Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer) occurred. Tree-child network is a kind of phylogenetic network with structural constraints. Existing approaches for tree-child network reconstruction can be slow for large data. In this paper, we present several computational approaches for bounding from below the number of reticulations in a tree-child network that displays a given set of rooted binary phylogenetic trees. Through simulation, we demonstrate that the new lower bounds on the reticulation number for tree-child networks can practically be computed for large tree data. The bounds can provide estimates of reticulation for relatively large data.
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A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the minimum phylogenetic network problem, in which phylogenetic trees are first inferred, and then the smallest phylogenetic network that displays all the trees is computed. The approach takes advantage of the fact that the theory of phylogenetic trees is mature, and there are excellent tools available for inferring phylogenetic trees from a large number of biomolecular sequences. A tree–child network is a phylogenetic network satisfying the condition that every nonleaf node has at least one child that is of indegree one. Here, we develop a new method that infers the minimum tree–child network by aligning lineage taxon strings in the phylogenetic trees. This algorithmic innovation enables us to get around the limitations of the existing programs for phylogenetic network inference. Our new program, named ALTS, is fast enough to infer a tree–child network with a large number of reticulations for a set of up to 50 phylogenetic trees with 50 taxa that have only trivial common clusters in about a quarter of an hour on average.
more » « less- Award ID(s):
- 1909425
- PAR ID:
- 10540529
- Publisher / Repository:
- Cold Spring Harbor Laboratory Press
- Date Published:
- Journal Name:
- Genome Research
- Volume:
- 33
- ISSN:
- 1088-9051
- Page Range / eLocation ID:
- 1053–1060
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer) occurred. Tree-child network is a kind of phylogenetic network with structural constraints. Existing approaches for tree-child network reconstruction can be slow for large data. In this study, we present several computational approaches for bounding from below the number of reticulations in a tree-child network that displays a given set of rooted binary phylogenetic trees. In addition, we also present some theoretical results on bounding from above the number of reticulations. Through simulation, we demonstrate that the new lower bounds on the reticulation number for tree-child networks can practically be computed for large tree data. The bounds can provide estimates of reticulation for relatively large data.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1101/gr.277669.123
