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An Experimental Test on the Probability of Extinction of New Genetic Variants

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An Experimental Test on the Probability of Extinction of New Genetic Variants ARTICLE Received 1 Nov 2012 | Accepted 8 Aug 2013 | Published 13 Sep 2013 DOI: 10.1038/ncomms3417 OPEN An experimental test on the probability of extinction of new genetic variants Ivo M. Chelo1, Judit Ne´dli1, Isabel Gordo1 & Henrique Teoto´nio1 In 1927, J.B.S. Haldane reasoned that the probability of fixation of new beneficial alleles is twice their fitness effect. This result, later generalized by M. Kimura, has since become the cornerstone of modern population genetics. There is no experimental test of Haldane’s insight that new beneficial alleles are lost with high probability. Here we demonstrate that extinction rates decrease with increasing initial numbers of beneficial alleles, as expected, by performing invasion experiments with inbred lines of the nematode Caenorhabditis elegans. We further show that the extinction rates of deleterious alleles are higher than those of beneficial alleles, also as expected. Interestingly, we also find that for these inbred lines, when at intermediate frequencies, the fate of invaders might not result in their ultimate fixation or loss but on their maintenance. Our study confirms the key results from classical population genetics and highlights that the nature of adaptation can be complex. 1 Instituto Gulbenkian de Cieˆncia, Apartado 14, P-2781-901 Oeiras, Portugal. Correspondence and requests for materials should be addressed to H.T. (email: [email protected]). NATURE COMMUNICATIONS | 4:2417 | DOI: 10.1038/ncomms3417 | www.nature.com/naturecommunications 1 & 2013 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3417 hen a new allele appears by mutation or recombina- in scoring GFP individuals could lead to inadvertent estimation of tion, it will be represented in very low numbers and it low extinction rates (see Methods). Wcan be lost even when it is adaptive. This idea was first Haldane’s assumption that competing alleles have independent formalized by J.B.S. Haldane when he deduced that the growth dynamics was easily achieved with the number of probability of fixation of a new beneficial allele is twice its fitness generations of selfing employed for the inbred line derivation, effect1. Haldane’s insight became the foundation of modern which makes them nearly isogenic because the average expected population genetics2–5 and has since been used to understand the heterozygosity across the genome is o0.01% (refs 3,27) (see limits of adaptation6–9, speciation rates10–12 and the extent of Methods). In line with this, we genotyped the inbred lines at differentiation between populations13,14, including those of 29 single-nucleotide polymorphisms (SNPs) and found no pathogens and their human hosts15–17. heterozygosity in them (Supplementary Data 1). Outcrossing Haldane’s result only applies to beneficial alleles and it depends among the inbred lines was expected to be of minor consequence on the invader and resident alleles having independent growth because C. elegans hermaphrodites can only cross-fertilize their dynamics that will compete in populations characterized by oocytes when mated with males29. Males were initially absent due discrete non-overlapping generations and stable sizes1,18–22. His to the derivation of the inbred lines by selfing, and neither approximation is further conditional on alleles having weak mutation nor selection for outcrossing was expected to increase fitness effects and on individuals having successful offspring male frequency for the short duration of the experiments26,30. numbers that follow Poisson distributions. Together, these Together, these observations imply that segregation and assumptions allow for genetic drift to be described as a recombination in the two inbred lines would be negligible branching process and for the probability of fixation to be during the experiments. The inbred lines were thus expected to calculated from selection coefficients, which in turn can be accurately model haploid, or allelic, growth dynamics that are measured in finite populations as the relative frequency changes independent of each other. of invader and resident alleles23. The critical prediction made by Haldane is that, even with a substantial selection advantage, the probability of extinction Beneficial alleles are lost by genetic drift. To test for a decrease declines with the number of individuals carrying the invading in extinction rates with the number of beneficial invaders, we beneficial allele. There are no explicit experimental tests of this performed experiments with two starting frequencies of the GFP prediction. Results concerning the extinction of beneficial alleles allele: either two or five GFP reproductively immature individuals are few24,25, with the most relevant ones coming from recent (late L4 larval stage) were introduced into populations with 103 experiments where it was shown that the probability of extinction wild-type individuals of the same stage. Multiple replicate inva- declines with increasing strength of selection24. In this latter sions were seeded and independently propagated for five gen- study, however, extinctions due to genetic drift had to be erations in the same discrete non-overlapping generations modelled because the manipulation of the number of invader experienced by the lab-adapted population during the preceding alleles was not possible. 