
$B_2$
. For instance, Proposition 9 states that if the local limit G of a sequence
$(G_n)$
is such that the directed random walk X gets trapped in a leaf with probability 1, then
Similarly, in Proposition 10 we provide an easy-to-check sufficient condition ensuring that
$\lim_n B_2(G_n) = B_2(G)$
.
In the next subsection, we state our main continuity result (on which our study of the
$B_2$
index of uniform leaf-labeled galled trees relies): that the
$B_2$
index is essentially continuous for a generic class of models of random phylogenetic networks known as blowups of Galton–Watson trees.
3.3. Blowups of Galton–Watson trees
Informally, a blowup of a random rooted tree T is a random phylogenetic network that is obtained by first sampling T and then replacing each internal vertex v by an independent realization
$\Gamma_{\!v}$
of a random phylogenetic network (identifying v with the root of
$\Gamma_{\!v}$
, and each of the children of v with a leaf of
$\Gamma_{\!v}$
; see Figure 6). In this construction, we require that
$\Gamma_{\!v}$
depend on
$d^+(v)$
only, where
$d^+(v)$
denotes the number of children of v in T, and that the matching between the leaves of
$\Gamma_{\!v}$
and the children of v be chosen uniformly at random and independently of everything else.
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
$v \in T$
has been ‘replaced’ by the network
$\Gamma_{\!v}$
; for instance, vertex 3 corresponds to the subgraph of G highlighted in blue, which is isomorphic to
$\Gamma_{\!3}$
.

Formally, let T be a random ordered tree—that is, T is rooted and the children of each vertex
$v \in T$
are ordered from 1 to
$d^+(v)$
—which we view as a subset of the Ulam–Harris tree
$\mathcal{U}$
(see, e.g., [Reference Janson16, Section 6]). Let
$\nu = (\nu_{k})_{k \geqslant 1}$
, where each
$\nu_k$
is a leaf-exchangeable probability distribution on the set of finite phylogenetic networks with k leaves labeled
$1, \ldots, k$
(by leaf-exchangeable, we mean invariant under permutation of the labels of the leaves). Finally, let
$\Gamma = (\Gamma_{\!v}^{k} \,:\, v \in \mathcal{U}, k \geqslant 1)$
be a family of independent phylogenetic networks such that
$\Gamma_{\!v}^{k} \sim \nu_{k}$
and
$\Gamma$
is independent of T.
The blowup of
$T$
with respect to
$\nu$
is the random phylogenetic network obtained from
$(T, \Gamma)$
by glueing the networks
$\Gamma_{\!v} \,:\!=\, \Gamma_{\!v}^{d^+\!(v)}$
, where v ranges over the internal vertices of T, as follows: for each internal vertex
$v \in T$
, let
$u_k$
denote the kth child of v, and for each non-leaf
$u_k$
, identify the root of
$\Gamma_{\!u_k}$
with the leaf of
$\Gamma_{\!v}$
labeled k. Note that the leaves of the resulting network G are not properly labeled, but that they are in bijection with the leaves of T (which are canonically labeled by the Ulam–Harris labeling). To get a leaf-labeled network, we can label the leaves of T (e.g. uniformly at random) and carry over the labels to G; this is irrelevant when we are considering label-invariant functions of G, such as the
$B_2$
index.
Blowups of Galton–Watson trees are a noteworthy class of random phylogenetic networks. Indeed,
-
• Prominent ‘combinatorial’ models of random phylogenetic networks—i.e. models that correspond to the uniform distribution on some relevant class of networks—can be obtained as blowups of (size-conditioned) Galton–Watson trees. For instance, Stufler [Reference Stufler27] proved that this is the case for uniform leaf-labeled level-k networks (and, therefore, for the galled trees considered here, as detailed in Subsection 3.4). Blowups of Galton–Watson trees can also result from biologically relevant evolutionary processes; see [Reference Bienvenu and Duchamps4].
-
• The constrained structure of blowups of Galton–Watson trees makes them highly tractable. In [Reference Stufler27], this was used to obtain asymptotic counting results for level-k networks, as well as an explicit description of their large-scale geometry. Another example illustrating these constraints is given in [Reference Bienvenu and Steel5], where it is proved that if a combinatorial model of phylogenetic networks can be obtained as a blowup of a Galton–Watson tree, then for any fixed subgraph S the fraction of the networks that contain S in the corresponding combinatorial class is either 0 or 1.
The tractability of blowups of Galton–Watson trees comes, with various degrees of directness, from that of the underlying trees. In particular, the remarkable asymptotic behavior of large size-conditioned critical Galton–Watson trees often plays a crucial role. Here we focus only on their local limit, which, as we will see, has a universal structure known as Kesten’s tree.
Definition 9. Let
$\eta = (\eta_i)_{i \geqslant 0}$
be a probability distribution on the integers such that
$\eta_0 > 0$
and
$\sum_{i \geqslant 0} i \eta_i = 1$
. The Kesten tree associated with
$\eta$
is the two-type (spine/regular) Galton–Watson tree
$T_*$
such that:
-
• regular vertices have offspring distribution
$\eta$
, and all of their children are regular vertices; -
• spine vertices have offspring distribution
$\hat{\eta}$
given by
$\hat{\eta}_i = i \eta_i$
, and exactly one of their children (whose order is chosen uniformly) is a spine vertex; -
• the root of
$T_*$
is a spine vertex.
A Kesten tree
$T_*$
is always infinite, and has exactly one ray
$v_0\to v_1\to \cdots$
starting from the root. This ray is known as the spine.
Let T be a Galton–Watson tree with critical offspring distribution
$\eta$
such that
$\eta_0 > 0$
. For all n such that
$\mathbb{P}{(\!\left|T\right|=n)}>0$
, where
$\left|T\right|$
denotes the number of leaves of T, let
$T_n$
denote a random tree distributed as T conditioned to have n leaves. It is well-known that
$T_n\to T_*$
in distribution for the local topology, where
$T_*$
is the Kesten tree associated with
$\eta$
; see, e.g., [Reference Janson16, Theorem 7.1].
Now let G be a blowup of T with respect to some family
$\nu$
of leaf-exchangeable finite random graphs, and let
$G_n$
be distributed as G conditioned to have n leaves, noting that
$G_n$
can equivalently be described as a blowup of
$T_n$
with respect to
$\nu$
. Because the blowup procedure is a local operation, the convergence of
$T_n$
to
$T_*$
implies that
$G_n \to G_*$
in distribution for the local topology, where
$G_*$
is a blowup of
$T_*$
with respect to
$\nu$
.
The following theorem, which we prove in Appendix F, is a continuity criterion for the
$B_2$
index of blowups of Galton–Watson trees.
Theorem 4. With the notation above, assuming that the offspring distribution
$\eta$
is critical, satisfies
$\eta_0>0$
, and has a finite third moment, we have:
-
(i)
$B_2(G_n) \to B_2(G_*)$
in distribution; -
(ii) for all
$p\geqslant 1$
,
$\mathbb{E}{[B_2(G_n)^p]} \to \mathbb{E}{[B_2(G_*)^p]}$
, and all these moments are finite.
Note the assumption in Theorem 4 that the offspring distribution
$\eta$
has a finite third moment. This is because, as already pointed out in Subsection 3.2, the mere convergence of
$G_n$
to
$G_*$
is not sufficient to get the convergence of
$B_2(G_n)$
: we also need to control the speed of convergence. Loosely speaking, we need an upper bound on the total variation distance between
$[G_n]_{k_n}$
and
$[G_*]_{k_n}$
, for suitable sequences
$(k_n)$
. This upper bound comes from a total variation bound for the convergence of Galton–Watson trees: see Proposition 12 in Appendix E. This total variation bound relies on a Berry–Esseen-type local central limit theorem, hence the third moment condition.
Combined with the independence between the base tree and the random networks used in the blowup procedure, the recursive structure of Galton–Watson trees makes it possible to get a simple expression for the expected value of the
$B_2$
index.
Theorem 5. Let T be a Galton–Watson tree whose offspring distribution
$\eta$
is such that
$\eta_0 > 0$
, and let G be a blowup of T with respect to
$\nu$
. Then
where
$\xi \sim \eta$
,
$f(0) = 0$
, and, for
$k \geqslant 1$
,
$f(k) = \mathbb{E}{[B_2(\Gamma_{\!k})]}$
, where
$\Gamma_{\!k} \sim \nu_k$
. If, in addition,
$\eta$
has mean 1 then denoting by
$T_*$
the Kesten tree associated with T and by
$G_*$
the blowup of
$T_*$
with respect to
$\nu$
, we have
where
$\smash{\hat{\xi}}\sim \hat{\eta}$
, the size-biased distribution associated with
$\eta$
; that is,
$\hat{\eta}_k = k\, \eta_k$
.
Proof. First, we use the recursive structure of G (see Figure 7) to characterize the distribution of
$B_2(G)$
. For this, note that
-
• With probability
$\eta_0$
, G is reduced to its root, and
$B_2(G) = 0$
. -
• With probability
$\eta_k$
, the root of T has k children and thus the network
$\Gamma$
associated with it is distributed as
$\nu_k$
. In that case, by the grafting property, (3.1)where
\begin{equation} B_2(G) \mathrel{\overset{d}{=}} B_2(\Gamma) + \sum_{i = 1}^k q_i\,B_2(G^{(i)}), \end{equation}
$G^{(1)}, \ldots, G^{(k)}$
are independent copies of G, and
$q_i$
is the probability that the directed random walk started from the root of
$\Gamma$
reaches its leaf labeled i.
Recursive structure of G (on the left) and of
$G_*$
(on the right). The network G is either reduced to a single vertex or obtained by grafting
$\xi$
independent copies of itself on the leaves of a network
$\Gamma \sim \nu_{\xi}$
. By contrast,
$G_*$
is never reduced to a single vertex: it is obtained by grafting
$\hat{\xi}-1$
independent copies of G and an independent copy of itself on the leaves of a network
$\Gamma_{\!*} \sim \nu_{\hat{\xi}}$
.

We now consider
$G_n$
the subgraph of G that corresponds to the blowup of
$[T]_n$
, for each
$n\geqslant 0$
. Note that
$G_{n+1}$
is composed of finite graphs grafted on
$G_n$
, and that the sequence
$(G_n)_{n\geqslant 0}$
increases to G: it is what we call a stub sequence of G (see Definition 14 in Appendix D). It is not hard to see—and it is proved in Proposition 11—that
$(B_2(G_n))_{n\geqslant 0}$
is non-decreasing and tends to
$B_2(G)$
. Let
$\xi$
denote the number of children of the root of T, and write
$\alpha_n\,:\!=\, \mathbb{E}[B_2(G_n)]$
for conciseness. Conditional on
$\{\xi = k\}$
, we have that
$q_i$
is independent of
$G^{(i)}$
and that
$\sum_{i=1}^k q_i = 1$
. Moreover, each network
$G^{(i)}$
is distributed as G. As a result, by taking expectations in (3.1), we get
\begin{align*} \begin{cases} \;\mathbb{E}{[B_2(G_{n+1}) | \xi = 0]} = 0, \\ \;\mathbb{E}{[B_2(G_{n+1}) | \xi = k]} = \alpha_n + f(k), \end{cases}\end{align*}
where
$f(k) \,:\!=\, \mathbb{E}{[B_2(\Gamma) | \xi = k]}$
. Plugging this in
$\alpha_{n+1} = \sum_{k\geqslant 0} \eta_k \, \mathbb{E}{[B_2(G_{n+1}) | \xi = k]}$
, we get
Solving for
$(\alpha_n)_{n\geqslant 0}$
, we obtain
\begin{align*} \alpha_0=0, \quad \alpha_1 = \mathbb{E}{[\,f(\xi)]}, \dots,\quad \alpha_n = \mathbb{E}{[\,f(\xi)]} \sum_{k=0}^{n-1}(1-\eta_0)^{k} ,\end{align*}
and by taking the limit as
$n\to\infty$
, we get
$\alpha_n \to \alpha \,:\!=\, \mathbb{E}{[B_2(G)]} = \eta_0^{-1} \mathbb{E}{[\,f(\xi)]}$
, proving the first part of the theorem.
Similarly, let
$\smash{\hat{\xi}}$
denote the number of leaves of the root of
$T_*$
, recalling that
$\smash{\hat{\xi}}\sim \hat{\eta}$
, where
$\hat{\eta}$
denotes the size-biased distribution associated with
$\eta$
. Let
$\Gamma_{\!*}$
denote the network associated with the root of
$T_*$
, and set
$\alpha_* \,:\!=\, \mathbb{E}{[B_2(G_*)]}$
. As previously, write
$q_i$
for the probability that the directed random walk started from the root of
$\Gamma_{\!*}$
goes through its leaf labeled i. Finally, let S denote the leaf of
$\Gamma_{\!*}$
through which the spine of
$G_*$
goes, and write
$I = \{1, \ldots, \hat{\xi}\} \setminus \{S\}$
. Then
where
$G^{(1)}, G^{(2)}, \ldots$
are independent copies of G, and
$G'_*$
is an independent copy of
$G_*$
. Similarly, we define
$(G_{*,n})_{n\geqslant 0}$
as a stub sequence of
$G_*$
by removing the part of the graph descending from the nth spinal vertex. Taking expectations and recalling that
$q_1 + \cdots + q_{\hat{\xi}} = 1$
, we get
In this expression,
$\mathbb{E}{[B_2(\Gamma_{\!*})]} = \mathbb{E}{[\,f(\smash{\hat{\xi}}\,)]}$
. Next, to compute
$\mathbb{E}{[q_S]}$
, note that
\begin{align*} \mathbb{E}{[q_S | \Gamma_{\!*}]} = \sum_{i = 1}^{\hat{\xi}} q_i\, \underbrace{\mathbb{P}{(S = i | \Gamma_{\!*})}}_{1/\hat{\xi}} = \frac{1}{\hat{\xi}},\end{align*}
from which it follows that
$\mathbb{E}{[q_S]} = \sum_{k \geqslant 1} \frac{\hat{\eta}_k}{k} =\sum_{k \geqslant 1} \eta_k = 1 - \eta_0 $
. Plugging this in (3.3) and solving for
$(\beta_{n})_{n\geqslant 0}$
, we obtain the desired expression for
$\mathbb{E}{[B_2(G_{*})]} = \lim_{n\to\infty} \beta_{n}$
.
