This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of the root and reticulation vertices, can be oriented as a directed nonbinary phylogenetic network. Moreover, we characterize when this is possible and show that, in such instances, the resulting directed nonbinary phylogenetic network is unique. In addition, without being given the location of the root and the reticulation vertices, we describe an algorithm for deciding whether an undirected binary phylogenetic network N can be oriented as a directed binary phylogenetic network of a certain class. The algorithm is fixed-parameter tractable (FPT) when the parameter is the level of N and is applicable to classes of directed phylogenetic networks that satisfy certain conditions. As an example, we show that the well-studied class of binary tree-child networks satisfies these conditions.

Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that orchard networks can be interpreted as trees with additional horizontal arcs. Therefore, they are closely related to tree-based networks, where the difference is that in tree-based networks the additional arcs do not need to be horizontal. Then, we use this new characterization to show that the space of orchard networks on n leaves with k reticulations is connected under the rNNI rearrangement move with diameter O(kn+ nlog (n)).

We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequences and runs in O((8 k) ^kpoly (n, t)) time, where n is the number of leaves of every tree, t is the number of trees, and k is the reticulation number of the constructed network. Moreover, we provide an efficient parallel implementation of the algorithm and show that it can deal with up to 100 input trees on a standard desktop computer, thereby providing a major improvement over previous phylogenetic network construction methods.

The unit distance graph G¹_Rd is the infinite graph whose nodes are points in R^d, with an edge between two points if the Euclidean distance between these points is 1. The 2-dimensional version G¹_R2 of this graph is typically studied for its chromatic number, as in the Hadwiger-Nelson problem. However, other properties of unit distance graphs are rarely studied. Here, we consider the restriction of G¹_Rd to closed convex subsets X of R^d. We show that the graph G¹_Rd[X] is connected precisely when the radius of r(X) of X is equal to 0, or when r(X) ≥ 1 and the affine dimension of X is at least 2. For hyperrectangles, we give bounds for the graph diameter in the critical case that the radius is exactly 1.

Head moves are a type of rearrangement moves for phylogenetic net-works. They have primarily been studied as part of other types of moves, such as rSPR moves. Here, we study head moves as a type of moves on themselves. We show that the tiers (k > 0) of phylogenetic network space are connected by local head moves. Then, we show tail moves and head moves are closely related: sequences of tail moves can be converted into sequences of head moves and vice versa, changing the length by at most a constant factor. Because the tiers of network space are connected by rSPR moves, this gives a second proof of the connectivity of these tiers. Furthermore, we show that these tiers have small diameter by reproving the connectivity a third time. As the head move neighbourhood is small in general, this makes head moves a good candidate for local search heuristics. Finally, we prove that finding the shortest sequence of head moves between two networks is NP-hard.

Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks. In particular, one needs to distinguish different networks and determine whether one network is contained in another. In this paper, we introduce cherry-picking networks, a class of networks that can be reduced by a so-called cherry-picking sequence. We then show how to compare such networks using their sequences. We characterize reconstructible cherry-picking networks, which are the networks that are uniquely determined by the sequences that reduce them, making them distinguishable. Furthermore, we show that a cherry-picking network is contained in another cherry picking network if a sequence for the latter network reduces the former network, provided both networks can be reconstructed from their sequences in a similar way (i.e., they are in the same reconstructible class). Lastly, we show that the converse of the above statement holds for tree-child networks, thereby showing that NETWORK CONTAINMENT, the problem of checking whether a network is contained in another, can be solved by computing cherry picking sequences in linear time for tree-child networks.

Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer. Recently, network-based Markov models of DNA sequence evolution have been introduced along with model-based methods for reconstructing phylogenetic networks. For these methods to be consistent, the network parameter needs to be identifiable from data generated under the model. Here, we show that the semi-directed network parameter of a triangle-free, level-1 network model with any fixed number of reticulation vertices is generically identifiable under the Jukes–Cantor, Kimura 2-parameter, or Kimura 3-parameter constraints.

Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive representation of evolutionary history compared to phylogenetic trees. Stochastic processes for generating random trees or networks are important tools in evolutionary analysis, especially in phylogeny reconstruction where they can be utilized for validation or serve as priors for Bayesian methods. However, as more network generators are developed, there is a lack of discussion or comparison for different generators. To bridge this gap, we compare a set of phylogenetic network generators by profiling topological summary statistics of the generated networks over the number of reticulations and comparing the topological profiles.

Phylogenetic networks are used to represent evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which stem from both biological and computational motivations. We study two network classes in this paper: tree-based networks and orchard networks. Tree-based networks are those that can be obtained by inserting edges between the edges of an underlying tree. Orchard networks are a recently introduced generalization of the class of tree-child networks. Structural characterizations have already been discovered for tree-based networks; this is not the case for orchard networks. In this paper, we introduce cherry covers—a unifying characterization of both network classes—in which we decompose the edges of the networks into so-called cherry shapes and reticulated cherry shapes. We show that cherry covers can be used to characterize the class of tree-based networks as well as the class of orchard networks. Moreover, we also generalize these results to non-binary networks.

Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one network is embedded in another. Here, we consider the Network Containment problem, which asks whether a given network is contained in another network. We give a linear-time algorithm to this problem for the class of tree-child networks using the recently introduced tree-child sequences by Linz and Semple. We implement this algorithm in Python and show that the linear-time theoretical bound on the input size is achievable in practice.

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree based on a model with speciation and duplication where duplications are clustered in duplication episodes. The goal is to minimize the number of such episodes. The second variant, Parental Hybridization, aims at inferring a species network based on a model with speciation and reticulation. The goal is to minimize the number of reticulation events. It is a variant of the well-studied Hybridization Number problem with a more generous view on which gene trees are consistent with a given species network. We show that these seemingly different problems are in fact closely related and can, surprisingly, both be solved in polynomial time, using a structure we call 'beaded trees'. However, we also show that methods based on these problems have to be used with care because the optimal species phylogenies always have a restricted form. To mitigate this problem, we introduce a new variant of Unrestricted Minimal Episodes Inference that minimizes the duplication episode depth. We prove that this new variant of the problem can also be solved in polynomial time.

Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks. To find bigger networks, one can attempt to combine small networks. In this paper, we study the Network Hybridization problem, a problem of combining networks into another network with low complexity. We characterize this complexity via a restricted problem, Tree-child Network Hybridization, and we present an FPT algorithm to efficiently solve this restricted problem.

The burning number of a graph was recently introduced by Bonato et al. Although they mention that the burning number generalises naturally to directed graphs, no further research on this has been done. Here, we introduce graph burning for directed graphs, and we study bounds for the corresponding burning number and the hardness of finding this number. We derive sharp bounds from simple algorithms and examples. The hardness question yields more surprising results: finding the burning number of a directed tree with one indegree-0 node is NP-hard, but FPT; however, it is W[2]complete for DAGs. Finally, we give a fixed-parameter algorithm to find the burning number of a digraph, with a parameter inspired by research in phylogenetic networks.

Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and regraft), and TBR (tree bisection and reconnection). Recently, these operations have been extended to unrooted phylogenetic networks-generalisations of phylogenetic trees that can model reticulated evolutionary relationships-where they are called NNI, PR, and TBR moves. Here, we study global and local properties of spaces of phylogenetic networks under these three operations. In particular, we prove connectedness and asymptotic bounds on the diameters of spaces of different classes of phylogenetic networks, including tree-based and level-k networks. We also examine the behaviour of shortest TBR-sequence between two phylogenetic networks in a class, and whether the TBR-distance changes if intermediate networks from other classes are allowed: for example, the space of phylogenetic trees is an isometric subgraph of the space of phylogenetic networks under TBR. Lastly, we show that computing the TBR-distance and the PR-distance of two phylogenetic networks is NP-hard.

Network reconstruction lies at the heart of phylogenetic research. Two well-studied classes of phylogenetic networks include tree-child networks and level-k networks. In a tree-child network, every non-leaf node has a child that is a tree node or a leaf. In a level-k network, the maximum number of reticulations contained in a biconnected component is k. Here, we show that level-k tree-child networks are encoded by their reticulate-edge-deleted subnetworks, which are subnetworks obtained by deleting a single reticulation edge, if k≥ 2. Following this, we provide a polynomial-time algorithm for uniquely reconstructing such networks from their reticulate-edge-deleted subnetworks. Moreover, we show that this can even be done when considering subnetworks obtained by deleting one reticulation edge from each biconnected component with k reticulations.

Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rooted Nearest Neighbour Interchange (rNNI) and rooted Subtree Prune and Regraft (rSPR). Recently, these moves were generalized to rooted phylogenetic networks, which are a more suitable representation of reticulate evolutionary histories, and it was shown that any two rooted phylogenetic networks of the same complexity are connected by a sequence of either rSPR or rNNI moves. Here, we show that this is possible using only tail moves, which are a restricted version of rSPR moves on networks that are more closely related to rSPR moves on trees. The connectedness still holds even when we restrict to distance-1 tail moves (a localized version of tail moves). Moreover, we give bounds on the number of (distance-1) tail moves necessary to turn one network into another, which in turn yield new bounds for rSPR, rNNI and SPR (i.e. the equivalent of rSPR on unrooted networks). The upper bounds are constructive, meaning that we can actually find a sequence with at most this length for any pair of networks. Finally, we show that finding a shortest sequence of tail or rSPR moves is NP-hard.

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree based on a model of speciation and duplication where duplications are clustered in duplication episodes. The goal is to minimize the number of such episodes. The second variant, Parental Hybridization, aims at inferring a species network based on a model of speciation and reticulation. The goal is to minimize the number of reticulation events. It is a variant of the well-studied Hybridization Number problem with a more generous view on which gene trees are consistent with a given species network. We show that these seemingly different problems are in fact closely related and can, surprisingly, both be solved in polynomial time, using a structure we call “beaded trees”. However, we also show that methods based on these problems have to be used with care because the optimal species phylogenies always have some restricted form. We discuss several possibilities to overcome this problem.