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Evaluating Gene Flow Using Selected Markers: A Case Study
Thomas Lenormanda, Thomas Guillemauda, Denis Bourguet1,a, and Michel Raymondaa Laboratoire Génétique et Environnement, Institut des Sciences de l'Evolution (UMR 5554), Université Montpellier II, 34095 Montpellier Cedex 5, France
Corresponding author: Thomas Lenormand, Laboratoire Génétique et Environnement, Institut des Sciences de l’Evolution (UMR 5554), Université Montpellier II, CC065 Place E. Bataillon, F-34095 Montpellier Cedex 5, France, lenorman{at}isem.univ-montp2.fr (E-mail).
Communicating editor: M. SLATKIN
| ABSTRACT |
|---|
The extent to which an organism is locally adapted in an environmental pocket depends on the selection intensities inside and outside the pocket, on migration, and on the size of the pocket. When two or more loci are involved in this local adaptation, measuring their frequency gradients and their linkage disequilbria allows one to disentangle the forcesmigration and selectionacting on the system. We apply this method to the case of a local adaptation to organophosphate insecticides in the mosquito Culex pipiens pipiens in southern France. The study of two different resistance loci allowed us to estimate with support limits gene flow as well as selection pressure on insecticide resistance and the fitness costs associated with each locus. These estimates permit us to pinpoint the conditions for the maintenance of this pocket of adaptation as well as the effect of the interaction between the two resistance loci.
ALTHOUGH evolutionary theory attempts mainly to explain past changes, its predictions can be tested by examining actual evolutionary processes in natural populations. To do so we must quantify the deterministic processes causing genetic evolution, namely, selection and gene flow, and take into account the unpredictable changes due to stochastic processes such as random drift and mutation. Among these factors only gene flow (and stabilizing selection) will oppose genetic differentiation between populations. Its evaluation is therefore required for the understanding of the evolution of populations in their "adaptive landscape" (for review, see ![]()
In most cases, it is possible to determine the relative magnitude of gene flow vs. drift, and thus estimate the degree of isolation of populations. This determination enables the evaluation of the effects of different kinds of selection, of the geographic scale of a local adaptation (![]()
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2). Estimating this finite variance requires knowledge of population sizes and of the patterns of isolation by distance (![]()
Another approach is to analyze directly the relative magnitude of gene flow vs. selection through clinal patterns that have been extensively studied theoretically for various selection models (![]()
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We have investigated the case of local adaptation of the mosquito Culex pipiens pipiens to organophosphate insecticides in the Montpellier area in France. This adaptation is conferred by resistance alleles at two major loci. Insecticide selection varies geographically, creating a pocket of adaptation. We have analyzed clinal patterns at these two loci to estimate selection intensities and gene flow. These estimates were used to evaluate the role of interaction between the two loci for the maintainance of the pocket of adaptation. Finally, we compared our estimates to direct or indirect estimates of selection intensity and gene flow in other studies.
| MATERIALS AND METHODS |
|---|
Culex pipiens and its environment:
Larval development of the mosquito C. p. pipiens takes place mainly in anthropic pools where insecticide control occurs. Females are presumably fertilized at emergence (WEIDHASS et al. 1973) and then search for their blood meal and a site to lay ~150200 eggs. Insecticides are applied during the breeding season, that is, approximately from April to October near Montpellier in southern France (see ![]()
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Genetics of resistance:
Two main loci are responsible for OP resistance in C. p. pipiens. The first locus, Ace.1, codes for an acetylcholinesterase (AChE1), the OP target (![]()
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Fitness of resistant mosquitoes:
The different resistance alleles contribute unequally to OP resistance: in southern France, insensitive acetylcholinesterase alleles confer in general a resistance higher than overproduced esterases (![]()
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Data collection:
Pupae were sampled on July 5, 1995 in 10 breeding sites along a 50-km north-south transect (Figure 1) across the treated and untreated areas studied by ![]()
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For each mosquito, resistance alleles at the Ester and Ace.1 loci were determined as follows. The thorax and the abdomen were used to detect overproduced esterases using starch-gel electrophoresis (Tris-Maleate-EDTA 7.4 buffer; ![]()
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Theoretical expectations:
Let us consider first the case of one locus. Let us note 1-si and 1-c, the probability that a susceptible and a resistant homozygote survive exposure to insecticide, and 1 and 1-c, the probability that they survive in the absence of insecticide. Further, si represents the fitness decrease due to insecticide exposure, and c the fitness cost of resistance. In the Montpellier area, insecticide treatments are restricted to the coastal belt (between 0 and L kilometers from the sea). For one locus with two alleles, the fitness of each genotype can be written as follows:
2 the ratio of the selection coefficient for x > L and 0
x < L.
