Evidence that adaptation in Drosophila is not limited by mutation at single sites

Abstract

Adaptation in eukaryotes is generally assumed to be mutation-limited because of small effective population sizes. This view is difficult to reconcile, however, with the observation that adaptation to anthropogenic changes, such as the introduction of pesticides, can occur very rapidly. Here we investigate adaptation at a key insecticide resistance locus (Ace) in Drosophila melanogaster and show that multiple simple and complex resistance alleles evolved quickly and repeatedly within individual populations. Our results imply that the current effective population size of modern D. melanogaster populations is likely to be substantially larger (> or = 100-fold) than commonly believed. This discrepancy arises because estimates of the effective population size are generally derived from levels of standing variation and thus reveal long-term population dynamics dominated by sharp--even if infrequent--bottlenecks. The short-term effective population sizes relevant for strong adaptation, on the other hand, might be much closer to census population sizes. Adaptation in Drosophila may therefore not be limited by waiting for mutations at single sites, and complex adaptive alleles can be generated quickly without fixation of intermediate states. Adaptive events should also commonly involve the simultaneous rise in frequency of independently generated adaptive mutations. These so-called soft sweeps have very distinct effects on the linked neutral polymorphisms compared to the standard hard sweeps in mutation-limited scenarios. Methods for the mapping of adaptive mutations or association mapping of evolutionarily relevant mutations may thus need to be reconsidered.

Figure 1. Haplotype network at Ace.

Alleles containing mutations I161V, G265A and F330Y are numbered 1, 2 and 3 respectively. Sizes of the circles correspond to the number of identical sequences representing each haplotype; tick marks along a branch indicate the number of mutations between two neighbouring haplotypes. Sensitive haplotypes are labelled with capital letters and resistant haplotypes with lowercase letters. Note that our sample is enriched for resistant haplotypes. Resistant NA alleles containing a single mutation (all at the first site) appear to have arisen on the common out-of-Africa haplotype L, with one specific L-related allele (labelled p) present at the highest frequency. The resistant AUS alleles also cluster together. AUS resistant alleles containing a single resistant mutation in the first or second site appear to have arisen either on the background of the common out-of-Africa sensitive haplotype L, or on the background of the specifically AUS haplotype N. The alleles containing two mutations in NA (first plus second or first plus third sites) are all related to the sensitive L haplotype and the common resistant allele (labelled p) containing the mutation in the first site. The 3-mutation alleles are present both in NA and AUS populations (v and w) and are the most closely related to the sensitive L haplotype. There are two resistant alleles containing single mutations in the first and the second site that we detected in AF. One of these is very similar to the AUS alleles containing the second mutation and is likely a migrant from out-of-Africa back to AF. The other appears to have arisen in situ in AF (u).

Figure 2. Soft sweeps at Ace.

The table shows segregating sites within the 1.5-kb region of Ace. Each strain is named according to the corresponding letter in Figure 1. When multiple strains shared the same haplotype, they were named with the same letter but with different numbers (i.e. w-1, w-2, w-3). For the names and origins of the strains refer to Table S1 and Table S2. The nucleotide position and the consensus sequence at the top of the table correspond to the y¹; cn¹ bw¹ sp¹ strain. The positions of the three resistant mutations are shaded. The table shows all sensitive haplotypes observed more than once as well as all haplotypes containing the resistant mutation at the first site (I161V) and the ones that contain all three resistant mutations.

Figure 3. Population dynamics of resistance adaptation for different Θ regimes.

(A) Frequency trajectories of resistant haplotypes from a typical simulation of a single population with Θ = 0.01 during the first 1500 generations after pesticides are applied. The selection scenario is s _1m = 0.05, s _2m = 0.1, s _3m = 0.2. Trajectories are shown for all resistant haplotypes that reached a population frequency above 2%. On the right, summary statistics for P _1m, P _3m, P _ss, and P _c estimated from 10⁵ runs are shown. (B) Frequency trajectories of a typical simulation run and summary statistics for a single population with Θ = 1. This simulation shows a soft sweep for the 3-mutation allele (two different haplotypes at high frequencies; their frequencies together add to 100%). Also, note that 2-mutation alleles do not rise to high frequencies before being taken over by the fitter 3-mutation alleles. (C) P _c for a variety of different selection, recombination, and population substructure scenarios as specified in Table S3. Probabilities P _c of each scenario are plotted against the average heterozygosity Θ_π of the entire population estimated from coalescent simulations.

Figure 4. Population dynamics of neutral and adaptive alleles in a population with a bottleneck.

(A) The population history similar to that inferred by Thornton and Andolfatto for D. melanogaster . Values of Θ_π and Watterson's Θ_w were obtained from coalescent simulations with 100 sampled genomes. (B) Same scenario as (A) except for the current population size is changed to 10⁸.