Note that since the function f in Theorem 5 satisfies
$f(k) \leqslant \log_2 k$
for
$k \geqslant 1$
, this implies that if G is a blowup of T then
$\mathbb{E}{[B_2(G)]} \leqslant \mathbb{E}{[B_2(T)]}$
. It is not too hard to see that we have the stronger statement
as proved in Corollary 3 in Appendix F. In particular, this immediately implies that if T is a random tree (not necessarily a Galton–Watson tree) and G is a blowup of T, then
$B_2(T)$
is second-order stochastically dominant over
$B_2(G)$
; see Corollary 4 in Appendix F.
Having introduced all the required tools, we now turn to the study of the
$B_2$
index of uniform leaf-labeled galled trees.
3.4. Application to leaf-labeled galled trees
Let us start by briefly recalling the blowup construction of uniform leaf-labeled galled trees introduced by Stufler [Reference Stufler27]; we refer the reader to that article for a rigorous justification of the sampling procedure outlined below.
Following [Reference Stufler27], let a head of size k be
-
• for
$k = 2$
, a galled tree with 2 labeled leaves; -
• for
$k \geqslant 3$
, a galled tree with a single gall of length
$k+1$
and k labeled leaves.
Let
$a_k$
denote the number of heads of size k, so that
$a_1 = 0$
,
$a_2 = 3$
, and
$a_3 = 9$
; see Figure 8. To count the number of heads of size
$k \geqslant 3$
, first orient the gall and choose the position of the reticulation in the gall (k possibilities), then label the k leaves (
$k!$
possibilities), and finally forget the orientation of the cycle, and observe that each head is obtained exactly twice. This reasoning also works for
$k = 2$
, but in that case we have to add the network consisting of a single cherry. Putting the pieces together, we get
$a_1 = 0$
and, for
$k \geqslant 2$
,
Next, let
$\nu = (\nu_k)_{k\geqslant 2}$
, where
$\nu_k$
denotes the uniform distribution on the heads of size k. It is not too hard to see that if
$T_n$
is a simply generated tree with n leaves (see, e.g., [Reference Janson16]) whose weight sequence is given by
$w_k = a_k / k!$
, then the blowup of
$T_n$
with respect to
$\nu$
is a uniform leaf-labeled galled tree.
The heads of size k used in the blowup construction of galled trees, for
$k =2$
(left) and
$k = 3$
(right). The blue dots are the roots, and the white squares are reticulations. Note that the heads are leaf-labeled.

To show that the simply generated tree
$T_n$
can also be obtained as a conditioned critical Galton–Watson tree, we must find an offspring distribution
$(\eta_k)_{k \geqslant 0}$
with mean 1 that is an exponential tilt of the weight sequence
$(w_k)_{k \geqslant 1}$
—that is, we must find
$\theta > 0$
such that
\begin{align*} \begin{cases} \eta_k = \theta^{k-1} \, w_k \text{ for } k \geqslant 1 \text{ and } \eta_0 = 1 - \sum_{k \geqslant 1} \eta_k & \text{(exponential tilt)}, \\ \sum_{k \geqslant 0} k\,\eta_k = 1 & \text{(criticality).} \end{cases}\end{align*}
Note that the specific form of this exponential tilt (where, to get a probability distribution, we change
$\eta_0$
—instead of multiplying all
$\eta_k$
’s by a constant) is because we are conditioning on the number of leaves (as opposed to the number of vertices).
To find
$\theta$
, set
$g(z) = \sum_{k\geqslant 1} w_k\, z^{k}$
, so that
$\sum_{k\geqslant 1}k\,\eta_k = 1 \iff g'(\theta) = 1$
. Elementary calculations then show that
from which we get
Note in passing that
$\theta$
is also the first-order term in the expansion of the generating function of galled trees at
$z = 1/8$
; see (2.2).
Let us recap the construction.
Proposition 2. Let
$T_n$
be a critical Galton–Watson tree conditioned to have n leaves whose offspring distribution
$(\eta_k)_{k \geqslant 0}$
is defined by
with
$\theta = (5 - \sqrt{17})/4$
. Let
$G_n$
be the blowup of
$T_n$
with respect to
$(\nu_k)_{k\geqslant 2}$
, where
$\nu_k$
denotes the uniform distribution on the set of heads of size k. Then
$G_n$
is uniformly distributed on the set of galled trees with n labeled leaves.
Since the offspring distribution
$\eta$
in Proposition 2 has a finite third moment, it follows from Theorem 4 that as
$n \to \infty$
,
$B_2(G_n)$
converges in distribution and in all moments to
$B_2(G_*)$
, where
$G_*$
is the local limit of
$G_n$
, which, as we have already seen, is the blowup with respect to
$\nu$
of the Kesten tree
$T_*$
associated with
$\eta$
. Therefore,
$\lim_n \mathbb{E}[B_2(G_n)] = \mathbb{E}{[B_2(G_*)]}$
can be computed with use of the expression given in Theorem 5.
Because when
$\xi = 2$
the head can be a cherry (whose structure differs from that of other heads, see Figure 8), it will be convenient to let
$\beta_k$
denote the expected
$B_2$
index of a network
$\Gamma_{\!k}$
sampled uniformly at random among the galled trees with a single gall of length
$k+1$
and k labeled leaves, and to write the function f from Theorem 5 as
$f(2) = \frac{1}{3} + \frac{2}{3} \beta_2$
for
$k = 2$
and
$f(k) = \beta_k$
for
$k\geqslant 3$
.
To compute
$\beta_k$
, orient the gall of
$\Gamma_{\!k}$
uniformly at random, and then number its vertices from 1 to k. For
$r = 0, \ldots, k-1$
, let
$\Gamma_{\!k,r}$
denote the realization of
$\Gamma_{\!k}$
whose reticulation is on the
$(r+1)$
th vertex of the gall—that is, there are r vertices on one side of the gall and
$k-r-1$
on the other. Letting
$\beta_{k, r} = B_2(\Gamma_{\!k, r})$
, we have
\begin{align*} \beta_{k, r} = \sum_{i = 1}^r \frac{i+1}{2^{i+1}} + \sum_{j = 1}^{k-r-1} \frac{j+1}{2^{j+1}} - \left(\frac{1}{2^{r+1}} + \frac{1}{2^{k-r}}\right) \log_2 \left(\frac{1}{2^{r+1}} + \frac{1}{2^{k-r}}\right).\end{align*}
Next we need to integrate over the position of the reticulation, as described by r in the parametrization above. Using the procedure described at the beginning of this subsection to enumerate the heads, we see that r is uniform on
$\{0, \ldots, k-1\}$
. Therefore,
\begin{equation} \beta_k = \frac{1}{k} \sum_{r = 0}^{k-1} \beta_{k, r}.\end{equation}
Finally, by substituting the expression for
$\eta_k$
from Proposition 2 in the expression given in Theorem 5, we get, in the notation of the theorem,
The following theorem summarizes the calculations of this section; compare with the results from Section 2.
Theorem 6. Let
$G_n$
be sampled uniformly at random among the set of galled trees with n labeled leaves. Then as
$n \to \infty$
,
$B_2(G_n)$
converges in distribution and in all moments to a random variable
$B_2(G_*)$
with finite moments of all orders. In particular,
\begin{align*} \mathbb{E}{[B_2(G_*)]} = \frac{1}{2\,\eta_0} \left(3\, \theta + \sum_{k \geqslant 2} (k+1)k\, \theta^{k-1} \beta_k \right),\end{align*}
where
$\theta$
and
$\eta_0$
are explicit algebraic constants given in Proposition 2, and
$\beta_k$
is given in (3.4). Numerically,
$\alpha_* = 2.707911858984\ldots$
.
Remark 3. The recursive structure of
$G^*$
could, in principle, be used to compute the higher moments of
$B_2(G^*)$
. Indeed, raising both sides of (3.2) to the power
$\ell$
and taking expectations, we get a recursion for
$\mathbb{E}{[B_2(G^*)^\ell]}$
involving
$\mathbb{E}{[B_2(G)^\ell]}$
and all lower-order moments. However, the computations quickly become tedious and we did not push this approach further.
Appendix A. The limit law via the method of moments
The main purpose of this appendix is to prove the technical estimate (2.9) (see Lemma 2 below) in order to complete the proof of Theorem 3. Set
\begin{align*}f_{\ell,1}(z)&\,:\!=\, \frac{1}{2}\sum_{\substack{\ell_1+\ell_2+\ell_3=\ell\\\ell_1,\ell_2<\ell}}\binom{\ell}{\ell_1,\ell_2,\ell_3}\frac{1}{2^{\ell_1+\ell_2}}A^{[\ell_1]}(z)A^{[\ell_2]}(z),\\f_{\ell,2}(z)&\,:\!=\,\sum_{k\geqslant 1}\sum_{\substack{\ell_1+\cdots+\ell_{k+2}=\ell\\\ell_j<\ell, 1\leqslant j\leqslant k+1}}\binom{\ell}{\ell_1,\ldots,\ell_{k+2}}\prod_{s=1}^{k}\frac{1}{2^{(s+1)\ell_s}}\hspace{-0.2em}\left(\frac{1}{2}+\frac{1}{2^{k+1}}\right)^{\ell_{k+1}}\hspace{-0.7em}\mu_{k,0}^{\ell_{k+2}}\\&\qquad\quad\times\prod_{s=1}^{k+1}A^{[\ell_s]}(z),\\f_{\ell,3}(z)&\,:\!=\,\frac{1}{2}\sum_{k,m\geqslant 1}\sum_{\substack{\ell_1+\cdots+\ell_{k+m+2}=\ell\\\ell_j<\ell,1\leqslant j\leqslant k+m+1}}\binom{\ell}{\ell_1,\ldots,\ell_{k+m+2}}\prod_{s=1}^{k}\frac{1}{2^{(s+1)\ell_s}}\prod_{t=1}^{m}\frac{1}{2^{(t+1)\ell_{k+t}}}\nonumber\\&\qquad\quad\times\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)^{\ell_{k+m+1}}\mu_{k,m}^{\ell_{k+m+2}}\prod_{s=1}^{k}A^{[\ell_s]}(z)\prod_{t=1}^{m+1}A^{[\ell_{k+t}]}(z)\end{align*}
so that
$f_{\ell}(z)=f_{\ell,1}(z)+f_{\ell,2}(z)+f_{\ell,3}(z)$
; see (2.6), where we have split the last sum of (2.6) into two parts since below we use the first (simpler) part to explain our ideas and then treat the second (more complicated) part without repeating the similar details. Moreover, set
and thus
where the notation is as in Section 2.
We first consider
$c_{\ell}$
, for which we have the following result.
Lemma 1. There exists a constant
$K>0$
such that
$c_{\ell}\leqslant K^\ell\ell!$
for all
$\ell\geqslant 0$
.
Proof. We prove the claim by induction on
$\ell$
, where we take
Note that by this choice, the claim holds for
$1\leqslant \ell\leqslant 9$
. In addition, it trivially holds for
$\ell=0$
. In addition, note that
$g_{\ell}(\rho)$
is increasing in
$\ell$
and
$g_1(\rho)\equiv 0.570194101601\ldots$
. Thus, by (A.1), we have to show that
for
$\ell\geqslant 10$
. We assume that this claim holds for
$\ell'<\ell$
and prove it for
$\ell$
. For this, we estimate
$c_{\ell,i}$
with
$i=1,2,3$
separately.
