A framework for representing reticulate evolution
In biology it is a very important task representing the evolution of the living world. Generally rooted trees are used to display the evolutionary relations. It is well known, however, that the real-world evolution is ``reticulate (= non-tree like) as a consequence of ``hybridizations and ``horizontal gene transfers. Therefore acyclic directed graphs (ADG) can be better tools to describe the evolution. This paper starts the systematic study of the usage of ADGs for this purpose. It discusses in details how one can use these objects to analyse evolutionary relationships, displaying more evolutionary trees in one ADG, where hybridizations are represented with vertices of higher in-degree. The paper also recognizes that, since hybridizations are relatively rare events, it is an important requirement to keep the number of vertices of higher in-degree low. A plausible set of definitions is introduced and important statements are proved for them.
- Reconstruction of LGT networks from tri-LGT-nets
- Reconstruction of certain phylogenetic networks from the genomes at their leaves
- Merging arcs to produce acyclic phylogenetic networks and normal networks
- Distinct-cluster tree-child phylogenetic networks and possible uses to study polyploidy
- Classes of explicit phylogenetic networks and their biological and mathematical significance
- Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes
- Trinets encode tree-child and level-2 phylogenetic networks
- Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks
- On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters
- Properties of normal phylogenetic networks
- Bounding the number of hybridisation events for a consistent evolutionary history
- Unique determination of some homoplasies at hybridization events
- Reconstruction of some hybrid phylogenetic networks with homoplasies from distances
- Computing quadratic entropy in evolutionary trees
- Accumulation phylogenies
- Restricted trees: simplifying networks with bottlenecks
- The rigid hybrid number for two phylogenetic trees
- Hybridization number on three rooted binary trees is EPT
- Modelling reticulate evolution
- Hybrid phylogenies with certain properties of regularity
- Reconstruction of certain phylogenetic networks from their tree-average distances
- Optimizing tree and character compatibility across several phylogenetic trees
- Combining Networks Using Cherry Picking Sequences
- Comparing and simplifying distinct-cluster phylogenetic networks
- Consensus clusters in Robinson-Foulds reticulation networks
- Topology of viral evolution
- Constructing the simplest possible phylogenetic network from triplets
- Beyond evolutionary trees
- Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph
- Finding agreement cherry-reduced subnetworks in level-1 networks
- A cluster reduction for computing the subtree distance between phylogenies
- Characterizing and transforming DAGs within the \(\mathfrak{I}\)-lca framework
- Simplifying and characterizing DAGs and phylogenetic networks via least common ancestor constraints
- Inferring DAGs and phylogenetic networks from least common ancestors
- Unique reconstruction of tree-like phylogenetic networks from distances between leaves
- Computing the minimum number of hybridization events for a consistent evolutionary history
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