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Methods for Rich Phylogenetic Inference Over Distributed Sexual Populations

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Genetic Programming Theory and Practice XX

Part of the book series: Genetic and Evolutionary Computation ((GEVO))

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Abstract

The structure of relatedness among members of an evolved population tells much of its evolutionary history. In application-oriented evolutionary computation (EC), such phylogenetic information can guide algorithm selection and tuning. Although traditional direct tracking approaches provide the perfect phylogenetic record, sexual recombination complicates management and analysis of this data. Taking inspiration from biological science, this work explores a reconstruction-based approach that uses end-state genetic information to estimate phylogenetic history after the fact. We apply recently developed “hereditary stratigraphy” genome annotations to lineages with sexual recombination to design devices germane to species phylogenies and gene trees. As shown through a series of validation experiments, the proposed instrumentation can discern genealogical history, population size changes, and selective sweeps. Fully decentralized by nature, these methods afford new observability at scale, in particular, for distributed EC systems. Such capabilities anticipate continued growth of computational resources available to EC. Accompanying open-source software aims to expedite the application of reconstruction-based phylogenetic analysis where pertinent.

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Notes

  1. 1.

    Reported experiments used 64-bit fingerprint values, which will exhibit even lower collision probabilities. However, numerical considerations impede precise calculation.

  2. 2.

    The smallest representable floating point value was set for fitness advantage treatment 0.0 so the introduced gene could be differentiated from the background gene. This value was small enough to have no meaningfully detectable effect on selection.

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Authors and Affiliations

  1. University of Michigan, Ann Arbor, USA

    Matthew Andres Moreno

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  1. Matthew Andres Moreno
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Correspondence to Matthew Andres Moreno .

Editor information

Editors and Affiliations

  1. School of Information, Communications and Media, University of Applied Sciences Upper Austria, Hagenberg, Austria

    Stephan Winkler

  2. Engineering Sciences Graduate Program, Tecnológico Nacional de México, IT de Tijuana, Tijuana, Baja California, Mexico

    Leonardo Trujillo

  3. Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA

    Charles Ofria

  4. School of Computing, Queen's University, Kingston, ON, Canada

    Ting Hu

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Moreno, M.A. (2024). Methods for Rich Phylogenetic Inference Over Distributed Sexual Populations. In: Winkler, S., Trujillo, L., Ofria, C., Hu, T. (eds) Genetic Programming Theory and Practice XX. Genetic and Evolutionary Computation. Springer, Singapore. https://doi.org/10.1007/978-981-99-8413-8_7

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  • DOI: https://doi.org/10.1007/978-981-99-8413-8_7

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  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-99-8412-1

  • Online ISBN: 978-981-99-8413-8

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