First, for
$c_{\ell,1}$
, we have
\begin{align}c_{\ell,1} & \leqslant \frac{1}{2}\sum_{\substack{\ell_1+\ell_2+\ell_3=\ell\\ \ell_1,\ell_2<\ell}}\frac{\ell!}{\ell_3!}\frac{1}{2^{\ell_1+\ell_2}}K^{\ell_1+\ell_2}\leqslant \frac{\ell!}{2}\sum_{\substack{\ell_1+\ell_2+\ell_3=\ell\\ \ell_1,\ell_2<\ell}}\frac{K^{\ell-\ell_3}}{2^{\ell-\ell_3}}\nonumber\\&=\frac{\ell!}{2}\left(\frac{K}{2}\right)^{\ell}\sum_{\substack{\ell_1+\ell_2+\ell_3=\ell\\ \ell_1,\ell_2<\ell}}\left(\frac{2}{K}\right)^{\ell_3}\leqslant \frac{\ell!}{2}\left(\frac{K}{2}\right)^\ell\sum_{\ell_3=0}^{\ell}\left(\frac{1}{256}\right)^{\ell_3}\sum_{\substack{\ell_1+\ell_2=\ell-\ell_3\\\ell_1,\ell_2<\ell}}1\nonumber\\&\leqslant K^{\ell}\ell!\left(\frac{1}{2}\right)^{\ell+1}\sum_{\ell_3=0}^{\ell}\left(\frac{1}{256}\right)^{\ell_3}(\ell-\ell_3+1)\nonumber\\&=K^{\ell}\ell!\left(\frac{1}{2}\right)^{\ell+1}\left(\frac{256}{255}\ell+\frac{256^{-\ell}}{65025}+\frac{65024}{65025}\right)\nonumber\\ & \leqslant 0.005390234525\ldots K^{\ell}\ell!,\end{align}
where in the estimate of the second line, we used that
$K\geqslant 512$
, and the last inequality holds for
$\ell\geqslant 10$
.
Next, we consider
$c_{\ell,2}$
. Here we first note that since
$\ell_1+\cdots+\ell_{k+2}=\ell$
, we have
$k+1$
degrees of freedom, i.e.
$\ell_{k+1}$
is fixed if
$\ell_{1},\ldots,\ell_{k}$
and
$\ell_{k+2}$
are decided. We replace
$c_{\ell_{k+1}}$
on the right-hand side of
$c_{\ell,2}$
by
$K^{\ell_{k+1}}\ell_{k+1}!$
except when
$\ell_{k+1}=0$
and
$\ell_{k+1}=1$
, where we replace it by
$\rho$
and
$c_1$
, respectively. This gives
\begin{equation}c_{\ell,2}\leqslant \frac{9}{16}\sum_{k\geqslant 1}\sideset{}{'}\sum\binom{\ell}{\ell_1,\ldots,\ell_{k+2}}\prod_{s=1}^{k}\frac{1}{2^{(s+1)\ell_s}}\mu_{k,0}^{\ell_{k+2}}\left(\prod_{s=1}^{k} c_{\ell_s}\right)K^{\ell_{k+1}}\ell_{k+1}!,\end{equation}
where
$\ell_{k+1}=\ell-\ell_1-\cdots-\ell_{k}-\ell_{k+2}$
, the second sum is over all
$0<\ell_1+\cdots+\ell_{k}+ \ell_{k+2}\leqslant \ell$
with
$\ell_j<\ell,1\leqslant j\leqslant k$
, and we have used that
$\xi_{k,\ell_{k+1}}\leqslant 9/16$
with
\begin{align*}\xi_{k,\ell_{k+1}}=\begin{cases}\rho&\text{if}\ \ell_{k+1}=0,\\\left(\frac{1}{2}+\frac{1}{2^{k+1}}\right)\frac{c_1}{K}&\text{if}\ \ell_{k+1}=1,\\\left(\frac{1}{2}+\frac{1}{2^{k+1}}\right)^{\ell_{k+1}}&\text{if}\ \ell_{k+1}\geqslant 2.\end{cases}\end{align*}
Next, by using
$\mu_{k,0}\leqslant 2$
and plugging the induction hypothesis for
$c_{\ell_s}$
into (A.3) except when
$s\neq k+1$
, where we again use
$\rho$
and
$c_1$
if
$\ell_s=0$
and
$\ell_s=1$
, we have
\begin{align}c_{\ell,2}&\leqslant \frac{9}{16}K^{\ell}\ell!\sum_{k\geqslant 1}\prod_{s=1}^{k}\left(\rho+\frac{c_1}{K2^{s+1}}+\sum_{\ell_s\geqslant 2}\frac{1}{2^{(s+1)\ell_s}}\right)\sum_{\ell_{k+2}=0}^{\infty}\frac{2^{\ell_{k+2}}}{K^{\ell_{k+2}}\ell_{k+2}!}\nonumber\\&\leqslant \frac{9e^{1/256}}{16}K^{\ell}\ell!\sum_{k\geqslant 1}\prod_{s=1}^{k}\left(\rho+\frac{c_1}{K2^{s+1}}+\frac{1}{2^{s+1}(2^{s+1}-1)}\right)\nonumber\\&=0.223033369804\ldots K^{\ell}\ell!,\end{align}
where we used that
$K\geqslant 512$
in the second last step and MAPLE to evaluate the numerical constant.
Similarly, by using
$\mu_{k,m}\leqslant 3$
, we obtain
\begin{align}c_{\ell,3}&\leqslant \frac{\rho e^{3/512}}{2}K^{\ell}\ell!\sum_{k\geqslant 1}\prod_{s=1}^{k}\left(\rho+\frac{c_1}{K2^{s+1}}+\frac{1}{2^{s+1}(2^{s+1}-1)}\right)\nonumber\\&\qquad\qquad\qquad\qquad\times\sum_{m\geqslant 1}\prod_{t=1}^{m}\left(\rho+\frac{c_1}{K2^{t+1}}+\frac{1}{2^{t+1}(2^{t+1}-1)}\right)\nonumber\\&=0.017199020110\ldots K^{\ell}\ell!.\end{align}
Combining (A.2), (A.4), and (A.5), we get
which proves the desired result.
We use this now to prove a similar result for
$d_{\ell}$
.
Lemma 2. There exists a constant
$K>0$
such that
$d_{\ell}\leqslant K^{\ell}\ell!$
for all
$\ell\geqslant 0$
.
Proof. We again use induction on
$\ell$
where the claim holds for
$\ell=0$
. Moreover, we choose K large enough such that the conclusion of Lemma 1 holds and in addition that:
-
•
$K\geqslant \max\left\{d_1,\sqrt{d_2/2},\ldots,\sqrt{d_9/9!},4608c'/c_1,4608d'/d_1\right\}$
; -
•
$\rho\geqslant \max\left\{3c_1/(4K),3^2c_2/(2! 4^2K^2),\ldots,3^{9}c_9/(9!4^9K^9)\right\}$
;
where
$c'\,:\!=\, \max\{c_1,\ldots,c_9\}$
and
$d'\,:\!=\, \max\{d_1,\ldots,d_9\}$
.
By item (i), the claim holds for all
$1\leqslant \ell\leqslant 9$
. Thus, we can assume that
$\ell\geqslant 10$
and that the claim holds for all
$\ell'<\ell$
. We are going to bound
$d_{\ell,i}$
for
$i=1,2,3$
.
First, for
$d_{\ell,1}$
, we have
\begin{align*}f'_{\ell,1}(z)&=\frac{1}{2}\sum_{\substack{\ell_1+\ell_2+\ell_3=\ell\\ \ell_1,\ell_2<\ell}}\binom{\ell}{\ell_1,\ell_2,\ell_3}\frac{1}{2^{\ell_1+\ell_2}}\left((A^{[\ell_1]})'(z)A^{[\ell_2]}(z)+A^{[\ell_1]}(z)(A^{[\ell_2]})'(z)\right)\end{align*}
and thus
\begin{align*}d_{\ell,1} & = \frac{1}{2}\sum_{\substack{\ell_1+\ell_2+\ell_3=\ell\\ \ell_1,\ell_2<\ell}}\binom{\ell}{\ell_1,\ell_2, \ell_3}\frac{1}{2^{\ell_1+\ell_2}}\left(d_{\ell_1}c_{\ell_2}+c_{\ell_1}d_{\ell_2}\right)\\&=\sum_{\substack{\ell_1+\ell_2+\ell_3=\ell\\ \ell_1,\ell_2<\ell}}\binom{\ell}{\ell_1,\ell_2, \ell_3}\frac{1}{2^{\ell_1+\ell_2}}c_{\ell_1}d_{\ell_2}.\end{align*}
Using the induction hypothesis and the estimate from Lemma 1, we obtain
\begin{equation}d_{\ell,1}\leqslant \sum_{\substack{\ell_1+\ell_2+\ell_3=\ell\\ \ell_1,\ell_2<\ell}}\frac{\ell!}{\ell_3!}\frac{1}{2^{\ell_1+\ell_2}}K^{\ell_1+\ell_2}\leqslant 0.010780469050\ldots K^{\ell}\ell!,\end{equation}
which is twice the bound from (A.2).
Next, for
$d_{\ell,2}$
, we have
\begin{align*}f'_{\ell,2}(z)=\sum_{k\geqslant 1}\sum_{\substack{\ell_1+\cdots+\ell_{k+2}=\ell\\ \ell_j<\ell,1\leqslant j\leqslant k+1}}&\binom{\ell}{\ell_1, \ldots,\ell_{k+2}}\prod_{s=1}^k\frac{1}{2^{(s+1)\ell_s}}\left(\frac{1}{2}+\frac{1}{2^{k+1}}\right)^{\ell_{k+1}}\mu_{k,0}^{\ell_{k+2}}\\&\times\left(\sum_{i=1}^{k+1}(A^{[\ell_i]})'(z)\prod_{\substack{1\leqslant j\leqslant k+1\\j\neq i}}A^{[\ell_j]}(z)\right)\end{align*}
and thus
\begin{align*}d_{\ell,2}&=\sum_{k\geqslant 1}\sum_{\substack{\ell_1+\cdots+\ell_{k+2}=\ell\\ \ell_j<\ell,1\leqslant j\leqslant k+1}}\binom{\ell}{\ell_1,\ldots,\ell_{k+2}}\prod_{s=1}^k\frac{1}{2^{(s+1)\ell_s}}\left(\frac{1}{2}+\frac{1}{2^{k+1}}\right)^{\ell_{k+1}}\mu_{k,0}^{\ell_{k+2}}\\&\qquad\qquad\qquad\times\left(\sum_{i=1}^{k+1}d_{\ell_i}\prod_{\substack{j=1\\j\neq i}}^{k+1}c_{\ell_j}\right)\\&=\sum_{k\geqslant 1}\sum_{\substack{\ell_1+\cdots+\ell_{k+2}=\ell\\ \ell_j<\ell,1\leqslant j\leqslant k+1}}\binom{\ell}{\ell_1,\ldots,\ell_{k+2}}\prod_{s=1}^k\frac{1}{2^{(s+1)\ell_s}}\left(\frac{1}{2}+\frac{1}{2^{k+1}}\right)^{\ell_{k+1}}\mu_{k,0}^{\ell_{k+2}}\\&\qquad\qquad\qquad\times\left(\sum_{i=1}^{k}d_{\ell_i}\prod_{\substack{j=1\\j\neq i}}^{k+1}c_{\ell_j}\right)\\&\quad+\sum_{k\geqslant 1}\sum_{\substack{\ell_1+\cdots+\ell_{k+2}=\ell\\ \ell_j<\ell,1\leqslant j\leqslant k+1}}\binom{\ell}{\ell_1,\ldots,\ell_{k+2}}\prod_{s=1}^k\frac{1}{2^{(s+1)\ell_s}}\left(\frac{1}{2}+\frac{1}{2^{k+1}}\right)^{\ell_{k+1}}\mu_{k,0}^{\ell_{k+2}}\\&\qquad\qquad\qquad\times d_{\ell_{k+1}}\prod_{j=1}^{k}c_{\ell_j}.\end{align*}
We use now both the estimate for
$c_{\ell}$
from Lemma 1 and the induction hypothesis for
$d_{\ell}$
except for
$0\leqslant \ell\leqslant 9$
. Moreover, we use
$\mu_{k,0}\leqslant 2$
(as in the proof of Lemma 1) and
which follows by item (ii) above and
which holds trivially. The rest is handled by similar ideas as in the proof of Lemma 1. Thus, we obtain
\begin{align*}d_{\ell,2}&\leqslant \rho e^{2/K} K^{\ell}\ell!\sum_{k\geqslant 1}\prod_{s=1}^k\left(\rho+\left(\sum_{i=1}^9\frac{c_i}{2^{i(s+1)}i!K^i}\right)+\frac{1}{2^{9(s+1)}(2^{s+1}-1)}\right)\\&\qquad\qquad\qquad\times\left(\sum_{s=1}^k\frac{1+\left(\sum_{i=1}^9\frac{d_i}{2^{i(s+1)}i!K^i}\right)+\frac{1}{2^{9(s+1)}(2^{s+1}-1)}}{\rho+\left(\sum_{i=1}^9\frac{c_i}{2^{i(s+1)}i!K^i}\right)+\frac{1}{2^{9(s+1)}(2^{s+1}-1)}}\right)\\&\hspace{1.25 em}+ e^{2/K} K^{\ell}\ell!\sum_{k\geqslant 1}\prod_{s=1}^k\left(\rho+\left(\sum_{i=1}^9\frac{c_i}{2^{i(s+1)}i!K^i}\right)+\frac{1}{2^{9(s+1)}(2^{s+1}-1)}\right).\end{align*}
Note that, by our choice of K,
\begin{align*}\sum_{i=1}^{9}\frac{c_i}{2^{i(s+1)}i!K^i}\leqslant \frac{9c'}{2^{s+1}K}\leqslant \frac{1}{512\cdot 2^{s+1}}\end{align*}
and likewise with the
$c_i$
’s replaced by
$d_i$
’s. Plugging this into the above expression and numerically evaluating it (again with MAPLE), we obtain
We finally consider
$d_{\ell,3}$
, which is treated in a similar fashion. First,
\begin{align*}f'_{\ell,3}(z)&=\frac{1}{2}\sum_{k\geqslant 1}\sum_{m\geqslant 1}\sum_{\substack{\ell_1+\cdots+\ell_{k+m+2}=\ell \\ \ell_j< \ell,1\leqslant j\leqslant k+m+1}}\binom{\ell}{\ell_1, \ldots,\ell_{k+m+2}}\prod_{s=1}^k\frac{1}{2^{(s+1)\ell_s}}\prod_{t=1}^m\frac{1}{2^{(t+1)\ell_{k+t}}}\\&\qquad\times\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)^{\ell_{k+m+1}}\mu_{k,m}^{\ell_{k+m+2}}\left(\sum_{i=1}^{k+m+1}(A^{[\ell_i]})'(z)\prod_{\substack{j=1\\j\neq i}}^{k+m+1}A^{[\ell_j]}(z)\right)\end{align*}
and thus
\begin{align*}d_{\ell,3}&= \frac{1}{2}\sum_{k\geqslant 1}\sum_{m\geqslant 1}\sum_{\substack{\ell_1+\cdots+\ell_{k+m+2}=\ell \\ \ell_j<\ell,1\leqslant j\leqslant k+m+1}}\binom{\ell}{\ell_1, \ldots,\ell_{k+m+2}}\prod_{s=1}^k\frac{1}{2^{(s+1)\ell_s}}\prod_{t=1}^m\frac{1}{2^{(t+1)\ell_{k+t}}}\\&\qquad\quad\times\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)^{\ell_{k+m+1}}\mu_{k,m}^{\ell_{k+m+2}}\left(\sum_{i=1}^{k+m}d_{\ell_i}\prod_{\substack{j=1\\j\neq i}}^{k+m+1}c_{\ell_j}\right)\\& \hspace{1 em} +\frac{1}{2}\sum_{k\geqslant 1}\sum_{m\geqslant 1}\sum_{\substack{\ell_1+\cdots+\ell_{k+m+2}=\ell \\ \ell_j<\ell,1\leqslant j\leqslant k+m+1}}\binom{\ell}{\ell_1, \ldots, \ell_{k+m+2}}\prod_{s=1}^k\frac{1}{2^{(s+1)\ell_s}}\prod_{t=1}^m\frac{1}{2^{(t+1)\ell_{k+t}}}\\&\qquad\quad\times\left(\frac{1}{2^{k+1}}+\frac{1}{2^{m+1}}\right)^{\ell_{k+m+1}}\mu_{k,m}^{\ell_{k+m+2}}d_{\ell_{k+m+1}}\prod_{i=1}^{k+m}c_{\ell_i}(z).\end{align*}
