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Genetics. 2019 Apr;211(4):1191-1204. doi: 10.1534/genetics.118.301565. Epub 2019 Feb 20.

Fast Estimation of Recombination Rates Using Topological Data Analysis.

Author information

1
Department of Integrative Biology, The University of Texas at Austin, Texas 78712.
2
Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912.
3
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 m_miyagi@g.harvard.edu.
4
Department of Mathematics, The University of Texas at Austin, Texas 78712.

Abstract

Accurate estimation of recombination rates is critical for studying the origins and maintenance of genetic diversity. Because the inference of recombination rates under a full evolutionary model is computationally expensive, we developed an alternative approach using topological data analysis (TDA) on genome sequences. We find that this method can analyze datasets larger than what can be handled by any existing recombination inference software, and has accuracy comparable to commonly used model-based methods with significantly less processing time. Previous TDA methods used information contained solely in the first Betti number ([Formula: see text]) of a set of genomes, which aims to capture the number of loops that can be detected within a genealogy. These explorations have proven difficult to connect to the theory of the underlying biological process of recombination, and, consequently, have unpredictable behavior under perturbations of the data. We introduce a new topological feature, which we call ψ, with a natural connection to coalescent models, and present novel arguments relating [Formula: see text] to population genetic models. Using simulations, we show that ψ and [Formula: see text] are differentially affected by missing data, and package our approach as TREE (Topological Recombination Estimator). TREE's efficiency and accuracy make it well suited as a first-pass estimator of recombination rate heterogeneity or hotspots throughout the genome. Our work empirically and theoretically justifies the use of topological statistics as summaries of genome sequences and describes a new, unintuitive relationship between topological features of the distribution of sequence data and the footprint of recombination on genomes.

KEYWORDS:

coalescent theory; population genetics; recombination; topological data analysis

PMID:
30787042
PMCID:
PMC6456321
[Available on 2020-04-01]
DOI:
10.1534/genetics.118.301565
[Indexed for MEDLINE]

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