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The Distribution of Fitness Effects Among Beneficial Mutations
H. Allen Orraa Department of Biology, University of Rochester, Rochester, New York 14627
Corresponding author: H. Allen Orr
Communicating editor: J. B. WALSH
| ABSTRACT |
|---|
We know little about the distribution of fitness effects among new beneficial mutations, a problem that partly reflects the rarity of these changes. Surprisingly, though, population genetic theory allows us to predict what this distribution should look like under fairly general assumptions. Using extreme value theory, I derive this distribution and show that it has two unexpected properties. First, the distribution of beneficial fitness effects at a gene is exponential. Second, the distribution of beneficial effects at a gene has the same mean regardless of the fitness of the present wild-type allele. Adaptation from new mutations is thus characterized by a kind of invariance: natural selection chooses from the same spectrum of beneficial effects at a locus independent of the fitness rank of the present wild type. I show that these findings are reasonably robust to deviations from several assumptions. I further show that one can back calculate the mean size of new beneficial mutations from the observed mean size of fixed beneficial mutations.
ADAPTATION is a two-step process: (i) alleles having different effects on fitness arise by mutation and (ii) those alleles that improve fitness tend to increase in frequency by natural selection. A good part of classical population genetics focuses on the second step of this process, including calculation of the probability that natural selection will fix a new favorable mutation (![]()
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This is unfortunate as a number of aspects of adaptive evolution depend on the distribution of beneficial fitness effects. For example, the mean increase in fitness that occurs during substitution of a beneficial mutation must depend on the spectrum of effects among new mutations presented to natural selection. Large jumps in fitness, for instance, are possible only if mutations of large favorable effect occur.
The most direct approach to finding the distribution of fitness effects among new beneficial mutations is empirical. But while possible in principle this approach has proved difficult in practice. There are two main problems: beneficial mutations are rare and beneficial mutations of small effect are difficult to detect. Because of this, study of experimental microbial populations would seem to provide the best hope of characterizing the distribution of beneficial effects: the combination of large population size and short generation time means that many beneficial mutations can be sampled in a short time (![]()
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Given these difficulties, it seems worth asking if population genetic theory can provide any insight into the expected distribution of beneficial effects among new mutations. ![]()
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Here I derive this distribution. I show that it has two surprising properties: (i) the distribution of fitness effects among new beneficial mutations is always exponential and (ii) the distribution is invariant; i.e., it has the same mean regardless of the starting fitness rank of the wild-type allele. Our key assumption is that the starting wild-type allele has relatively high fitness.
| THE MODEL AND RESULTS |
|---|
The biological scenario:
Following GILLESPIE's (1983, 1984, 1991) "mutational landscape" model, I consider a population that was, until recently, well adapted to the environment. In particular, I consider a population that is essentially fixed for a wild-type sequence that wasuntil the recent environmental changethe fittest available at the gene. Following the environmental change, the wild type has dropped in fitness. The wild-type sequence can mutate to many alternative sequences. Of these, natural selection is essentially constrained to surveying those that differ from wild type by single-point mutations, as first pointed out by ![]()
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Although we know little about the fitnesses of mutant sequences at any gene, it is clear that most of the m mutations will be less fit than the present wild type. This follows from two facts. First, environments are autocorrelated through time, making it unlikely that the best sequence today will be the worst tomorrow (![]()
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Distribution of beneficial effects:
To find the distribution of fitness effects among those few mutations that are beneficial, we first rank the absolute fitnesses of the m mutant and one wild-type sequences: the fittest allele is given rank 1, the next fittest rank 2, and so on (Fig 1). The wild-type allele has rank i, where i is small. If a typical gene is L = 1000 bp long, then m = 3000 and i might range from, say, 2 to 25. The fitness gaps between adjacent alleles are labeled
1,
2, etc., as shown in Fig 1. Thus a mutation from wild-type allele i to favorable allele i - 1 improves absolute fitness by
W =
i-1, while a mutation from wild-type allele i to favorable allele 1 improves fitness by
W =
i-1 + ... +
2 +
1. The overall distribution, f(
W|i), of fitness effects among beneficial mutations when starting from wild-type allele i is the mixed distribution formed by considering all such possibilities. In symbols,
![]() |
(1) |
where f(
W|i, j) is the probability density of fitness effects when mutating from an allele of rank i to a beneficial allele of rank j.
