Evidence map›Paper›PMID 38489353›Full record

ArticlePLoS computational biology2024

Evolutionary graph theory beyond pairwise interactions: Higher-order network motifs shape times to fixation in structured populations.

Yang Ping Kuo, Oana Carja

Abstract read
In one paragraph

Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed.

  1. Local negative frequency dependence can decrease global coexistence in fragmented populations.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  2. Article
  3. Article
  4. Colonization times in Moran process on graphs.PLoS computational biology · 2025
    Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Fixation dynamics on hypergraphs.PLoS computational biology · 2023
    Article
  10. Suppressors of fixation can increase average fitness beyond amplifiers of selection.Proceedings of the National Academy of Sciences of the United States of America · 2022
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Yang Ping KuoComputational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.ORCID 0000-0002-5211-3328
Oana CarjaComputational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.ORCID 0000-0002-4296-2326

Funding

Integrated Interdisciplinary, inter-university PhD Program Computational Biology (T32)T32EB009403 · NIBIB · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI BAHAR, IVET, BAR-JOSEPH, ZIV · 2009 to 2023
$4.4M
From pattern to function: eco-evolutionary representations of complex spatial structure for the new era of spatial biologyR35GM147445 · NIGMS · CARNEGIE-MELLON UNIVERSITY · PI Oana Carja · 2022 to 2026
$1.9M
NIBIB NIH HHS T32 EB009403NIGMS NIH HHS R35 GM147445
6 · The paper itself

Abstract

To design population topologies that can accelerate rates of solution discovery in directed evolution problems or for evolutionary optimization applications, we must first systematically understand how population structure shapes evolutionary outcome. Using the mathematical formalism of evolutionary graph theory, recent studies have shown how to topologically build networks of population interaction that increase probabilities of fixation of beneficial mutations, at the expense, however, of longer fixation times, which can slow down rates of evolution, under elevated mutation rate. Here we find that moving beyond dyadic interactions in population graphs is fundamental to explain the trade-offs between probabilities and times to fixation of new mutants in the population. We show that higher-order motifs, and in particular three-node structures, allow the tuning of times to fixation, without changes in probabilities of fixation. This gives a near-continuous control over achieving solutions that allow for a wide range of times to fixation. We apply our algorithms and analytic results to two evolutionary optimization problems and show that the rate of solution discovery can be tuned near continuously by adjusting the higher-order topology of the population. We show that the effects of population structure on the rate of evolution critically depend on the optimization landscape and find that decelerators, with longer times to fixation of new mutants, are able to reach the optimal solutions faster than accelerators in complex solution spaces. Our results highlight that no one population topology fits all optimization applications, and we provide analytic and computational tools that allow for the design of networks suitable for each specific task.

Indexed as

Biological EvolutionMutation RateAlgorithmsMathematicsMutation

Identifiers

PMID38489353
PMCPMC10971782

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.