Quantifying genetic innovation: mathematical foundations for the topological study of reticulate evolution

DOI10.1137/18M118150XMaRDI QIDQ4959843zbMATH OpenOpenAlexWikidataFDO

Authors Michael Lesnick, R. Rabadán, Daniel I. Scholes Rosenbloom

Publication date 7 April 2020

Published in SIAM Journal on Applied Algebra and Geometry (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1804.01398

zbMATH Keywords

persistent homologytopological data analysisrecombinationreticulate evolution

Mathematics Subject Classification ID

Problems related to evolution (92D15) Persistent homology and applications, topological data analysis (55N31)

Abstract: A topological approach to the study of genetic recombination, based on persistent homology, was introduced by Chan, Carlsson, and Rabad'an in 2013. This associates a sequence of signatures called barcodes to genomic data sampled from an evolutionary history. In this paper, we develop theoretical foundations for this approach. First, we present a novel formulation of the underlying inference problem. Specifically, we introduce and study the novelty profile, a simple, stable statistic of an evolutionary history which not only counts recombination events but also quantifies how recombination creates genetic diversity. We propose that the (hitherto implicit) goal of the topological approach to recombination is the estimation of novelty profiles. We then study the problem of obtaining a lower bound on the novelty profile using barcodes. We focus on a low-recombination regime, where the evolutionary history can be described by a directed acyclic graph called a galled tree, which differs from a tree only by isolated topological defects. We show that in this regime, under a complete sampling assumption, the $1^{m}athrmst$ barcode yields a lower bound on the novelty profile, and hence on the number of recombination events. For $i>1$, the $i^{mathrmth}$ barcode is empty. In addition, we use a stability principle to strengthen these results to ones which hold for any subsample of an arbitrary evolutionary history. To establish these results, we describe the topology of the Vietoris--Rips filtrations arising from evolutionary histories indexed by galled trees. As a step towards a probabilistic theory, we also show that for a random history indexed by a fixed galled tree and satisfying biologically reasonable conditions, the intervals of the $1^{mathrmst}$ barcode are independent random variables. Using simulations, we explore the sensitivity of these intervals to recombination.

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Cited in

(11)

• Vietoris-Rips and Čech complexes of metric gluings
• A primer on persistent homology of finite metric spaces
• On a coupled map lattice formulation of the evolution of genetic sequences
• On homotopy types of Vietoris-Rips complexes of metric gluings
• The arithmetic topology of genetic alignments
• On Vietoris-Rips complexes of hypercube graphs
• Operations on Metric Thickenings
• Topological signatures for population admixture
• New families of stable simplicial filtration functors
• The evolution of genetic topologies
• On Vietoris–Rips Complexes (with Scale 3) of Hypercube Graphs

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