140 generations. As total offspring numbers before sampling can Here we use highly replicated experiments in the hermaphro- reach several tens of thousands (Supplementary Fig. S1), there ditic nematode Caenorhabditis elegans to introduce beneficial will be great culling to maintain constant population sizes of alleles at precise low numbers in a resident population composed N ¼ 103, and thus the distributions of successful offspring num- of deleterious alleles to test Haldane’s prediction. bers most likely follow Poisson distributions18. The probability of extinction (Pext) was measured as the proportion of replicate invasions that failed to show the GFP Results allele when scored in adult worms, before reproduction, for two The C. elegans model system. We started by deriving a collection consecutive generations (see Methods). Though extinction of of inbred lines through self-fertilization of hermaphrodites of a invaders is expected to predominantly occur in the first few polymorphic population that had been adapted for 140 genera- generations, genetic drift will nonetheless lead to further loss until tions to laboratory conditions. These laboratory conditions tens to hundreds of generations, depending on the initial number involved maintaining stable census population sizes of 104 indi- of invaders and strength of selection (Supplementary Fig. S2). viduals, and effective population sizes of 103, under discrete non- Note, however, that running the experiments for longer periods at overlapping generations26,27. In preliminary trials, the derived the large population sizes employed would allow mutations to inbred lines were characterized for embryo to adult survival, with start accumulating31,32. the one showing the lowest values (here referred to as the wild- Results from the two invasion experiments show, as expected, type line) being chosen as the potentially deleterious surrogate for that the Pext was higher when invader alleles started from lower the resident allele. frequencies (Fig. 1a,b). In particular, by generation 5, the GFP In parallel, we introgressed a green fluorescent protein (GFP) allele was lost from 37% of the replicates when it started the genetic construct into the lab-adapted population (see Methods), invasions from two individuals (n ¼ 35, bootstrap 95% confidence while maintaining genetic diversity, and then also enforced self- interval (CI) ¼ 23–51%), but only lost from 12.5% of the fertilization to derive another collection of inbred lines homo- replicates when starting from five individuals (n ¼ 56, bootstrap zygous for GFP. One of these GFP lines (here referred to as the 95% CI ¼ 5–21%). To confirm that these results were not biased GFP line) was arbitrarily chosen as the potentially beneficial by an insufficient number of replicates, we next sought to surrogate for the invader allele. Note that although henceforth we determine if selection on the GFP allele was congruent among the refer to the wild-type and the GFP inbred lines as two different two invasion experiments. ‘alleles’, these lines differ among them at many loci throughout For this, we numerically simulated the expected change in GFP the genome with each being composed of isogenic diploid allele frequency during the invasion experiments as a function of individuals. Defining the invader and resident alleles in this its relative fitness, while accounting for the total number of manner prevents artifactual positive results due to the GFP individuals and the life cycle of the populations. Specifically, the introgression. Though GFP expression is fully penetrant and relative growth rates of GFP and wild-type alleles were modelled highly visible across larval and adult life-history stages, and is as 1 þ s and 1, respectively, with s being defined as a selection further known to be stably inserted into the genome28, difficulties coefficient3. We estimate selection not by an analytical approach, 2 NATURE COMMUNICATIONS | 4:2417 | DOI: 10.1038/ncomms3417 | www.nature.com/naturecommunications & 2013 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3417 ARTICLE ab 60 0.5 ) ext 50 Two individuals Five individuals P 0.4 40 0.3 30 20 0.2 Number
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