Colonization times in Moran process on graphs
Language English Country United States Media electronic-ecollection
Document type Journal Article
PubMed
40324007
PubMed Central
PMC12052132
DOI
10.1371/journal.pcbi.1012868
PII: PCOMPBIOL-D-24-02021
Knihovny.cz E-resources
- MeSH
- Population Density MeSH
- Humans MeSH
- Mutation MeSH
- Computer Simulation MeSH
- Population Dynamics * MeSH
- Selection, Genetic MeSH
- Stochastic Processes MeSH
- Computational Biology MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
Moran Birth-death process is a standard stochastic process that is used to model natural selection in spatially structured populations. A newly occurring mutation that invades a population of residents can either fixate on the whole population or it can go extinct due to random drift. The duration of the process depends not only on the total population size n, but also on the spatial structure of the population. In this work, we consider the Moran process with a single type of individuals who invade and colonize an otherwise empty environment. Mathematically, this corresponds to the setting where the residents have zero reproduction rate, thus they never reproduce. The spatial structure is represented by a graph. We present two main contributions. First, in contrast to the Moran process in which residents do reproduce, we show that the colonization time is always at most a polynomial function of the population size n. Namely, we show that colonization always takes at most [Formula: see text] expected steps, and for each n, we identify the slowest graph where it takes exactly that many steps. Moreover, we establish a stronger bound of roughly [Formula: see text] steps for undirected graphs and an even stronger bound of roughly [Formula: see text] steps for so-called regular graphs. Second, we discuss various complications that one faces when attempting to measure fixation times and colonization times in spatially structured populations, and we propose to measure the real duration of the process, rather than counting the steps of the classic Moran process.
See more in PubMed
Kimura M. Evolutionary rate at the molecular level. Nature 1968;217(5129):624–6. doi: 10.1038/217624a0 PubMed DOI
Bürger R. The mathematical theory of selection, recombination, and mutation. Wiley; 2000.
Ewens WJ. Mathematical population genetics: theoretical introduction. vol. 27. Springer; 2004.
Sharma N, Traulsen A. Suppressors of fixation can increase average fitness beyond amplifiers of selection. Proc Natl Acad Sci U S A 2022;119(37):e2205424119. doi: 10.1073/pnas.2205424119 PubMed DOI PMC
Durrett R, Levin S. The importance of being discrete (and spatial). Theor Popul Biol 1994;46(3):363–94. doi: 10.1006/tpbi.1994.1032 DOI
Frean M, Rainey PB, Traulsen A. The effect of population structure on the rate of evolution. Proc Biol Sci 2013;280(1762):20130211. doi: 10.1098/rspb.2013.0211 PubMed DOI PMC
Lieberman E, Hauert C, Nowak MA. Evolutionary dynamics on graphs. Nature 2005;433(7023):312–6. doi: 10.1038/nature03204 PubMed DOI
Yagoobi S, Traulsen A. Fixation probabilities in network structured meta-populations. Sci Rep 2021;11(1):17979. doi: 10.1038/s41598-021-97187-6 PubMed DOI PMC
Yagoobi S, Sharma N, Traulsen A. Categorizing update mechanisms for graph-structured metapopulations. J R Soc Interface 2023;20(200):20220769. doi: 10.1098/rsif.2022.0769 PubMed DOI PMC
Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran process with environmental heterogeneity. Proc Roy Soc A. 2023:479(2271);20220685.
Svoboda J, Joshi S, Tkadlec J, Chatterjee K. Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating. arXiv preprint. 2024. https://arxiv.org/abs/2401.14914 PubMed PMC
Kaveh K, Komarova NL, Kohandel M. The duality of spatial death-birth and birth-death processes and limitations of the isothermal theorem. R Soc Open Sci 2015;2(4):140465. doi: 10.1098/rsos.140465 PubMed DOI PMC
Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants that modify population structure. J R Soc Interface 2023;20(208):20230355. doi: 10.1098/rsif.2023.0355 PubMed DOI PMC
Moran PAP. Random processes in genetics. In: Mathematical proceedings of the cambridge philosophical society. vol. 54. Cambridge University Press; 1958. p. 60–71.
