Operads and Phylogenetic Trees

zbMATH Open1411.18014arXiv1512.03337MaRDI QIDQ4563202FDOQ4563202

Authors: John Baez, Nina Otter 

Publication date: 7 June 2018

Abstract: We construct an operad $mathrmPhyl$ whose operations are the edge-labelled trees used in phylogenetics. This operad is the coproduct of $mathrmCom$, the operad for commutative semigroups, and $[0,infty)$, the operad with unary operations corresponding to nonnegative real numbers, where composition is addition. We show that there is a homeomorphism between the space of $n$-ary operations of $mathrmPhyl$ and $mathcal{T}_{n}imes[0,infty{)}^{n+1}$, where $mathcal{T}_n$ is the space of metric $n$-trees introduced by Billera, Holmes and Vogtmann. Furthermore, we show that the Markov models used to reconstruct phylogenetic trees from genome data give coalgebras of $mathrmPhyl$. These always extend to coalgebras of the larger operad $mathrmCom+[0,infty]$, since Markov processes on finite sets converge to an equilibrium as time approaches infinity. We show that for any operad $O$, its coproduct with $[0,infty]$ contains the operad $W(O)$ constucted by Boardman and Vogt. To prove these results, we explicitly describe the coproduct of operads in terms of labelled trees.

Full work available at URL: https://arxiv.org/abs/1512.03337

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zbMATH Keywords

treesMarkov processesoperadsphylogenetic trees

Mathematics Subject Classification ID

Trees (05C05)

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Cited In (1)

• Systematics and symmetry in molecular phylogenetic modelling: perspectives from physics

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