|
Equation 1 shows that if we knew
1,
2, ... ,
i-1 we would know the distribution of fitness effects among beneficial mutations. Although we have not specified the distribution of allelic fitnesses, we can, surprisingly, still say something about these fitness spacings. The reason, as ![]()
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For our purposes, the most important of these limit theorems describes the spacings,
j, between the top several draws, i.e., the fittest several alleles. Although for any particular wild-type sequence and set of mutants the
j's are constants, these extreme spacings will in general be random variables. Extreme value theory shows that these
j's are asymptotically independent exponentially distributed random variables regardless of the distribution of allelic fitnesses. Theory also shows that these spacings grow smaller as one moves toward the median allele as shown in Fig 1. In particular, E[
j] = E[
1]/j, where the constant E[
1] depends on the form of the distribution of allelic fitnesses (![]()
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Because we know the distribution of the top spacing,
1, we also know the distribution of beneficial effects when i = 2 and only one favorable mutant is available. It is
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(2) |
In words, this distribution is exponential with mean E[
1], as first noted by ![]()
But what if the wild-type allele has rank i = 3 and two favorable mutants are possible? If the population were to jump to the second-best allele, we have f(
W|i = 3, j = 2) = (2/E[
1])exp(-2
W/E[
1]); if the population were to jump to the best allele, we have (from the convolution), f(
W|i = 3, j = 1) = (2/E[
1])[exp (-
W/E[
1]) - exp(-2
W/E[
1])]. Substituting the previous two equations in (1), we find that the overall distribution of beneficial fitness effects is f(
W|i = 3) = (1/E[
1]) exp(-
W/E[
1]). This distribution is identical to that when starting at i = 2. Remarkably, this independence from fitness rank is a general result. This is proved in the next section where the moment-generating function (mgf) of f(
W|i) is derived.
The general result:
To find the mgf of f(
W|i) we first find the mgf for
W conditional on mutating to a favorable allele of rank j (where j < i as the mutation is beneficial). Because
W|i, j =
j +
j+1 + ... +
i-1 and each
n is independent, the mgf for
W|i, j equals the product of the mgf's for the individual
n. But the
n's are exponentially distributed with means E[
k] = E[
1]/k. The conditional mgf is thus
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(3) |
The overall distribution of fitness effects is a mixture distribution, i.e., one weighted by the probability of mutating to each favorable allele (Equation 1). Because the mgf of a mixture distribution equals the weighted average of the conditional mgf's (![]()
j
i - 1, we have
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(4) |
This is the mgf for an exponential distribution with mean E[
1] and is independent of i. Thus the distribution of fitness effects among beneficial mutations is exponential with mean E[
1] independent of the fitness rank of the wild-type allele. The spectrum of mutational fitness effects available to adaptation is, in other words, invariant: although the value of E[
1] might vary from gene to gene, the expected distribution of beneficial effects at a given locus is independent of the fitness rank of the current wild type, where we assume only that wild-type fitness rank is high enough to use extreme value theory.
Fig 2 shows the results of exact computer simulations that test the accuracy of the above asymptotic theory. A gene of length L = 1000 bp was simulated. For each distribution of allelic fitnesses, the fitnesses of m = 3000 mutant alleles plus one wild type were randomly drawn from the distribution of allelic fitnesses, ranked in fitness, and the difference in fitness between the wild type and a randomly chosen beneficial mutation was recorded. Allelic fitnesses were assumed to be exponential, gamma, or half-normal (see Fig 2 legend for parameter values). Simulations were begun with wild-type fitness ranks of i = 2, 10, or 25 (these different ranks translate into considerable differences in starting wild-type fitnesses given the distributions of allelic fitnesses used). Ten thousand replicates were performed for each set of conditions. Fig 2 shows that the theory nicely predicts the distribution of fitness effects among beneficial mutations regardless of the underlying distribution of allelic fitnesses. More important, the distribution of fitness effects among beneficial mutations is approximately invariant over a wide range of i, including those where it was unclear whether extreme value theory would hold (e.g., i = 25), although some deviations appear at large i in the half-normal case. Because these deviations grow as i increases, it would seem unwise to extrapolate our results to much larger i (see Fig 2 legend).
|
It might seem that our results may simply reflect the memoryless property of exponential distributions. Many familiar distributions have an "exponential tail" in the sense that, as x gets large, (1 - F(x + y))/(1 - F(x))
exp(-cy), where c is a constant; in words, the probability of an increase of size y falls off exponentially and is independent of the precise "starting point," x. The memoryless property of exponential tails cannot, however, fully explain our results. Many distributions of the Gumbel type do not show such tail behavior, e.g., normal or lognormal distributions and those that are bounded on the right. Nonetheless, these distributions still have independent exponential extreme spacings and still give rise to an exponential distribution of fitness effects among new beneficial mutations. Our results hold asymptotically for all distributions in the domain of attraction of the Gumbel extreme value distribution whether or not they have "exponential tails" (see the Appendix).