Using
$\mu_{k,m}\leqslant 3$
(see the proof of Lemma 1) and arguments as above, we obtain
\begin{align}&d_{\ell,3}\leqslant \rho e^{3/K} K^\ell \ell!\sum_{k\geqslant 1}\prod_{s=1}^k\left(\rho+\frac{c_1}{512\cdot2^{(s+1)}K}+\frac{1}{2^{9(s+1)}(2^{s+1}-1)}\right)\nonumber\\&\times \hspace{-0.1cm}\left(\sum_{s=1}^k\frac{1+\frac{d_1}{512\cdot2^{(s+1)}}+\frac{1}{2^{9(s+1)}(2^{s+1}-1)}}{\rho+\frac{c_1}{512\cdot2^{(s+1)}}+\frac{1}{2^{9(s+1)}(2^{s+1}-1)}}\right)\sum_{k\geqslant 1}\prod_{s=1}^k\left(\rho+\frac{c_1}{512\cdot2^{(s+1)}}+\frac{1}{2^{9(s+1)}(2^{s+1}-1)}\right)\nonumber\\&\ +\frac{e^{3/K}K^\ell \ell!}{2}\left(\sum_{k\geqslant 1}\prod_{s=1}^k\left(\rho+\frac{c_1}{512\cdot2^{(s+1)}}+\frac{1}{2^{9(s+1)}(2^{s+1}-1)}\right)\right)^2\nonumber\\&\ =0.141422204463\ldots K^{\ell}\ell!.\end{align}
Combining (A.6), (A.7), and (A.8), we obtain
Finally, for
$\ell\geqslant 10$
,
\begin{align*}d_{\ell}&\leqslant \frac{d_{\ell,1}+d_{\ell,2}+d_{\ell,3}}{g_{10}(\rho)}-\frac{g_{10}'(\rho)}{g_{10}(\rho)}c_{\ell}\\&\leqslant 0.869090272578\ldots K^{\ell}\ell!\end{align*}
since
$-g_{\ell}'(\rho)/g_{\ell}(\rho)$
decreases to 0 and
$g_{10}(\rho)= 0.986940779096\ldots$
and
$-g_{10}'(\rho)/g_{10}(\rho)=0.062876303286\ldots$
. This proves the claim.
Appendix B. The boundary of a phylogenetic network
Recall from Subsection 3.2 that to extend the definition of
$B_2$
to infinite phylogenetic networks, we need the notion of a ‘boundary’ of a network that includes not only the vertices in which the directed random walk X can get trapped (i.e. the leaves) but also all of the distinct ways in which it can escape to infinity (i.e. the ends, see Definition 6). This motivated Definition 7 of the boundary
$\partial G$
of a phylogenetic network G as
$\partial G = \mathcal{L} \cup \mathcal{E}$
, where
$\mathcal{L}$
and
$\mathcal{E}$
denote the set of leaves and the set of ends of G, respectively.
In this appendix, we show that
$\partial G$
can be embedded in a suitable compact metric space
$(\mathcal{K},\, d_{\mathcal{K}})$
, and that the escape point
$X_{\infty}$
of the directed random walk X is a well-defined random variable in
$\mathcal{K}$
. We also discuss some topological properties of the boundary
$\partial G$
, in particular its connection with the Martin boundary.
Let us start by introducing some notation. We write
$u\preccurlyeq v$
to indicate that u is an ancestor of v, i.e. that there exists a finite directed path from u to v in G. For any vertex
$v \in G$
, we denote by
the set of ancestors of v. Finally, for any set of vertices
$S \subset G$
, we use the short notation
$[S]_k$
for the set
$S \cap [G]_k$
of vertices of S at height at most k in G.
Definition 10. Let G be a phylogenetic network. Set
and equip
$\mathcal{K}$
with the distance
$d_{\mathcal{K}}$
defined by
with the convention
$\sup \emptyset = 0$
.
It is readily checked that
$(\mathcal{K}, d_{\mathcal{K}})$
is a compact metric space (using a diagonal argument and the local finiteness of G to show compactness).
Because the map
$v\in G\mapsto \bar{v}\in \mathcal{K}$
is injective, the vertices of G can be seen as points of
$\mathcal{K}$
. The next proposition shows that the ends of G can also be embedded in
$\mathcal{K}$
; more precisely, they are points of
$\mathrm{cl}(G)$
, the topological closure of G in
$\mathcal{K}$
.
Proposition 3. Let G be a phylogenetic network, and let
$\mathcal{E}$
denote its end set. For each
$x \in \mathcal{E}$
, define
where
$v\in r$
means that the ray r goes through the vertex v. Then the map
is injective. Furthermore, for any ray
$r = (v_n)_{n \geqslant 0}$
, we have
$\bar{v}_n \to\bar{x}$
in
$(\mathcal{K}, d_{\mathcal{K}})$
, where x is the end associated with r.
Proof. First, let us show that
$\bar{x}\in \mathcal{K}$
for any
$x\in \mathcal{E}$
. Fix
$x \in \mathcal{E}$
,
$v \in \bar{x}$
, and
$u \preccurlyeq v$
. We must show that
$u \in \bar{x}$
, i.e. that x contains a ray that goes through u. Let
$r\in x$
be such that
$v \in r$
. Because G is rooted and
$u \preccurlyeq v$
, there exists a path that goes from the root of G to u, and then from u to v. Let r
′ be the ray that starts with this path and then continues along r. Since
$r'$
$r$
, we have
$r' \in x$
, concluding the proof that
$\bar{x} \in \mathcal{K}$
.
Let us now show that
$x\mapsto \bar{x}$
is injective. Consider
$x, y \in \mathcal{E}$
such that
$\bar{x}=\bar{y}$
, and fix two rays
$r = (v_i)_{i\geqslant 0}\in x$
and
$r' = (v'_i)_{i\geqslant 0}\in y$
. To show that
$x = y$
, we must show that
$r$
$r'$
, and for this it suffices to show a ray that intersects r and r
′ infinitely many times. The key is to show that for all
$i\geqslant 0$
, there exists
$j \geqslant 0$
such that
$v_i \preccurlyeq v'_j$
—indeed, by symmetry we then get that there exists
$k \geqslant 0$
such that
$v'_j \preccurlyeq v_k$
, etc., and by a straightforward concatenation procedure we can build a ray that goes to and fro between vertices of r and vertices of r
′. By assumption,
$\bar{x} = \bar{y}$
and thus
$v_i \in \bar{y}$
. As a result, there exists a ray
$r''$
$r'$
such that
$v_i \in r''$
, and since r
″ intersects r
′ infinitely many times, there exists
$u \in r''$
,
$u \succcurlyeq v_i$
such that
$u \in r'$
, concluding the proof of the injectivity of
$x\mapsto \bar{x}$
.
Finally, consider any ray
$r = (v_n)_{n\geqslant 0}$
, letting x denote the corresponding end. Let us show that
$\bar{v}_n \to \bar{x}$
as
$n \to \infty$
, i.e. let us fix some
$k\geqslant 0$
and show that
$[\bar{x}]_k = [\bar{v}_i]_k$
for all i large enough. Let
$v\in [\bar{x}]_k$
, and pick
$r_v\in x$
such that
$v\in r_v$
. Because
$r_v$
$r$
, there exists
$i_v\in \mathbb{N}$
such that
$v\preccurlyeq v_{i_v}$
. Since
$[G]_k$
is finite, we can define
Thus,
$[\bar{x}]_k \subset \bar{v}_i$
for all
$i\geqslant N_k$
. Moreover, because
$\bar{x}\in \mathcal{K}$
we also have
$\bar{v}_i\subset \bar{x}$
for all
$i\geqslant 0$
. As a result,
$[\bar{x}]_k = [\bar{v}_i]_k$
for all
$i\geqslant N_k$
, concluding the proof.
Proposition 3 shows that the vertices and the ends of G can be embedded in
$\mathcal{K}$
(in the rest of this appendix, we thus identify
$v\in G$
with
$\bar{v}\in \mathcal{K}$
and simply drop the notation
$\bar{v}$
), and it immediately implies the following corollary.
Corollary 1. Let G be a phylogenetic network and let
$(X_t)_{t \geqslant 0}$
be the directed random walk on G. Then
$X_t$
converges almost surely in
$(\mathcal{K},\, d_{\mathcal{K}})$
to a random variable
$X_{\infty} \in \partial G$
.
Remark 4. Note that there is no connection between the boundary
$\partial G$
and the topological boundary of G in
$\mathcal{K}$
; that is,
$\mathrm{cl}(G) \setminus \mathrm{int}(G)$
. Indeed
-
(i) Because the vertices of G are isolated points in
$\mathcal{K}$
, they all belong to the interior of G, i.e. G is open in
$\mathcal{K}$
, whereas leaves belong to
$\partial G$
. -
(ii) Although
$\mathcal{E} \subset \mathrm{cl}(G)$
, not all limit points are ends: as Figure 9 shows, limit points can correspond to the union of ends.Figure 9.As previously, the root is highlighted in blue and the edges are pointing downwards. In this example, the sequence
$(\ell_n)$
has a limit
$m \in \mathcal{K} \setminus \partial G$
. 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
$\mathcal{K}$
of a sequence of points of
$\partial G$
is always either a leaf or a union of ends.
We close this appendix by briefly discussing the connection with a standard notion of a boundary for transient random walks: the Martin boundary. Let us start by recalling its definition in our setting; we refer the reader to [Reference Kemeny, Snell and Knapp18, Chapter 10] for a more general definition.
Let
$\mathbb{P}_{u}{\,\cdot\,}$
denote probabilities conditional on the directed random walk X being started from u, instead of from the root. The Martin kernel of X is defined as
Note that the functions
$M(u,\, \cdot\,)$
are bounded, since
As a result, there is a canonical compactification of G on which all functions
$M(u, \,\cdot\,)$
extend continuously (see, e.g., [Reference Woess29, Theorem 7.3]). This compactification, which we denote by
$\,\widehat{\!G}$
, is known as the Martin compactification of G. The Martin boundary of G is then defined as
$\,\widehat{\!G} \setminus G$
.
Equivalently, a sequence
$(v_n)$
of vertices of G converges in
$\,\widehat{\!G}$
if and only if
$M(u, v_n)$
converges for all
$u\in G$
. The Martin boundary consists of all limit points of sequences
$(v_n)$
that escape to infinity (in the sense that
$h(v_n) \to \infty$
, where h(v) denotes the height of v).
Although the Martin boundary and our boundary
$\partial G$
are both designed to capture the asymptotic behavior of X (and both make it possible to define an almost-sure limit for
$X_t$
), they are distinct notions and there does not seem to be a simple relationship between them; in particular, one is not finer than the other.
Two phylogenetic networks for which the Martin boundary differs from
$\mathcal{K}$
. 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.

