Defining phylogenetic networks using ancestral profiles

DOI10.1016/J.MBS.2021.108537zbMATH Open1475.92114OpenAlexW3120743784WikidataQ129176613 ScholiaQ129176613MaRDI QIDQ2240236FDOQ2240236

Authors Allan Bai, Charles Semple, Péter L. Erdős, Mike Steel 

Publication date 8 November 2021

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2012.00109

zbMATH Keywords

tree-child networksorchard networksaccumulation phylogeniesancestral profilespath-tuples

Mathematics Subject Classification ID

Problems related to evolution (92D15)

Abstract: Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is to consider its `ancestral profile' (the number of paths from each ancestral vertex to each leaf). In general, this information does not uniquely determine the underlying phylogenetic network. A recent paper considered a new class of phylogenetic networks called `orchard networks' where this uniqueness was claimed to hold. Here we show that an additional restriction on the network, that of being `stack-free', is required in order for the original uniqueness claim to hold. On the other hand, if the additional stack-free restriction is lifted, we establish an alternative result; namely, there is uniqueness within the class of orchard networks up to the resolution of vertices of high in-degree.

Recommendations

• A class of phylogenetic networks reconstructable from ancestral profiles
• Tree-based unrooted phylogenetic networks
• Reconstructibility of unrooted level-\(k\) phylogenetic networks from distances
• Orchard networks are trees with additional horizontal arcs
• Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks

Cites work

• scientific article; zbMATH DE number 1865935 (Why is no real title available?)
• A class of phylogenetic networks reconstructable from ancestral profiles
• Caterpillars on three and four leaves are sufficient to binary normal networks
• Determining phylogenetic networks from inter-taxa distances
• On cherry-picking and network containment
• Phylogenetic networks with every embedded phylogenetic tree a base tree
• Properties of normal phylogenetic networks
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Cited in

(4)

• Classes of explicit phylogenetic networks and their biological and mathematical significance
• Autopolyploidy, allopolyploidy, and phylogenetic networks with horizontal arcs
• Orchard networks are trees with additional horizontal arcs
• A class of phylogenetic networks reconstructable from ancestral profiles

Describes a project that uses

Uses Software

• PhyloNetwork

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