Robustness of results:
The above results are asymptotically independent of the shape of the distribution of allelic fitnesses (so long as it is of the Gumbel type) and i (so long as it is small). The above results are also robust to strong selection; indeed no weak selection approximations have been made.
Two assumptions, however, are potentially important. First, I assumed that each of the m mutations appears with equal frequency. It is easy to show that unequal mutation rates do not affect the above findings so long as all alleles are equally likely to have a given fitness rank; i.e., mutationally common alleles are no more or less likely to have a given fitness rank than are mutationally rare alleles. Formally, the chance that the next mutation has rank j is
, where Pr{k} is the probability that the next mutation is to a particular allele k of the m possible. So long as all alleles are equally likely to have a given fitness rank, it is trivially true that
, whether or not Pr{k} is the same for all m alleles. Considering only that subset of mutations that are beneficial, an analogous argument shows that Pr{j|j < i} = 1/(i - 1), as in Equation 4. Thus Equation 4and our key conclusionremains correct whether or not all alleles are mutated to with equal frequencies. This was confirmed in computer simulations (not shown).
Second, following ![]()
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|
|
| DISCUSSION |
|---|
Following ![]()
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W) among new beneficial mutations is exponential. More surprisingly, the distribution of beneficial effects shows an invariance property: it remains the same regardless of the fitness rank (and thus fitness) of the wild-type allele. Natural selection will, therefore, choose from the same spectrum of mutational effects whether adaptation starts from the second-best possible allele (i = 2) or one that is considerably worse (e.g., i = 10).
These results depend on robust limit theorems from extreme value theory and so are quite general. They are independent of the distribution of allelic fitness (so long as it is of the Gumbel type), starting wild-type fitness (so long as it is high), strength of selection, and heterogeneity in mutation rates across sites. Although our results rest on asymptotic theory and so must be viewed as approximations (especially as different parent distributions converge on the extreme value distribution at different rates), computer simulations suggest that they are good approximations. Our results also hold in both sexual and asexual species and recombining and nonrecombining chromosome regions. There would seem to be good reason, then, for thinking that the distribution of beneficial fitness effects among new mutations at a locus might be generally approximately exponential and invariant. (There could, of course, be exceptions. One predicted by the present theory involves any locus at which the wild type is of very low fitness. Extreme value theory does not hold here. Another is where the distribution of allelic fitnesses has a very lumpy tail; see the above simulations.)
Though counterintuitive, the invariance property among beneficial mutations can be explained heuristically. If adaptation starts from a high-quality wild-type allele (i = 2), the jump to the best allele usually involves medium-sized fitness increases (
1; see Fig 1). But if adaptation starts from a lower-quality allele (i = 3), jumps to better alleles involve some fitness increases that are usually smaller than before (
2) and an equal number that are usually larger than before (
1 +
2). On average these balance and the mean fitness increase is unchanged. This argument generalizes for any starting wild-type fitness rank i, so long as it is small.
It is important to note that our results concern fitness increases, not selection coefficients. Selection coefficients are fitness increases normalized by wild-type fitness: s =
W/W+, where W+ is the fitness of the wild-type allele. Because for any given i,
W and W+ are both random variables, it is easy to show that selection coefficients do not enjoy the above invariance property. Instead the mean selection coefficient among beneficial mutations is E[s] = E[
1/(W1 -
1 - ...