For codominance (d = 0) and
= 1, ![]()
/4, with k2 =
where
is the standard deviation of parent-offspring distance measured along one dimension. Such clines cannot be characterized only by their slope, in contrast to numerous other cases (![]()
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The full analytical treatment in the case of two loci in a semi-infinite environment has not been performed, although ![]()
Descriptive analysis:
In order to test for the presence of frequency gradients at each resistance allele along the transect, data were fitted to descriptive cline models. Allelic distributions were fitted according to a scaled negative exponential. For instance, the frequencies of the four esterase alleles were modeled as follows:
- Ester1: f1(x) = h1.e-a1.x2
- Ester2: f2(x) = h2.(1 - h1).e-a2.x2
- Ester4: f4(x) = h4.(1 - h1 - h2.(1 - h1)).e-a4.x2
- Ester0: f0(x) = 1 - f1(x) -f2(x) - f4(x),
where a1, a2, a4, h1, h2, and h4 are estimated parameters. The phenotypic distributions were computed by using these allelic distributions and by assuming each locus at Hardy-Weinberg equilibrium. The phenotype was considered to be a three-state or seven-state random variable for the Ace.1 and Ester locus, respectively (see Table 1). The likelihood of a sample was computed from the phenotypic multinomial distribution.
Departure from Hardy-Weinberg proportions was tested in each population at the Ester locus by a likelihood ratio test. For an overall test, P values of each test were combined across populations using Fisher's method (![]()
A linkage disequilibrium measure D = freq{S,O} - freq{S} x freq{O} was computed for each population and tested by an exact test on the contingency table ({S},{R}) x ({O},{E}) using the Genepop software (ver. 3.1a; ![]()
Simulations:
In order to estimate migration and selection, we used deterministic simulations to infer the allelic distribution at equilibrium because the analytical solution is intractable and requires the assumption of weak selection. One-dimension clines were simulated by a series of demes connected by migration as described in ![]()
The migration variance was measured by
2t/2, which is the variance of this distribution when a > t and where
is the distance between demes. Selection coefficients were combined additively. The order of the processes was assumed to be reproduction-migration-selection, as should be the case for C. pipiens.
Migration and selection estimations:
The method of estimation is based on the principle that all resistance allele frequencies should be clinal, decreasing from south to north (Figure 1). As a consequence, the mixing of genotypes by migration from populations along these clines should create heterozygote deficiencies at each locus (Wahlund effect) and positive linkage disequilibrium between loci. This disequilibrium is predicted to be maximal at a medium distance from the coast (x
L) where the most dissimilar genotypes are mixed. Migration and selection parameters were estimated conjointly such that the expected frequencies, computed using the simulation described above, and observed frequencies were as close as possible.
We focused our study on the differences between susceptible and resistance alleles within and between loci rather than on the transient polymorphism or allele replacements at each locus. For such a purpose, we pooled individuals carrying at least one resistance allele at each locus. The phenotype was considered therefore to be a four-state ({S,O}, {S,E}, {R,O} and {R,E}; see Table 1) random variable, and the likelihood of a sample was computed from its multinomial distribution. Eleven parameters are needed to describe the system. Among them, three can be estimated from external data: the recombination rate (r = 14.5%), the size of the treated area (L = 20 km), and the epistasis for resistance (zero). Furthermore, we assumed that epistasis for fitness costs was negligible. These estimations and assumptions allowed us to investigate the selection intensities (sa,
a for the Ace.1 locus and se,
e, for the Ester locus) and the migration variance (
2). To evaluate the influence of the dominance level on the estimation of the migration variance, three cases of dominance for both loci were considered: recessivity (d = -1), codominance (d = 0), and dominance (d = 1). The influence of the recombination rate was also investigated for codominance at both loci.
Model comparisons and tests:
Maximum likelihood estimates (MLE) of parameters were computed conjointly using the Metropolis algorithm adapted from N. H. BARTON (![]()
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| RESULTS |
|---|
Resistance allele frequencies and linkage disequilibria:
The frequencies of the different phenotypes combined at both loci are given in Table 2. The Hardy-Weinberg expectation was not rejected at the Ester locus (global test over populations P = 0.87). The linkage disequilibrium estimates between Ester and Ace.1 (D) and their corresponding P value are indicated in Table 2. A positive D is observed (Table 2D > 0, combined test across populations P = 5.10-5) that peaks (46%) near the ecotone transition, which is consistent with a linkage disequilibrium created by migration.
|
Descriptive models:
At the Ace.1 locus, a clinal pattern is detected for both Ace.1R and Ace.1RS alleles (Table 3). The presence at high frequencies of the duplication (0.33 on the coast, Table 4) is thus strongly supported, and its cline explains well the pattern of apparent excess of heterozygotes in the transect. These two similar clines explain 88% of the total deviance at Ace.1 locus. However, the frequency of the duplicated allele Ace.1RS is underestimated by assuming Hardy-Weinberg proportions because a heterozygote deficiency due to migration is expected. At the Ester locus, the model explains 77% of the total deviance. Significant and similar clinal patterns were found for all esterase resistance alleles, even for Ester2, which is rare (Table 3 and Table 4). These results are consistent with the hypothesis that, for each locus, the selection pressures acting on resistance alleles are similar, that is, that the main differences in selection pressure are between susceptible and resistance alleles.
