Orchard networks are trees with additional horizontal arcs (Q2155699)

Let us consider the class of phylogenetic \textit{orchard networks}. Such a phylogenetic network has been defined as one that can be reduced to a single node by either deleting one leaf from a pair of leaves with a common parent, or by deleting an internal edge (arc) whose both endpoints are parents of leaves. The authors show that such networks, can be characterized in a more natural way. They are exactly those networks that can be obtained from phylogenetic trees by inserting horizontal (when the original tree is drawn with the root at the top and all edges directed downwards) arcs. Unlike other tree-based networks, orchard networks have a time-consistency property -- the between-lineages arc links points which coexist at the same time, assuming that the underlying tree/network is time calibrated. Other tree-based networks may have non-horizontal arcs, e.g., linking internal nodes from different time points. Based on the new representation the Authors show that the space of orchard networks is connected under \textit{rooted nearest neighbour interchange}. Such move is defined as follows, let \(p,c,w,x,y,z\) be nodes in the network such that \((z,w)\) is an arc; either \((x,y)\) or \((y,x)\) is an arc; \(p\) and \(c\) are the parent and child of \(x\) that are not \(y\); and \(\{p,c\}\cap\{z,w\}=\emptyset\). Let \(e\) be the arc that has \(x\) and \(y\) as its endpoints. Then the rooted nearest neighbour interchange move is to replace the arcs \((p,x)\), \((x,c)\), and \((z,w)\) with \((p,c)\) and \((z,x)\).