Enumeration of coalescent histories for caterpillar species trees and p-pseudocaterpillar gene trees

DOI10.1016/J.AAM.2021.102265zbMATH Open1471.92232arXiv2103.13464OpenAlexW3193312128MaRDI QIDQ820935FDOQ820935

Authors: Egor Alimpiev, Noah A. Rosenberg 

Publication date: 29 September 2021

Published in: Advances in Applied Mathematics (Search for Journal in Brave)

Abstract: For a fixed set $X$ containing $n$ taxon labels, an ordered pair consisting of a gene tree topology $G$ and a species tree $S$ bijectively labeled with the labels of $X$ possesses a set of coalescent histories -- mappings from the set of internal nodes of $G$ to the set of edges of $S$ describing possible lists of edges in $S$ on which the coalescences in $G$ take place. Enumerations of coalescent histories for gene trees and species trees have produced suggestive results regarding the pairs $(G,S)$ that, for a fixed $n$, have the largest number of coalescent histories. We define a class of 2-cherry binary tree topologies that we term $p$-pseudocaterpillars, examining coalescent histories for non-matching pairs $(G,S)$, in the case in which $S$ has a caterpillar shape and $G$ has a $p$-pseudocaterpillar shape. Using a construction that associates coalescent histories for $(G,S)$ with a class of "roadblocked" monotonic paths, we identify the $p$-pseudocaterpillar labeled gene tree topology that, for a fixed caterpillar labeled species tree topology, gives rise to the largest number of coalescent histories. The shape that maximizes the number of coalescent histories places the "second" cherry of the $p$-pseudocaterpillar equidistantly from the root of the "first" cherry and from the tree root. A symmetry in the numbers of coalescent histories for $p$-pseudocaterpillar gene trees and caterpillar species trees is seen to exist around the maximizing value of the parameter $p$. The results provide insight into the factors that influence the number of coalescent histories possible for a given gene tree and species tree.

Full work available at URL: https://arxiv.org/abs/2103.13464

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zbMATH Keywords

phylogeneticsCatalan numbersDyck pathscoalescent historiesmonotonic paths

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Problems related to evolution (92D15) Exact enumeration problems, generating functions (05A15) Taxonomy, cladistics, statistics in mathematical biology (92B10)

Cites Work

• A \textit{Mathematica} version of Zeilberger's algorithm for proving binomial coefficient identities
• Coalescent histories for discordant gene trees and species trees
• Analytic combinatorics
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• Catalan Numbers
• There are no caterpillars in a wicked forest
• Enumeration of lonely pairs of gene trees and species trees by means of antipodal cherries
• Roadblocked monotonic paths and the enumeration of coalescent histories for non-matching caterpillar gene trees and species trees
• Catalan's trapezoids

Cited In (8)

• Enumeration of lonely pairs of gene trees and species trees by means of antipodal cherries
• Enumeration of compact coalescent histories for matching gene trees and species trees
• The distributions under two species-tree models of the number of root ancestral configurations for matching gene trees and species trees
• Roadblocked monotonic paths and the enumeration of coalescent histories for non-matching caterpillar gene trees and species trees
• There are no caterpillars in a wicked forest
• A lattice structure for ancestral configurations arising from the relationship between gene trees and species trees
• The distributions under two species-tree models of the total number of ancestral configurations for matching gene trees and species trees
• How to Obtain the Complete List of Caterpillars

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