i-1)], which shrinks slightly with smaller i. Numerical work shows, however, that the distribution of s remains roughly exponential over small i (not shown; see also ![]()
The above theory, when combined with previous work, allows us to back calculate the mean fitness effect of new beneficial mutations from the mean fitness effect of fixed beneficial mutations, which are much more easily assayed in microbial experimental evolution work. Because large beneficial mutations have a greater chance of going to fixation than do small ones, the mean fitness increase among fixed beneficial mutations will obviously exceed (or at least equal) that among new beneficial mutations. ![]()
Wfixed] = 2(i - 1)E[
1]/i. This quantity ranges between E[
1] and 2E[
1]. Because the present theory shows that E[
1] asymptotically equals the mean fitness effect of new beneficial mutations, it immediately follows that
![]() |
(5) |
i.e., the mean effect of new beneficial mutations is bounded between one-half and one times the mean effect of fixed beneficial mutations. Although this back calculation assumes that beneficial mutations enjoy independent fates, many asexual microbes having small genomes can be made to evolve under experimental conditions of effective sexuality (e.g., sufficiently small population sizes that beneficial mutations arise one at a time). It thus appears that a notoriously elusive quantitythe mean fitness effect of new beneficial mutationscan be estimated in a way that is, at least in principle, straightforward.
Although theoretical population genetics has historically focused on neutral and deleterious mutations, recent theory has turned to adaptation (![]()
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Wnew] = E[
1]. In sexuals this distribution then gets transformed by probabilities of fixation into one of mean E[
Wfixed] = 2(i - 1)E[
1]/i (![]()
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W is also roughly exponential). Thus both the distribution of beneficial effects among new mutations and the distribution of effects among the mutations ultimately fixed should be roughly exponential, at least when adaptation uses new mutations and approaches a constant optimum. It will obviously be of some importance to determine if similar patterns characterize adaptation when evolution proceeds from the standing genetic variation and/or approaches a moving optimum.
| ACKNOWLEDGMENTS |
|---|
I thank N. Barton, A. Betancourt, P. Gerrish, J. Gillespie, J. P. Masly, D. Presgraves, M. Turelli, and two anonymous reviewers for helpful discussions or comments. I especially thank L. de Haan, I. Weissman, and D. Zelterman for helpful discussions of extreme value theory. This work was supported by National Institutes of Health grant 2R01 G51932-06A1 and by The David and Lucile Packard Foundation.
Manuscript received October 10, 2002; Accepted for publication January 5, 2003.
| APPENDIX |
|---|
Most "ordinary" distributions belong to the Gumbel type (also known as type III). Here I briefly review the conditions for a distribution to belong to this type. My discussion is based loosely on that of ![]()
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Consider a parent distribution with probability density function (pdf) f(x) and cumulative distribution function (cdf) F(x). If we randomly draw a very large number, n, of values from this distribution, record the maximum value, and repeat this process many times, we will find that the distribution of the maximum (or of a linear function of the maximum) often tends to a limiting distribution, the so-called extreme value distribution. In reality, there are three extreme value distributions. "Ordinary" distributions like the normal, lognormal, exponential, gamma, etc., are in the domain of attraction of the Gumbel extreme value distribution; this is often casually referred to as the extreme value distribution. The cdf of the Gumbel distribution is
(y) = exp(-exp(-y)), where y is a linear function of the original random variable x. Many (though not all) bounded distributions are in the domain of attraction of another extreme value distribution, while exotic distributions like the Cauchy (whose moments are undefined) are in the domain of attraction of a third extreme value distribution. All of these extreme value distributions hold asymptotically as n
.
Parent distributions in the domain of attraction of the Gumbel distribution may have unbounded or bounded tails. The rightmost endpoint of the parent distribution is denoted xF, where xF
and f(x) = 0 for x > xF. If f(x) has a negative derivative over an interval (x0, xF), a sufficient condition for f(x) to be in the domain of attraction of the Gumbel extreme value distribution is that
![]() |
(A1) |
It is easy to show that familiar distributions like the exponential, gamma, normal, lognormal, etc., fulfill this condition.
The necessary and sufficient condition for f(x) to be in the domain of attraction of the Gumbel extreme value distribution has also been found. It is
![]() |
(A2) |
where g(t) is a strictly positive function. It is important to note that this condition is not identical to having an "exponential tail" in the usual sense of (1 - F(t + x))/(1 - F(t))
exp(-x) for large t. The reason is that g(t) need not be a constant. Indeed in the case of the normal and lognormal distributions, as well as in the case of bounded distributions, g(t) is not a constant. Nonetheless, these distributions are in the domain of attraction of the Gumbel extreme value distribution.
If the maximum of a distribution converges to a particular extreme value distribution, the second and third, etc., largest-order statistics will converge to an asymptotic distribution of related functional form; i.e., these order statistics belong to the same type as the maximum. ![]()
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