For instance, the phylogenetic network G given in Figure 10A provides an example of a sequence of vertices that converges in
$\mathcal{K}$
to an end
$x \in \partial G$
, but that does not converge in
$\,\widehat{\!G}$
: indeed, assume that the weights
$(\epsilon_n)$
given in Figure 10A satisfy
Let A be the event that the directed random walk X started from the root of G goes through one of the central edges
$(v_1\to v_2), (v_2\to v_3), \ldots$
; that is,
Using union bounds, we see that
If X goes to u and then never crosses to the right through one of the central edges, then it goes through
$v_{2n}$
. As a result, letting
${A}^{\mathsf{c}} $
denote the complement of A, we have
Conversely, if X goes to u and then visits
$v_{2n+1}$
, then it must have crossed to the right using one of the central edges, so
Similarly, we get
$\mathbb{P}{(u'\in X, v_{2n}\in X)} \leqslant \frac{1}{2}\delta$
and
$\mathbb{P}{(u'\in X, v_{2n+1}\in X)} \geqslant \frac{1}{2}(1-\delta)$
. As a result,
\begin{align*} \begin{cases} \mathbb{P}{\big(u\in X | v_{2n}\in X\big)} \geqslant \dfrac{1}{2}(1-\delta) \geqslant \dfrac{3}{8}, \\[6pt] \mathbb{P}{\big(u\in X | v_{2n+1}\in X\big)} \leqslant \dfrac{\delta}{1-\delta} \leqslant \dfrac{1}{3} , \end{cases}\end{align*}
from which it follows that
$(v_n)$
does not converge in
$\,\widehat{\!G}$
, whereas it does in
$\mathcal{K}$
, since
$\partial G$
consists of a single end.
Conversely, the phylogenetic network G
′ given in Figure 10B provides an example of a sequence that converges in the Martin boundary
$\,\widehat{\!G}\,'$
, but not in
$\mathcal{K}'$
: indeed, it is readily computed that
from which it follows that the sequence
$(u_1,v_1,u_2,v_2,\dots)$
converges in
$\,\widehat{\!G}\,'$
. Yet this sequence does not converge in
$\mathcal{K}$
, because the subsequences
$(u_n)$
and
$(v_n)$
have different limits.
Appendix C. Properties of the entropy
To make this article self-contained, in this appendix we recall the definition of the entropy of a probability measure on a general (i.e. not necessarily countable) space, as well as some of its main properties. The results are presented mostly without proofs, and we refer the reader to [Reference Martin and England22, Chapter 2] for a detailed treatment.
Let us start by recalling the definition of the entropy of a countable partition.
Definition 11. Let
$(\Omega, \mathscr{A}, \mu)$
be a probability space, and let
$\pi$
be a countable measurable partition of
$\Omega$
. Then the entropy of
$\pi$
with respect to
$\mu$
is given by
A key property of the entropy, which we refer to as its monotonicity, is given by the next proposition. Recall that a partition
$\pi$
is said to be finer than a partition
$\pi'$
if for all
$B \in \pi$
there exists
$B'\in\pi'$
such that
$B \subset B'$
. We write
$\pi \preccurlyeq \pi'$
to indicate that the partition
$\pi$
is finer than
$\pi'$
.
Proposition 4. (Monotonicity of the entropy) Let
$\pi$
and
$\pi'$
be two (countable) measurable partitions. If
$\,\pi' \preccurlyeq \pi$
then
$H_{\mu}(\pi') \geqslant H_{\mu}(\pi)$
.
In particular, Proposition 4 justifies—and is trivially preserved by—the following extension of Definition 11 to uncountable partitions.
Definition 12. Let
$(\Omega, \mathscr{A}, \mu)$
be a probability space, and let
$\pi$
be a measurable partition of
$\Omega$
. The entropy of
$\pi$
with respect to
$\mu$
is given by
The entropy of the probability distribution
$\mu$
is then defined as
The monotonicity of the entropy entails that, letting
$\sigma$
denote the partition into singletons,
$H(\mu) = H_{\mu}(\sigma)$
. In particular, if
$\Omega$
is countable then we recover the familiar definition of Shannon entropy:
If
$\mu$
has a non-atomic part then its entropy is infinite. This is sometimes used as an equivalent definition of the entropy (see, e.g., [Reference Martin and England22, Definition 2.14]), but we provide a short proof of this equivalence below. Before stating it, we point out an elementary but useful fact. Since the proof involves only straightforward calculations, we omit it.
Proposition 5. Let
$(\Omega, \mathscr{A}, \mu)$
be a probability space, and let
$\pi$
be a measurable partition of
$\,\Omega$
. Assume that
$\pi'$
is obtained from
$\pi$
by fragmenting one of its block B such that
$\mu(B) > 0$
, and let
$\pi_B$
denote the corresponding partition of B. Then
where
$\mu_B$
denotes the conditional probability distribution induced on B by
$\mu$
.
Proposition 6. Let
$(\Omega, \mathscr{A}, \mu)$
be a probability space. If
$\mu$
has a non-atomic part of positive mass then
$H(\mu) = +\infty$
.
Proof. Let
$(A_i)_{i\geqslant 1}$
denote the family of distinct atoms of
$\mu$
. Let
$A=\bigcup_i A_i$
, and note that by assumption
$\mu({A}^{\mathsf{C}}) > 0$
. Define
By Proposition 5, we have
Thus, to finish the proof it suffices to show that
$H(\mu_{{A}^{\mathsf{C}}}) = +\infty$
.
By Lyapunov’s theorem on non-atomic measures (see, e.g., [Reference Artstein2]), for all n it is possible to find a measurable partition
$\pi_n = \{B_1, \dots, B_n\}$
of
${A}^{\mathsf{C}}$
such that
$\mu(B_i)=\mu({A}^{\mathsf{C}})/n$
for all
$i\in \{1, \dots, n\}$
. It follows that
Since n can be arbitrarily large, this concludes the proof.
Finally, we close this appendix with a useful lemma for refining sequences of partitions. For this, we first introduce some vocabulary and notation. Given a partition
$\pi$
, we denote by
-
•
$\pi[x]$
the block of
$\pi$
that contains x; -
•
$\sim_{\pi}$
the equivalence relation associated with
$\pi$
.
Definition 13. We say that a sequence
$(\pi_n)$
of partitions of a set E converges to the partition
$\pi$
if, for all
$x, y \in E$
, there exists N such that, for all
$n \geqslant N$
,
Remark 5. Equivalently,
$(\pi_n)$
converges to
$\pi$
if and only if
$\lim_n \pi_n[x] = \pi[x]$
for every
$x \in E$
, i.e. if and only if
$\unicode{x1D7D9}_{\pi_n[x]}$
converges pointwise to
$\unicode{x1D7D9}_{\pi[x]}$
for all
$x\in E$
.
Lemma 3. Let
$(\pi_n)$
be a sequence of measurable partitions on a probability space
$(\Omega,\mathscr{A},\mu)$
. If
$(\pi_n)$
converges to a partition
$\pi$
, such that
$\pi\preccurlyeq \pi_n$
for all
$n\geqslant 0$
, then
$\pi$
is measurable and
In particular, if
$\pi$
is the partition into singletons, the limit is
$H(\mu)$
.
Proof. The fact that
$\pi$
is measurable can be deduced from Remark 5. This remark is also the key to the rest of the proof. Indeed, since
$\pi_n[x] \to \pi[x]$
for all
$x\in \Omega$
,
For any measurable partition
$\sigma$
, define the following measurable function:
\begin{align*} f^\sigma\colon\, x\in \Omega\, \longmapsto \begin{cases} -\log_2\big(\mu(\sigma[x])\big) &\text{if } \mu(\sigma[x])>0, \\ \infty & \text{otherwise}. \end{cases}\end{align*}
By (B1),
$f^{\pi_n}\to f^{\pi}$
pointwise. Noting that, in view of Proposition 6,
$H_{\mu}(\sigma)=\int f^\sigma \,d\mu$
, we deduce from Fatou’s lemma that
This concludes the proof, since, by Proposition 4,
$H_{\mu}(\pi_n) \leqslant H_{\mu}(\pi)$
for all n.
Appendix D. Properties of the
$B_2$
index
In this appendix, we list and prove miscellaneous properties of the
$B_2$
index. Let us start with something elementary, but fundamental—namely, the fact that the grafting property holds for infinite phylogenetic networks.
Proposition 7. Let
$G_1$
and
$G_2$
be two phylogenetic networks, and let G be the phylogenetic network obtained by identifying a leaf
$\ell \in G_1$
with the root of
$G_2$
. Then
where
$p_{\ell}$
denotes the probability that the directed random walk on
$G_1$
ends in
$\ell$
.
Since the proof of Proposition 7 is a straightforward application of the analogous Proposition 5 for the entropy, we do not detail it.
Next, let us prove the measurability of
$B_2$
. This technicality is needed to ensure that the
$B_2$
index of a random phylogenetic network is a well-defined random variable.
Proposition 8. Let
$\mathbb{G}$
denote the space of phylogenetic networks, equipped with the local topology and its Borel
$\sigma$
-field. The function
$B_2\colon \mathbb{G} \to \mathbb{R}\cup\{+\infty\}$
is measurable.
Proof. We will show that
$B_2$
can be expressed as a pointwise limit of continuous functions from
$\mathbb{G}$
to
$\mathbb{R}$
.
Let G be a fixed phylogenetic network, and let
$X=(X_n)_{n\geqslant 0}$
be the directed random walk on G, started from the root. Note that X is the only source of randomness, and that, for any
$n \geqslant 0$
, the distribution of
$X_n$
depends only on
$[G]_n$
. Therefore, the functions
are continuous for the local topology (recall that
$\bar{X}_n$
denotes the set of ancestors of
$X_n$
in G, and that we use the short notation
$[\bar{X}_n]_k = \bar{X}_n \cap [G]_k$
). Furthermore, we gave in Definition 10 a compactification
$\mathcal{K}$
of G in which
$X_n$
converges almost surely to
$X_{\infty}$
and in which, by definition, the functions
$x \mapsto [\bar{x}]_k$
are continuous, for all k. Therefore, for any
$k\geqslant 1$
and
$A \subset [G]_k$
, by dominated convergence,
This implies that
where
$\mu$
is the distribution of
$X_{\infty}$
on
$\mathcal{K}$
, and
$\pi_k$
is the partition defined by
Because the map
$x\mapsto \bar{x}$
is injective (see Proposition 3), as
$k\to\infty$
the partition
$\pi_k$
tends to the partition into singletons. Therefore, by Lemma 3 and definition of
$B_2$
,
concluding the proof.
We now provide tools to study the continuity of
$B_2$
. We focus on easy-to-check sufficient conditions that are likely to hold for biologically relevant models of phylogenetic networks.
Proposition 9. Let
$(G_n)$
be a sequence of phylogenetic networks converging locally to G. Assume that the directed random walk on G ends in a leaf almost surely. Then
Proof. Let
$\mathcal{L}$
be the leaf set of G, and let
$\mathcal{L}_k = \{\ell \in \mathcal{L} \,:\, h(\ell) \leqslant k\}$
be the set of leaves at height at most k. As always, write X for the directed random walk on G, and
$X_{\infty}$
for its limit on the boundary of G. Finally, let
$p_{\ell} = \mathbb{P}{(X_{\infty}=\ell)}$
.
Since
$\mathbb{P}{(X_{\infty} \in \mathcal{L})} = 1$
, we have
$B_2(G) = -\!\sum_{\ell \in \mathcal{L}} p_{\ell} \log_2 p_{\ell}$
, and since
$\mathcal{L} = \operatorname{lim\!\uparrow\,}_k \mathcal{L}_k$
, it follows that
Now fix some b such that
$0< b <B_2(G)$
, and let k be such that the sum in the expression above be greater than b. Fix
$n_0$
such that
$[G_n]_k=[G]_k$
for all
$n\geqslant n_0$
. Then, for all
$n\geqslant n_0$
,
This shows that
$\liminf_n B_2(G_n) \geqslant b$
. Our letting
$b\to B_2(G)$
concludes the proof.
Proposition 10. Let
$(G_n)$
be a sequence of finite phylogenetic networks that converge locally to G. Assume that, for a sequence
$(k_n)$
satisfying
$[G_n]_{k_n}=[G]_{k_n}$
, we have
where
$h(X_{\infty})$
is the height of the limit of the directed random walk on G, and
$\left|{G_n}\right|$
denotes the number of leaves of
$G_n$
. Then
Proof. Let us write
$q_n = \mathbb{P}{(h(X_{\infty}) > k_n)}$
. Since
$\log \left|{G_n}\right|$
cannot tend to 0 (except in the trivial case where G is a finite DAG with a single leaf), we must have
$q_n\to 0$
. This means that
$\mathbb{P}{(X_{\infty} \in \mathcal{L})} = 1$
, where
$\mathcal{L}$
denotes the leaf set of G. As a result, by Proposition 9 it suffices to show
where
$p_{\ell} = \mathbb{P}{(X_{\infty} = \ell)}$
. Let us write
$\mathcal{L}_{k_n}^{n}$
(respectively
$\mathcal{L}_{>k_n}^n$
) for the set of leaves in
$G_n$
at height at most
$k_n$
(respectively at least
$k_n+1$
). For any leaf
$\ell\in G_n$
, write
$\smash{p_{\ell}^{(n)}}$
for the probability that the directed random walk on
$G_n$
ends in
$\ell$
. Notice that, since
$[G_n]_{k_n}=[G]_{k_n}$
,
and that, since
$(p^{(n)}_{\ell}\! / q_n \,:\, \ell \in \mathcal{L}_{>k_n}^{n})$
is a probability distribution, Jensen’s inequality gives
\begin{align*} -\frac{1}{q_n}\sum_{{\ell \in \mathcal{L}_{ > k_n}^{n}}}\; p^{(n)}_{\ell} \log_2p^{(n)}_{\ell} \leqslant \log_2\Bigg(\sum_{{\ell \in \mathcal{L}_{>k_n}^{n}}}\;\; \frac{p^{(n)}_{\ell}}{q_n}\cdot\frac{1}{p^{(n)}_{\ell}} \Bigg) \leqslant \log_2\bigg(\frac{\left|{G_n}\right|}{q_n}\bigg).\end{align*}
It follows that
where the first term on the right-hand side tends to
$B_2(G)$
, while the second one tends to 0 because
$q_n\to 0$
and
$q_n \log_2 |G_n|\to 0$
by hypothesis.