KIMURA M. On the probability of fixation of mutant genes in a population. Genetics 1962;47(6):713–9. doi: 10.1093/genetics/47.6.713 PubMed DOI PMC
Kimura M. Average time until fixation of a mutant allele in a finite population under continued mutation pressure: Studies by analytical, numerical, and pseudo-sampling methods. Proc Natl Acad Sci U S A 1980;77(1):522–6. doi: 10.1073/pnas.77.1.522 PubMed DOI PMC
Slatkin M. Fixation probabilities and fixation times in a subdivided population. Evolution. n.d.;35(4):477–88. PubMed
Whitlock MC. Fixation probability and time in subdivided populations. Genetics 2003;164(2):767–79. doi: 10.1093/genetics/164.2.767 PubMed DOI PMC
Broom M, Rychtář J. An analysis of the fixation probability of a mutant on special classes of non-directed graphs. Proc R Soc A 2008;464(2098):2609–27. doi: 10.1098/rspa.2008.0058 DOI
Hadjichrysanthou C, Broom M, Rychtář J. Evolutionary games on star graphs under various updating rules. Dyn Games Appl 2011;1(3):386–407. doi: 10.1007/s13235-011-0022-7 DOI
Monk T, Green P, Paulin M. Martingales and fixation probabilities of evolutionary graphs. Proc R Soc A 2014;470(2165):20130730. doi: 10.1098/rspa.2013.0730 DOI
Díaz J, Goldberg LA, Mertzios GB, Richerby D, Serna M, Spirakis PG. Approximating fixation probabilities in the generalized Moran process. Algorithmica 2012;69(1):78–91. doi: 10.1007/s00453-012-9722-7 DOI
Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Amplification on undirected population structures: comets beat stars. Sci Rep 2017;7(1):82. doi: 10.1038/s41598-017-00107-w PubMed DOI PMC
Möller M, Hindersin L, Traulsen A. Exploring and mapping the universe of evolutionary graphs identifies structural properties affecting fixation probability and time. Commun Biol. 2019;2:137. doi: 10.1038/s42003-019-0374-x PubMed DOI PMC
Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Population structure determines the tradeoff between fixation probability and fixation time. Commun Biol. 2019;2:138. doi: 10.1038/s42003-019-0373-y PubMed DOI PMC
Monk T, van Schaik A. Correction to “Wald’s martingale and the conditional distributions of absorption time in the Moran process”. Proc Math Phys Eng Sci 2020;476(2242):20200731. doi: 10.1098/rspa.2020.0731 PubMed DOI PMC
Kuo YP, Carja O. Evolutionary graph theory beyond pairwise interactions: Higher-order network motifs shape times to fixation in structured populations. PLoS Comput Biol 2024;20(3):e1011905. doi: 10.1371/journal.pcbi.1011905 PubMed DOI PMC
Galanis A, Göbel A, Goldberg LA, Lapinskas J, Richerby D. Amplifiers for the Moran Process. J ACM 2017;64(1):1–90. doi: 10.1145/3019609 DOI
Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Commun Biol. 2018;1:71. doi: 10.1038/s42003-018-0078-7 PubMed DOI PMC
Goldberg LA, Lapinskas J, Lengler J, Meier F, Panagiotou K, Pfister P. Asymptotically optimal amplifiers for the Moran process. Theor Comput Sci. 2019;758:73–93. doi: 10.1016/j.tcs.2018.08.005 DOI
Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. Nat Commun 2021;12(1):4009. doi: 10.1038/s41467-021-24271-w PubMed DOI PMC
Nowak MA. Evolutionary dynamics: exploring the equations of life. Harvard University Press; 2006.
