Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory

Overview

Journal Commun Biol

Specialty Biology

Date 2018 Oct 2

PMID 30271952

Citations 28

Authors

Andreas Pavlogiannis

Josef Tkadlec

Krishnendu Chatterjee

Martin A Nowak

Affiliations

Soon will be listed here.

Abstract

Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures.

Citing Articles

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References

Lang G, Rice D, Hickman M, Sodergren E, Weinstock G, Botstein D . Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature. 2013; 500(7464):571-4. PMC: 3758440. DOI: 10.1038/nature12344. View

Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak M . Fast and strong amplifiers of natural selection. Nat Commun. 2021; 12(1):4009. PMC: 8242091. DOI: 10.1038/s41467-021-24271-w. View

McCandlish D, Epstein C, Plotkin J . Formal properties of the probability of fixation: identities, inequalities and approximations. Theor Popul Biol. 2014; 99:98-113. DOI: 10.1016/j.tpb.2014.11.004. View

Maruyama T . A Markov process of gene frequency change in a geographically structured population. Genetics. 1974; 76(2):367-77. PMC: 1213071. DOI: 10.1093/genetics/76.2.367. View

Komarova N, Shahriyari L, Wodarz D . Complex role of space in the crossing of fitness valleys by asexual populations. J R Soc Interface. 2014; 11(95):20140014. PMC: 4006240. DOI: 10.1098/rsif.2014.0014. View

Mannik J, Driessen R, Galajda P, Keymer J, Dekker C . Bacterial growth and motility in sub-micron constrictions. Proc Natl Acad Sci U S A. 2009; 106(35):14861-6. PMC: 2729279. DOI: 10.1073/pnas.0907542106. View

Rusconi R, Garren M, Stocker R . Microfluidics expanding the frontiers of microbial ecology. Annu Rev Biophys. 2014; 43:65-91. PMC: 4076152. DOI: 10.1146/annurev-biophys-051013-022916. View

Galajda P, Keymer J, Chaikin P, Austin R . A wall of funnels concentrates swimming bacteria. J Bacteriol. 2007; 189(23):8704-7. PMC: 2168927. DOI: 10.1128/JB.01033-07. View

Hauert C, Doebeli M . Spatial structure often inhibits the evolution of cooperation in the snowdrift game. Nature. 2004; 428(6983):643-6. DOI: 10.1038/nature02360. View

10.

Dai L, Vorselen D, Korolev K, Gore J . Generic indicators for loss of resilience before a tipping point leading to population collapse. Science. 2012; 336(6085):1175-7. DOI: 10.1126/science.1219805. View

11.

Desai M, Fisher D, Murray A . The speed of evolution and maintenance of variation in asexual populations. Curr Biol. 2007; 17(5):385-94. PMC: 2987722. DOI: 10.1016/j.cub.2007.01.072. View

12.

Kaveh K, Komarova N, 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. PMC: 4448870. DOI: 10.1098/rsos.140465. View

13.

Barrick J, Yu D, Yoon S, Jeong H, Oh T, Schneider D . Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature. 2009; 461(7268):1243-7. DOI: 10.1038/nature08480. View

14.

Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M . Amplification on Undirected Population Structures: Comets Beat Stars. Sci Rep. 2017; 7(1):82. PMC: 5427850. DOI: 10.1038/s41598-017-00107-w. View

15.

Keymer J, Galajda P, Muldoon C, Park S, Austin R . Bacterial metapopulations in nanofabricated landscapes. Proc Natl Acad Sci U S A. 2006; 103(46):17290-5. PMC: 1635019. DOI: 10.1073/pnas.0607971103. View

16.

Shakarian P, Roos P, Johnson A . A review of evolutionary graph theory with applications to game theory. Biosystems. 2011; 107(2):66-80. DOI: 10.1016/j.biosystems.2011.09.006. View

17.

Hindersin L, Traulsen A . Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics. PLoS Comput Biol. 2015; 11(11):e1004437. PMC: 4636432. DOI: 10.1371/journal.pcbi.1004437. View

18.

Slatkin M . FIXATION PROBABILITIES AND FIXATION TIMES IN A SUBDIVIDED POPULATION. Evolution. 2017; 35(3):477-488. DOI: 10.1111/j.1558-5646.1981.tb04911.x. View

19.

Debarre F, Hauert C, Doebeli M . Social evolution in structured populations. Nat Commun. 2014; 5:3409. DOI: 10.1038/ncomms4409. View

20.

Allen B, Lippner G, Chen Y, Fotouhi B, Momeni N, Yau S . Evolutionary dynamics on any population structure. Nature. 2017; 544(7649):227-230. DOI: 10.1038/nature21723. View