Finally, we close this appendix by providing a useful tool to compute the
$B_2$
index of a fixed infinite network G. This essentially consists in chopping the network at its cut-vertices and using the grafting property—but there is a small subtlety (namely, showing that the resulting non-decreasing sequence of
$B_2$
indices, which is trivially bounded above by the
$B_2(G)$
, actually reaches it in the limit). To give a clean statement, let us introduce some vocabulary.
Definition 14. A stub of a phylogenetic network G is any phylogenetic network
$S \subset G$
that can be obtained by removing all out-going edges from a set of cut-vertices of G and keeping the connected component containing the root. We write
$S \sqsubset G$
to indicate that S is a stub of G. A stub sequenceof G is an increasing sequence of stubs
$S_n \sqsubset S_{n+1} \sqsubset G$
such that
$\lim_n S_n = G$
.
Proposition 11. Let
$(S_n)$
be a stub sequence of G. Then
Proof. For any stub
$S \sqsubset G$
, let
$\pi_S$
be the partition of
$\partial G$
defined by the following equivalence relation:
To see that this is indeed an equivalence relation, recall that the leaves of S are either leaves or cut-vertices in G, and note that for all
$x \in \partial G$
, the set
$\bar{x}$
contains at most one leaf of S. The transitivity of
$\sim_S$
then follows readily.
Note that the partitions
$\pi_{S_n}$
are refining along the stub sequence
$(S_n)$
, and that they converge simply (see Definition 13) to
$\pi_G$
, the partition into singletons. Indeed, pick
$x\neq y$
and assume that
$x\sim_{S_n}y$
for all n. For each n, let
$v_n$
be the unique leaf of
$S_n$
in
$\bar{x} \cap \bar{y}$
. Then
-
• If
$\{v_n \,:\, n \geqslant 1\}$
is finite then there exists
$\ell$
such that
$v_n = \ell$
for all n large enough. By the local convergence of
$S_n$
to G, this vertex
$\ell$
is a leaf of G, and therefore
$x = y = \ell$
, yielding a contradiction. -
• If
$\{v_n \,:\, n \geqslant 1\}$
is infinite then
$v_1, v_2, \ldots$
are cut-vertices of G and they lie on a ray
$r \subset \bar{x} \cap \bar{y}$
. This entails
$x = y$
: indeed, let
$r_x \in x$
and
$r_y \in y$
. For all n, since
$v_n \in \bar{x}$
and
$v_n$
is a cut-vertex of G,
$v_n \in r_x$
. As a result,
$r_x$
intersects r infinitely many times. Similarly,
$r_y$
intersects r infinitely many times. Thus, we have
$r_x$
$r_y$
, and therefore
$x = y$
, again yielding a contradiction.
Finally, note that
$B_2(S_n) = H_{\mu}(\pi_{S_n})$
, where
$\mu$
is the distribution of
$X_{\infty}$
, and that, by definition,
$B_2(G) = H_{\mu}(\pi_G)$
. Thus, the proposition follows from Lemma 3.
Appendix E. Total variation bound for the convergence of Galton–Watson trees
In this appendix, we provide a total variation bound to quantify the speed of convergence of conditioned Galton–Watson trees to Kesten’s tree. Let us start by setting/recalling some notation.
In the remainder of this appendix,
$\xi$
will denote a random variable taking values in
$\mathbb{N} = \{0, 1, 2, \ldots\}$
, with mean 1 and such that
$\mathbb{P}{(\xi=0)}>0$
. Likewise,
$T \sim \mathrm{GW}(\xi)$
will be a Galton–Watson tree with offspring distribution
$\xi$
, which we view as an ordered tree. Recall that, for any tree
$\mathbf{t}$
, we denote the number of leaves of
$\mathbf{t}$
by
$\left|\mathbf{t}\right|$
. As in Subsection 3.3, for any n such that
$\mathbb{P}{(|{T}|=n)}>0$
, we write
$T_n$
for a random tree distributed as T conditioned to have n leaves. Note that whenever we state something about
$T_n$
, we implicitly assume that n is taken so that
$\mathbb{P}{(|{T}|=n)}>0$
. Finally, we denote by
$T_*$
the Kesten tree associated with T, i.e. the local limit of
$T_n$
as
$n\to\infty$
(see Definition 9), and we write
$\hat{\xi}$
for a random variable such that
$\mathbb{P}{\big(\hat{\xi}=n\big)}=n\,\mathbb{P}{(\xi=n)}$
for all
$n \geqslant 1$
(thus,
$\hat{\xi}$
is distributed as the number of children of the vertices that lie on the spine of
$T_*$
).
Let us now introduce a truncation of
$T_*$
: for each
$k\geqslant 0$
, let
$v_k$
be the kth vertex on the spine of
$T_*$
, with
$v_0$
being the root, and let
$T_*^k$
be the leaf-pointed rooted tree obtained from
$T_*$
by removing all descendants of
$v_k$
(other than
$v_k$
itself) and letting
$v_k$
be the distinguished leaf. The distribution of
$T_*^k$
is easily computed: let
$\mathbf{t}$
denote a finite ordered tree with a distinguished leaf
$v_k$
at height k, and write
$\mathbf{v}=(v_0,v_1,\dots,v_k)$
for the path from the root of
$\mathbf{t}$
to its distinguished leaf
$v_k$
. Then, by construction of
$T_*$
,
\begin{align*} \mathbb{P}{(T_*^k=\mathbf{t})} &= \Bigg(\prod_{i=0}^{k-1}\mathbb{P}{(\hat{\xi}=d_{v_i})}\cdot \frac{1}{d_{v_i}}\Bigg) \Bigg(\!\!\prod_{\;v\in \mathbf{t}\setminus \mathbf{v}}\!\! \mathbb{P}{(\xi=d_{v})} \Bigg) \\[0.5ex] &= \prod_{{ v\in \mathbf{t}\setminus \{v_k\}}}\, \mathbb{P}{(\xi=d_{v})} \\[1ex] &= \frac{\mathbb{P}{(T=\mathbf{t})}}{\mathbb{P}{(\xi=0)}},\end{align*}
where
$d_v$
denotes the number of children of vertex v and, by a slight abuse of notation, we write
$\{T=\mathbf{t}\}$
for the event that the Galton–Watson tree T is equal to the non-pointed version of the tree
$\mathbf{t}$
. Moreover, note that
${\mathbb{P}{(T=\mathbf{t})}}/ {\mathbb{P}{(\xi=0)}}$
is also the probability that T ‘starts’ with the leaf-pointed tree
$\mathbf{t}$
, i.e. that T can be obtained by grafting a tree T
′ on the distinguished leaf of
$\mathbf{t}$
. Writing
$\{\mathbf{t}\subset T\}$
for this event, we therefore have
Also note that, conditional on
$\{\mathbf{t}\subset T\}$
, the subtree of T descending from the distinguished leaf of
$\mathbf{t}$
is a
$\mathrm{GW}(\xi)$
tree.
Next, let us build a pointed tree
$T_n^k$
from
$T_n$
, as we did for
$T_*^k$
. Conditional on
$T_n$
, let
$u_n$
be chosen uniformly at random among the n leaves of
$T_n$
. If
$u_n$
is at height at least k then let
$v_{n,k}$
be the vertex at distance k from the root on the path to
$u_n$
, and define
$T_n^k$
to be the tree obtained from
$T_n$
by removing all vertices descending from
$v_{n,k}$
(other than
$v_{n, k}$
itself) and letting
$v_{n,k}$
be the distinguished vertex. On the event that
$u_n$
is at height less than k, the definition of
$T_n^k$
is irrelevant; we define it to be the tree reduced to a single node. From this construction, note that for any
$\mathbf{t}$
finite ordered tree with a distinguished leaf at height k,
\begin{align} \mathbb{P}{(T_n^k=\mathbf{t})} &= \frac{n-|\mathbf{t}|+1}{n}\cdot\frac{\mathbb{P}{(\mathbf{t}\subset T, \, \left|{T}\right|=n)}}{\mathbb{P}{(|{T}|=n)}} \nonumber\\ &=\frac{n-\left|\mathbf{t}\right|+1}{n}\cdot \mathbb{P}{(\mathbf{t}\subset T)} \cdot \frac{\mathbb{P}{(|{T}|=n-\left|\mathbf{t}\right|+1)}}{\mathbb{P}{(|{T}|=n)}} \nonumber\\ &= \mathbb{P}{(T_*^k=\mathbf{t})} \cdot \frac{f(n-\left|\mathbf{t}\right|+1)}{f(n)}, \end{align}
where
$f(n)\,:\!=\, n\,\mathbb{P}{(|{T}|=n)}$
.
With these definitions, we are ready to state the main result of this appendix.
Proposition 12. If
$\,\mathbb{E}{[\xi^3]}<\infty$
then for any sequence of integers
$(k_n)_{n\geqslant 0}$
such that
$k_n=o(\sqrt{n})$
, we have
Remark 6. The fact that the total variation distance between
$T_n^{k_n}$
and
$T_*^{k_n}$
tends to 0 whenever
$k_n = o(\sqrt{n})$
appears, in slightly different forms, in the literature: a similar result, but where
$T_n$
is conditioned on its number of vertices, can be found in [Reference Kersting19, Theorem 5]—without any moment assumption besides
$\mathbb{E}{[\xi]} = 1$
, and for any sequence
$k_n=o(n/a_n)$
, with
$a_n$
being any sequence such that
$\sum_{i=1}^n\xi_i/a_n$
converges in distribution (where
$\xi_i$
are independent and identically distributed (i.i.d.) replicates of
$\xi$
). Stufler [Reference Stufler26, Theorem 5.2] also provided a closely related result for fringe subtrees, under a finite variance assumption. What is new here is the explicit speed of convergence
$k_n/\sqrt{n}$
, which we need to show the convergence of all moments of
$B_2(G_n)$
to those of
$B_2(G_*)$
in the proof of Theorem 4.
The third moment assumption is needed in our proof to get a Berry–Esseen-type estimate, but this may be a superfluous assumption. It would be interesting to see whether similar bounds can be obtained in the critical case without any moment assumption (similarly to Theorem 5 in [Reference Kersting19]), but this is beyond the scope of this paper.
Finally, note that the proof that we develop would be essentially the same if
$T_n$
were conditioned on the number of vertices, or if we looked at fringe subtrees.
The proof of Proposition 12 relies on the following lemma.
Lemma 4. With the same notation as above,
-
(i) if
$\,\mathbb{E}{[\xi^3]}<\infty$
, then there exists a constant
$c_1 > 0$
such that along any sequence of n such that
$\mathbb{P}{(|{T}|=n)}>0$
,
\begin{align*} f(n) = n\,\mathbb{P}{(|{T}|=n)} = \frac{c_1}{\sqrt{n}} + O(n^{-1}); \end{align*}
-
(ii) if
$\mathbb{E}{[\xi^2]}<\infty$
then for any sequence of integers
$(k_n)_{n\in \mathbb{N}}$
such that
$k_n=o(\sqrt{n})$
, we have
\begin{align*} \mathbb{P}{(|{T_*^{k_n}}| \geqslant n)} = \Theta\Big(\frac{k_n}{\sqrt{n}}\Big). \end{align*}
Proof. (i) By Minami’s correspondence [Reference Minami23, Theorem 2], we have
where v(T
′) denotes the number of vertices of T
′, and T
′ is a
$\mathrm{GW}(\xi')$
tree whose offspring distribution is given by
\begin{align*} \xi' = \sum_{i=1}^{Z}Y_i ,\end{align*}
with
$\mathbb{P}{(Z=n)} = \mathbb{P}{(\xi>0)}^n\, \mathbb{P}{(\xi=0)}$
for all
$n\geqslant 0$
, and where the variables
$Y_i$
are i.i.d., independent of Z, and distributed as
$(\xi-1 \mid \xi>0)$
. It is easy to see that T
′ is critical and that
$\xi'$
has a finite third moment.
Next, we use the well-known fact (see, e.g., [Reference Dwass10]) that
where the
$\xi'_i$
are i.i.d. copies of
$\xi'$
. Since
$\xi'$
has a finite third moment, the asymptotic expansion given in (i) follows readily from a Berry–Esseen-type estimate for the local central limit theorem [Reference Petrov24, Chapter VII, Theorem 6].