Hathcock D, Strogatz SH. Fitness dependence of the fixation-time distribution for evolutionary dynamics on graphs. Phys Rev E. 2019;100(1–1):012408. doi: 10.1103/PhysRevE.100.012408 PubMed DOI
Ann Goldberg L, Lapinskas J, Richerby D. Phase transitions of the Moran process and algorithmic consequences. Random Struct Algorithms 2019;56(3):597–647. doi: 10.1002/rsa.20890 DOI
Díaz J, Goldberg LA, Richerby D, Serna M. Absorption time of the Moran process. Random Struct Alg 2016;49(1):137–59. doi: 10.1002/rsa.20617 DOI
Allen B, Lippner G, Chen Y-T, Fotouhi B, Momeni N, Yau S-T, et al.. Evolutionary dynamics on any population structure. Nature 2017;544(7649):227–30. doi: 10.1038/nature21723 PubMed DOI
McAvoy A, Allen B. Fixation probabilities in evolutionary dynamics under weak selection. J Math Biol 2021;82(3):14. doi: 10.1007/s00285-021-01568-4 PubMed DOI
Durocher L, Karras P, Pavlogiannis A, Tkadlec J. Invasion dynamics in the biased voter process. In: Proceedings of the Thirty-First International Joint Conference on Artificial Intelligence. 2022. p. 265–71. doi: 10.24963/ijcai.2022/38 DOI
Brendborg J, Karras P, Pavlogiannis A, Rasmussen AU, Tkadlec J. Fixation maximization in the positional Moran process. AAAI 2022;36(9):9304–12. doi: 10.1609/aaai.v36i9.21160 DOI
M Altrock P, Traulsen A. Fixation times in evolutionary games under weak selection. New J Phys 2009;11(1):013012. doi: 10.1088/1367-2630/11/1/013012 DOI
Gao S, Liu Y, Wu B. The speed of neutral evolution on graphs. J R Soc Interface 2024;21(215):20230594. doi: 10.1098/rsif.2023.0594 PubMed DOI PMC
Ibsen-Jensen R, Chatterjee K, Nowak MA. Computational complexity of ecological and evolutionary spatial dynamics. Proc Natl Acad Sci U S A 2015;112(51):15636–41. doi: 10.1073/pnas.1511366112 PubMed DOI PMC
Allen B, Sample C, Jencks R, Withers J, Steinhagen P, Brizuela L, et al.. Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs. PLoS Comput Biol 2020;16(1):e1007529. doi: 10.1371/journal.pcbi.1007529 PubMed DOI PMC
Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS Comput Biol 2020;16(1):e1007494. doi: 10.1371/journal.pcbi.1007494 PubMed DOI PMC
Brewster DA, Nowak MA, Tkadlec J. Fixation times on directed graphs. PLoS Comput Biol 2024;20(7):e1012299. doi: 10.1371/journal.pcbi.1012299 PubMed DOI PMC
Komarova NL, Rodriguez-Brenes IA, Wodarz D. Laws of spatially structured population dynamics on a lattice. Physics. 2022;4(3):812–32.
Cormen TH, Leiserson CE, Rivest RL, Stein C. Introduction to algorithms. MIT Press; 2022.
Monk T, van Schaik A. Martingales and the characteristic functions of absorption time on bipartite graphs. R Soc Open Sci 2021;8(10):210657. doi: 10.1098/rsos.210657 PubMed DOI PMC
Adlam B, Chatterjee K, Nowak MA. Amplifiers of selection. Proc R Soc A 2015;471(2181):20150114. doi: 10.1098/rspa.2015.0114 DOI
Hindersin L, Traulsen A. Counterintuitive properties of the fixation time in network-structured populations. J R Soc Interface 2014;11(99):20140606. doi: 10.1098/rsif.2014.0606 PubMed DOI PMC
Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977;81(25):2340–61. doi: 10.1021/j100540a008 DOI