(ii) Let us fix a sequence
$k_n = o(\sqrt{n})$
. By construction of Kesten’s tree, we have
\begin{equation} \big|{T_*^{k_n}}\big|-1 \overset{d}{=} \sum_{i=1}^{k_n} X_i,\end{equation}
where the
$X_i$
are independent and distributed as
$\sum_{i=1}^{Y}\left|T_i\right|$
, where Y is distributed as
$\hat{\xi}-1$
and the
$T_i$
are i.i.d.
$\mathrm{GW}(\xi)$
trees.
Similarly to the proof of (i), using a standard local central limit theorem—this time requiring only a finite second moment for
$\xi$
—we get
$\mathbb{P}{(|{T}|\geqslant n)} \sim C_1n^{-1/2}$
for some constant
$C_1>0$
(for a complete proof in a more general case, see, e.g., [Reference Kortchemski21, Theorem 3.1]). Because
$\hat{\xi}-1$
has a finite expectation, we also have
$\mathbb{P}{(X_1\geqslant n)} \sim C_2n^{-1/2}$
for the variables
$X_i$
in (B2), for some constant
$C_2>0$
. Therefore,
$X_1$
is in the domain of attraction of a
$(1/2)$
-stable distribution and we can apply Heyde’s large deviation theorem [Reference Heyde14]: for any non-decreasing sequence
$(x_m)$
such that
$\sum_{i=1}^m X_i/x_m \to 0$
in probability, we have
\begin{align*} \mathbb{P}{\Bigg(\sum_{i=1}^m X_i \geqslant x_n\Bigg)} = \Theta\big(m\,\mathbb{P}{(X_1 \geqslant x_n)}\big) = \Theta\Big(\frac{m }{\sqrt{x_n}}\Big).\end{align*}
Since
$k_n=o(\sqrt{n})$
and since
$X_1$
is in the domain of a
$(1/2)$
-stable distribution, we have
$\sum_{i=1}^{k_n} X_i/n \to 0$
in probability, and so the equation above translates to
\begin{align*} \mathbb{P}{(|T_*^{k_n}| \geqslant n)} = \mathbb{P}{\Bigg(\sum_{i=1}^{k_n} X_i \geqslant n\Bigg)} = \Theta\Big(\frac{k_n}{\sqrt{n}}\Big),\end{align*}
concluding the proof.
Proof of Proposition
12. Recall from (B1) that for any fixed tree
$\mathbf{t}$
with a distinguished leaf at height k, we have
with
$f(n)=n\mathbb{P}{(|{T}|=n)}$
. This implies that, if we let
$(\!\cdot\!)_+$
denote the positive part,
\begin{align} d_{\mathrm{TV}}\big(T_n^k,\, T_*^k\big) &= \sum_{\mathbf{t}}\big(\mathbb{P}{\big(T_*^k=\mathbf{t}\big)} - \mathbb{P}{\big(T_n^k=\mathbf{t}\big)}\big)_+ \nonumber \\[1ex] &\leqslant \mathbb{P}{\big(|T_*^k| > \tfrac{n}{2}\big)} + \hspace{-0.75em} \sum_{\quad\mathbf{t}\,:\,\left|\mathbf{t}\right|\leqslant n/2} \hspace{-1.4em} \big(\mathbb{P}{\big(T_*^k=\mathbf{t}\big)} - \mathbb{P}{\big(T_n^k=\mathbf{t}\big)}\big)_+ \nonumber \\ &= \mathbb{P}{\big(|T_*^k| > \tfrac{n}{2}\big)} + \mathbb{E}{\Bigg[\bigg(1-\frac{f(n-|T_*^k|+1)}{f(n)}\bigg)_{\!+}\!\! \cdot\, \unicode{x1D7D9}_{\big\{|T_*^k|\leqslant \tfrac{n}{2}\big\}}\Bigg]}. \end{align}
Using Lemma 4(i), we see that as
$n\to\infty$
and uniformly for all
$\ell \leqslant n/2$
such that
$f(n-\ell+1)>0$
,
\begin{align*} \frac{f(n-\ell+1)}{f(n)} = \frac{\frac{c_1}{\sqrt{n - \ell + 1}} + O(n^{-1})}{\frac{c_1}{\sqrt{n}} + O(n^{-1})} = \sqrt{\frac{n}{n - \ell + 1}} + O(n^{-1/2}) .\end{align*}
Because
$(\frac{n}{n-\ell+1})^{1/2}\geqslant 1$
, this gives
and by plugging this into (B3), we obtain
Finally, since
$T_n$
has exactly n leaves, the following lower bound is obtained immediately:
Considering a sequence
$k_n=o(\sqrt{n})$
and using Lemma 4(ii) readily concludes the proof of the proposition.
Appendix F. Blowups of Galton–Watson trees: proofs
In this appendix, we prove the results stated in Subsection 3.3. Most of the appendix is devoted to the proof of Theorem 4, but more elementary and general results about the
$B_2$
index of blowups of (not necessarily random) trees are also given.
Throughout this appendix, we use the notation and assumptions of Appendix E:
$T\sim \mathrm{GW}(\xi)$
is a Galton–Watson tree with offspring distribution
$\xi$
, and we assume that
$\xi$
is critical, with
$\mathbb{P}{(\xi=0)}>0$
and
$\mathbb{E}{[\xi^3]}<\infty$
. We denote by
$T_n$
(respectively
$T_*$
) the corresponding tree conditioned on having n leaves (respectively Kesten tree).
We also use the notation of Subsection 3.3:
$G_n$
and
$G_*$
denote blowups of
$T_n$
and
$T_*$
with respect to a fixed sequence of distributions
$\nu=(\nu_k)_{k\geqslant 1}$
. Finally, for any G blowup of T and for each vertex
$u\in T$
, we let
$\Gamma_{\!u} \sim \nu_{d^+(u)}$
denote the random network associated with u in the blowup construction of G.
In the statement of the next lemma, let us write
$(u_i)_{i\geqslant 0}$
for the vertices along the spine of
$T_*$
, and for each
$i\geqslant 0$
let
$v_i$
be the root of
$\Gamma_{u_i}$
.
Lemma 5. Let
$p_k=p_{v_k}$
denote the probability (conditional on
$G_*$
) for the directed random walk on
$G_*$
, started from the root, to reach
$v_k$
. Then
-
(i)
$\mathbb{E}{[p_k]} = (1-\eta_0)^k$
, -
(ii)
$p_k = O((1-\eta_0)^k)$
almost surely,
where
$\eta_0 = \mathbb{P}{(\xi =0)} >0$
.
Proof. For
$k\geqslant 0$
, let
$G_*^k$
denote the almost surely finite network obtained from
$G^*$
by removing all (strict) descendants of
$v_k$
—with the notation of Appendix E, this is a blowup of
$T_*^k$
with respect to
$\nu$
. Let us now fix
$k\geqslant 0$
and define D to be the out-degree of
$u_k$
, i.e. the number of leaves of
$\Gamma_{u_k}$
. For each
$i = 1, \ldots, D$
, let then
$q_i$
denote the probability, conditional on
$\Gamma_{u_k}$
, for a random walk started from
$v_k$
to pass through the ith leaf of
$\Gamma_{u_k}$
. Because
$\Gamma_{u_k}$
is leaf-exchangeable, we have
and because
$u_{k+1}$
is chosen uniformly among the children of
$u_k$
,
Integrating this with respect to D, we get
Because the out-degrees of the vertices are i.i.d. on the spine of
$T_*$
, it follows that
$(1-\eta_0)^{-k}p_k$
is a positive martingale. As a result, it converges almost surely to a non-negative random variable. This concludes the proof.
We are now ready to prove Theorem 4, whose statement we recall here for convenience.
Theorem 1. (Repeated from Subsection 3.3.) With the notation above, assuming that
$\xi$
satisfies
$\mathbb{E}{[\xi]} = 1$
,
$\mathbb{P}{(\xi = 0)} > 0$
, and
$\mathbb{E}{[|\xi|^3]} < +\infty$
, we have
-
(i)
$B_2(G_n) \to B_2(G_*)$
in distribution. -
(ii) For all
$p\geqslant 1$
,
$\mathbb{E}{[B_2(G_n)^p]} \to \mathbb{E}{[B_2(G_*)^p]}$
, and all these moments are finite.
Proof. The proof of the convergence in distribution consists in building a coupling of
$(G_n)_{n\geqslant 1}$
and
$G_*$
such that any subsequence of
$(B_2(G_n))_{n\geqslant 0}$
has a subsequence that converges to
$B_2(G_*)$
almost surely. To prove the convergence of moments, we show that, for all
$m \geqslant 1$
, the sequence
$(\mathbb{E}{[B_2(G_n)^m]})_{n \geqslant 1}$
is bounded.
Let us describe our coupling: First, pick any sequence of integers
$(k_n)_{n\geqslant 1}$
such that
for some
$\varepsilon > 0$
. Then, build
$(G_*, T_*)$
as in Subsection 3.3: let
$\mathcal{U}$
denote the Ulam–Harris tree, and let
$\Gamma = (\Gamma_{\!v}^{k} \,:\, v \in \mathcal{U}, k \geqslant 1)$
be a family of independent phylogenetic networks such that
$\Gamma_{\!v}^{k} \sim \nu_{k}$
. Finally, sample
$T_*$
independently of
$\Gamma$
, and let
$G_*$
be the blowup obtained from
$(T_*, \Gamma)$
.
Next, conditional on
$T_*$
, build a sequence
$(G_n, T_n)_{n\geqslant 1}$
as follows: for each
$n \geqslant 1$
, sample a conditioned
$\mathrm{GW}(\xi)$
tree
$T_n$
with n leaves, independently of
$\Gamma$
and in such a way that
where the truncated trees
$T_n^{k}$
and
$T_*^k$
are defined as in Appendix E. Finally, let
$G_n$
be the blowup obtained from
$T_n$
and
$\Gamma$
.
Let us now show that any subsequence of
$(B_2(G_n))_{n \geqslant 1}$
has a subsequence that converges to
$B_2(G_*)$
almost surely—and, therefore, in distribution. By a standard result (see, e.g., [Reference Billingsley7, Theorem 2.6]), this will prove that
$B_2(G_n) \to B_2(G_*)$
in distribution. First, note that since
$k_n = o(\sqrt{n})$
, by Proposition 12 we have
As a result, along any increasing sequence of integers there exists a subsequence, whose range we denote by A, such that
Thus, by the Borel–Cantelli lemma, there exists a random
$n_0$
such that, for all
$n\in A\cap [n_0,\infty[$
, we have
$T_n^{k_n}=T_*^{k_n}$
—and, therefore,
$G_n^{k_n}=G_*^{k_n}$
.
As previously, for each k let
$v_k$
denote the distinguished leaf of
$G_n^{k}$
and let
$p_k = p_{v_k}$
denote the probability that the directed random walk reaches it. Since on the event
$\{G_n^{k_n}=G_*^{k_n}\}$
, the network
$G_n$
can be obtained from
$G_*^k$
by grafting a network with at most n leaves on
$v_k$
, by Proposition 1 we have
Because
$k_n \gg \log\log n$
, by Lemma 5 the term
$p_{k_n} \log_2 n$
vanishes almost surely. Finally, by Proposition 11,
$B_2(G_*^{k_n}) \to B_2(G_*)$
almost surely. As a result,
$B_2(G_n) \to B_2(G_*)$
along the subsequence indexed by A, concluding the proof of point (i).
It remains to show the convergence of all moments of
$B_2(G_n)$
. Because we have already proved the convergence in distribution, it is sufficient to show that for all
$m\geqslant 1$
,
$\mathbb{E}{[B_2(G_n)^m]}$
is bounded: indeed, this implies that
$(B_2(G_n)^m)_{n\geqslant 1}$
is uniformly integrable—which, together with the convergence in distribution, implies the convergence of moments (see, e.g., [Reference Kallenberg17, Lemma 5.11]).
Note that
Using
$(a+b)^m \leqslant 2^{m-1}(a^m + b^m)$
for
$a, b \geqslant 0$
, bounding
$\unicode{x1D7D9}_{\{G_n^{k_n} = G_*^{k_n}\}}$
by 1, and taking expectations, we get
Recalling that
$\log \log n \ll k_n \ll n^{1/2-\epsilon}$
and that
$d_{\mathrm{TV}}(T_n^{k_n}, T_*^{k_n}) = O(k_n / \sqrt{n})$
, we see that the first term on the right-hand side vanishes as
$n\to\infty$
. So does
$\mathbb{E}{[p_{k_n}^m]} (\!\log_2 n)^m$
, since
$p_{k_n}^m \leqslant p_{k_n}$
and, by Lemma 5,
$\mathbb{E}{[p_{k_n}]} = (1-\eta_0)^{k_n}$
with
$(1-\eta_0)<1$
. Finally,
$B_2(G_*^{k_n})\leqslant B_2(G_*)$
. Therefore, to conclude the proof it suffices to show that
$\mathbb{E}{[B_2(G_*)^m]}$
is finite.
Let us fix some notation: let
$u_k$
denote the kth vertex along the spine of
$T_*$
, and let
$\Gamma_{\!u_k}$
be the corresponding network in the blowup construction of
$G_*$
. Let
$\hat{\xi}_k$
be the number of leaves of
$\Gamma_{\!u_k}$
, and for
$i = 1, \ldots, \hat{\xi}_k$
let
$q_{k, i}$
be the probability that the directed random walk started from the root of
$G_*$
goes through the ith leaf of
$\Gamma_{\!u_k}$
. Note that, because of the leaf-exchangeability of
$\Gamma_{\!u_k}$
, we can assume that for all
$k\geqslant 0$
the spine goes through the first leaf of
$\Gamma_{\!u_k}$
, so that
$q_{k, 1} = p_{k+1}$
. Finally, let us write
$G_{k,i}$
for the finite phylogenetic network consisting of the ith leaf of
$\Gamma_{\!u_k}$
and all of its descendants. With this notation, by the grafting property,
\begin{align*} B_2(G_*) = \sum_{k\geqslant 0} \Bigg( p_k\, B_2(\Gamma_{\!u_k}) + \sum_{i=2}^{\hat{\xi}_k} q_{k,i}\, B_2(G_{k,i}) \Bigg).\end{align*}
Therefore,
\begin{equation} \mathbb{E}{[B_2(G_*)^m]} \leqslant 2^{m-1} \left(\! \mathbb{E}{\Bigg[\!\Bigg(\sum_{k\geqslant 0}p_k\,B_2(\Gamma_{\!u_k})\!\Bigg)^m\Bigg]} + \mathbb{E}{\Bigg[\!\Bigg(\sum_{k\geqslant 0}\sum_{i=2}^{\hat{\xi}_k} q_{k,i} B_2(G_{k,i})\Bigg)^m\Bigg]} \right).\end{equation}
To bound the first term on the right-hand side, note that since
$p_k^m \leqslant p_{k}$
and since
$p_{k}$
is independent of
$\Gamma_{\!u_k}$
,
Using
$\mathbb{E}{[p_{k}]} = (1-\eta_0)^{k}$
and
$B_2(\Gamma_{\!u_k}) \leqslant \log_2 \hat{\xi}_k$
, we obtain
Since
$\xi$
has a finite variance, it follows that
$\hat{\xi}$
has a finite mean, and therefore that
$\mathbb{E}{[(\!\log_2 \hat{\xi})^m]} < \infty$
. Thus, if we let
$\left\lVert \cdot \right\rVert_{m} = \mathbb{E}{[\left|{\,\cdot\,}\right|^m]}^{1/m}$
denote the
$L^m$
-norm then
As a result, by the triangle inequality,
\begin{align*} \Bigg\|\sum_{k\geqslant 0}p_kB_2(\Gamma_{\!u_k})\Bigg\|_m \leqslant \sum_{k\geqslant 0}\left\lVert{p_k\, B_2(\Gamma_{\!u_k})}\right\rVert_{m} < \infty .\end{align*}
Finally, to bound the second term in (F1), note that
$\sum_{k\geqslant 0} \sum_{i = 2}^{\hat{\xi}_k} q_{k, i} = 1$
almost surely. Thus, Jensen’s inequality gives
\begin{align*} \mathbb{E}{\Bigg[\Bigg(\sum_{k\geqslant 0}\sum_{i=2}^{\hat{\xi}_k} q_{k,i}\, B_2(G_{k,i})\Bigg)^m\Bigg]} \leqslant \mathbb{E}{\Bigg[\,\sum_{k\geqslant 0}\sum_{i=2}^{\hat{\xi}_k} q_{k,i}\, B_2(G_{k,i})^m\Bigg]} = \mathbb{E}{\big[B_2(G)^m\big]},\end{align*}
where G is a blowup of T, the Galton–Watson tree with offspring distribution
$\xi$
(the last equality follows from the fact that the
$G_{k, i}$
’s are independent of the
$q_{k, i}$
’s and are all distributed as G). Thus, to finish the proof it suffices to note that, since
$B_2(G) \leqslant \log_2 \left|{T}\right|$
, where
$\left|{T}\right|$
denotes the number of leaves of T, we have
Indeed, it is classic (see also Lemma 4) that
$\mathbb{P}{(|{T}| \geqslant n)}=\Theta(n^{-1/2})$
, which implies that
$(\!\log_{2}\left|{T}\right|)^m$
is integrable. This concludes the proof.
Let us close this appendix by listing further properties of the
$B_2$
index of blowups of trees. Although some of these properties are not related to Galton–Watson trees, the reason why we list them here is that proving them requires some of the vocabulary and notation of this appendix, and that they all follow readily from the following elementary proposition.
Proposition 13. Let
$\mathbf{t}$
be a fixed tree, and let G be the blowup of
$\,\mathbf{t}$
with respect to some family of random networks
$\nu = (\nu_k)_{k\geqslant 1}$
. Let X denote the directed random walk on
$\mathbf{t}$
, and for all
$v \in \mathbf{t}$
, let
$p_v = \mathbb{P}{(v\in X)}$
. Then
\begin{align*} \mathbb{E}{[B_2(G)]} = \sum_{v \in \mathbf{t}} p_v f(d^{+}(v)) = \mathbb{E}{\Bigg[\sum_{t\geqslant 0} f(d^{+}(X_t))\Bigg]} ,\end{align*}
where
$d^+(v)$
denotes the outdegree of v in
$\mathbf{t}$
, and
$f \colon k \mapsto \mathbb{E}{[B_2(\Gamma_{\!k})]}$
, with
$\Gamma_{\!k}\sim \nu_k$
and the convention
$f(0) = 0$
.
Proof. Let
$\rho$
denote the root of
$\mathbf{t}$
and, for conciseness, write
$\delta \,:\!=\, d^+(\rho)$
for its out-degree. Let
$\Gamma_{\!\rho} \sim \nu_{\delta}$
denote the random network associated with
$\rho$
in the blowup construction of G. Finally, let
$\mathbf{t}_1, \ldots, \mathbf{t}_{\delta}$
denote the subtrees of
$\mathbf{t}$
subtended by the children of
$\rho$
, and let
$G_1, \ldots, G_{\delta}$
be the corresponding blowups with respect to
$\nu$
.
Since G is obtained by grafting
$G_1, \ldots, G_{\delta}$
on the leaves of
$\Gamma_{\!\rho}$
, by the grafting property we have
\begin{equation} B_2(G) = B_2(\Gamma_{\!\rho}) + \sum_{i = 1}^{\delta} q_{\rho}(i) \, B_2(G_i) ,\end{equation}
where
$q_{\rho}(i)$
denotes the probability that the directed random walk on
$\Gamma_{\!\rho}$
ends at its ith leaf. Note that
$q_{\rho}$
is a random probability distribution on
$\{1, \ldots, \delta\}$
, and that it follows from the definition of blowups that
-
(i) being a deterministic function of
$\Gamma_{\!\rho}$
,
$q_{\rho}$
is independent of
$(G_1, \ldots, G_{\delta})$
; -
(ii) by the leaf-exchangeability of
$\Gamma_{\!\rho}$
,
$q_{\rho}$
is exchangeable.
As a result, taking expectations in (F2), we get
\begin{align*} \mathbb{E}{[B_2(G)]} = f(\delta) + \frac{1}{\delta} \sum_{i = 1}^{\delta} \mathbb{E}{[B_2(G_i)]} ,\end{align*}
and
$\mathbb{E}{[B_2(G)]} = \sum_{v \in \mathbf{t}} p_v f(d^{+}(v))$
follows by induction. Finally, to see that this is also
$\mathbb{E}{[\sum_{t\geqslant 0} f(d^{+}(X_t))]}$
, it suffices to note that
$p_v = \sum_{t\geqslant 0} \mathbb{P}{(X_t = v)}$
for any internal vertex v, and that
$\sum_{v \in \mathbf{t}} \unicode{x1D7D9}_{\{X_t = v\}} = 1$
almost surely for all
$t\geqslant 0$
.
By ‘not blowing up’ the base tree
$\mathbf{t}$
in Proposition 13 (i.e. by using star trees for the networks by which internal vertices are replaced in the blowup, so that the tree is left unchanged), we immediately get the following simple expression for the
$B_2$
index of a tree. This expression does not seem to have been pointed out previously in the literature.
Corollary 2. For any tree
$\mathbf{t}$
, we have
where
$d^+(v)$
denotes the out-degree of v in
$\mathbf{t}$
, and
$p_v = \big(\prod_u d^{+}(u)\big)^{-1}$
, where the product runs over the vertices on the path from the root of
$\mathbf{t}$
to v, excluding v.
Because
$f(k) \leqslant \log_2 k$
, Proposition 13 also has the following corollary.
Corollary 3. Let
$\mathbf{t}$
be a fixed tree, and let G be a blowup of
$\,\mathbf{t}$
. Then
Note, however, that the inequality in Corollary 3 holds only after integration with respect to the blowup procedure. In particular, if T is a random tree and G is a blowup of T, then
$B_2(T)$
does not necessarily stochastically dominate
$B_2(G)$
. To see this, let
$T = \mathbf{t}$
be deterministic, and note that it is then possible to have
$B_2(G) > B_2(\mathbf{t})$
. This implies that, in that case, there is not monotone coupling of
$B_2(G)$
and
$B_2(T)$
.
Nevertheless, as the next corollary shows,
$B_2(T)$
is second-order stochastically dominant over
$B_2(G)$
. Very loosely speaking, this means that—in addition to being no smaller in expectation—
$B_2(T)$
is more predictable than
$B_2(G)$
.
Corollary 4. Let T be a tree, and let G be a blowup of T. Then
$B_2(T)$
is second-order stochastically dominant over
$B_2(G)$
; that is, for every non-decreasing concave function
$\phi$
,
Proof. Let
$\phi$
be a non-decreasing concave function. First, by Corollary 3, we have
$\mathbb{E}{[B_2(G) | T]} \leqslant B_2(T)$
, and therefore
As a result, by Jensen’s inequality,
concluding the proof.
Finally, note that Proposition 13 yields a simple derivation of the expression that was already given in Theorem 5 for the expected value of the
$B_2$
index of blowups of Galton–Watson trees. Before detailing this, let us briefly compare the two approaches: Recall that the proof of Theorem 5 used the recursive structure of Galton–Watson trees (i.e. the branching property) together with the independence between the base tree and the networks used in the blowup procedure to get a distributional equation for
$B_2(G)$
. In a way, Proposition 13 isolates the part of the proof of Theorem 5 where the independence between the base tree and the networks is used, and in the proof below we use the branching property to recover the expression given in Theorem 5; what justifies presenting the two proofs is that the way the branching property is used is different.
Corollary 5. Let T be a Galton–Watson tree with offspring distribution
$\xi$
and let G be a blowup of T with respect to a family of networks
$\nu = (\nu_k)_{k\geqslant 1}$
. Then
where
$f(0) = 0$
and, for
$k\geqslant 1$
,
$f(k) = \mathbb{E}{[B_2(\Gamma_{\!k})]}$
, where
$\Gamma_{\!k} \sim \nu_k$
, and with the convention
$0/0 = 0$
.
Proof. First, let us deal with degenerate cases: When
$\mathbb{P}{(\xi = 1)} = 1$
, the tree T is an infinite path, and therefore G has exactly one end, which implies
$B_2(G) = 0$
. Since
$f(1) = 0$
, the proposition holds with the convention
$0/0 = 0$
. In the case where
$\xi$
is not almost surely equal to 1 and where
$\mathbb{P}{(\xi = 0)} = 0$
, we have
$B_2(G) = +\infty$
and the proposition also holds.
Now, assume that
$\mathbb{P}{(\xi =0)}> 0$
. Note that, by the branching property,
\begin{align*} \sum_{t\geqslant 0} f(d^{+}(X_t)) \mathrel{\overset{d}{=}} \sum_{i = 1}^{N} f\big(\xi^+_i\big),\end{align*}
where
$(\xi_i^+)_{i\geqslant 1}$
are i.i.d. copies of
$(\xi \mid \xi > 0)$
, the variable
$\xi$
is conditioned to be positive, and N is a geometric variable on
$\{0, 1, \ldots\}$
with parameter
$\eta_0 \,:\!=\, \mathbb{P}{(\xi = 0)}$
that is independent of
$(\xi_i^+)_{i\geqslant 1}$
. As a result, by Wald’s formula,
because
$f(0) = 0$
. This concludes the proof.
Funding information
Part of this work was done while FB was at the Institute for Theoretical Studies of ETH Zürich and was supported by Dr. Max Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation. FB and J-JD were in part supported by the Agence Nationale de la Recherche, France, under grant ANR-24-CE40-7154. MF and T-CY were in part supported by the National Science and Technology Council, Taiwan, under grant NSTC-111-2115-M-004-002-MY2.
Competing interests
There are no competing interests to declare that arose during the preparation of or the publication process for this article.






n=8
p1
1/8
p3
1/16+1/8
G1
G2
k+m⩾1
B2([G]k)=𝟙{k is odd}
A
B
C
ℵ0=Card(N)
D
2ℵ0=Card(R)
v1→v2→⋯
(Gn′)
Gn
Gn′
vn
Gn→G
B2(Gn)=B2(G)+pvnB2(Gn′)
v∈T
Γv
Γ3
G∗
ξ
Γ∼νξ
G∗
ξ^−1
Γ∗∼νξ^
k=2
k=3
(ℓn)
m∈K∖∂G
K
∂G
K