|
|
Migration-selection models:
The migration-selection models explain 9293% of the total deviance (Table 5 and Figure 2). The maximum likelihood estimate of the parent-offspring standard deviation measured on one dimension is
= 6.6 km.gen-
(support limits 4.88.7 km.gen-1/2) when codominance is assumed at both loci. It should be underlined that the expected linkage disequilibrium does not peak at the ecotone transition, as in the case of an infinite environment (see ![]()
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Effect of the linkage:
As in the case of a single locus, the ratio of selection intensities in treated and untreated areas (
2) and the selection-migration ratio (k) depend only on the relative magnitude of selection vs. gene flow for each locus (data not shown). However, the linkage between the two loci (14.5%) has a noticeable effect on the Ester locus: in order to maintain the Ester cline at the same frequency in the absence of selection on Ace.1, selection (or k2) would have to be 26% higher. In contrast, to maintain the Ace.1 cline at the same level, k2 need only be increased by 7% in the absence of selection on the Ester locus.
Dominance effect:
The different hypotheses of dominance do not have an important effect neither on the estimation of migration variance (
range 6.67.1) nor on its support limits (Table 5). In fact, for given frequency gradients, the estimation depends mainly on the linkage disequilibrium pattern, as previously pointed out by ![]()
Recombination effect:
The estimate of the migration variance strongly depends on the recombination rate between Ace.1 and Ester: for the same migration variance, the closer the loci the higher the linkage disequilibrium. The recombination rate (r) of 14.5% was estimated between Ester and Ace.1 based on 503 individuals (T. LENORMAND, T. GUILLEMAUD, D. BOURQUET and M. RAYMOND, unpublished results). Figure 3 shows the joint support area for r and
, assuming codominance at both loci. Support limits of
are not affected by error measurements on the recombination rate (see Figure 3).
|
Selection intensities:
Estimations of selection intensities may not be as robust as the estimation of
, because they depend on the assumptions of dominance. However, the different cases of dominance that were investigated are not equally likely (Table 5). In particular, models considering dominance at Ace locus (models AC in Table 5) are ~20 times less likely than those that consider recessivity (models GI). In contrast, for a given dominance on the Ace.1 locus, there are no noticeable differences between models considering different dominance levels on the Ester locus. When considering only the most likely models (EI), selection intensity is likely to be ~0.12 on Ace.1 (sa) and ~0.055 on Ester (se). For codominance at both loci (model E), these selection intensities give an estimate of the insecticide selection pressure (si
0.30 for Ace.1 and
0.16 for Ester) and of the intensities of the fitness costs (c
0.11 and
0.06 for Ace.1 and Ester, respectively).
| DISCUSSION |
|---|
Validity of the assumptions:
The analysis of clinal patterns allowed us to infer in a single step the different parameters that are relevant to describe the dynamics of local adaptation, i.e., gene flow and selection coefficients in the different part of the environment for each locus. Additionally, the model developed permits us to explain 92% of the total deviance of the data in a quite economical manner. However, many simplifications were assumed, and external estimations were used for some parameters. We will discuss these points in turn.
Models of selection:
We assumed that the different resistance alleles at each locus were subjected to the same selection pressure. This is probably not true since allele replacements were observed over the last 20 years (![]()
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External estimation of parameters: We supposed that the summer clines were observed at migration-selection equilibrium. This is of course not exactly true, because selection intensities vary during the year. However, the high selection pressure and migration variance estimated are consistent with very rapid adjustments of frequencies. Moreover, frequencies, as well as selection intensities, are autocorrelated in time: adjustments to selection intensities require only limited changes in frequency.
We assumed a symmetric binomial migration distribution with a reflecting condition on the sea coast. Departures from this assumption could exist due to several factors. First, the migration distribution may be more leptokurtic. This may not strongly affect the peak of linkage disequilibrium at the ecotone transition (see ![]()
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Comparison with other estimates:
Direct measures of dispersal:
Many studies have investigated the active dispersal of Culex species by mark-recapture experiments. Although none consider C. p. pipiens, plenty of data is available for C. p. quinquefasciatus, the tropical subspecies of C. pipiens (![]()
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Migration-drift equilibrium:
The relative magnitude of gene flow vs. drift has been evaluated in southern France by ![]()
allows us to disentangle drift and migration and to estimate average effective population densities. We reanalyzed the allozymic data from ![]()
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2), where De is the density of mosquitoes (![]()
2 is 16.3 individuals. Using our estimate of
= 6.6 km·gen-
, the estimate of the density De is 0.37 individuals per km2. This result is surprising when compared to the mosquito densities observed in the field during the breeding season (104107 individuals/km2; ![]()
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Selection intensities:
We found that insecticide selection on Ace.1 locus (si
0.30) was higher than on Ester locus (si
0.16). This is consistent with the resistance ratio associated with these loci: the insensitive AChE1 confers a higher level of resistance. However, even if selection has been clearly associated with OP insecticides, it has never been measured in natural populations. The evaluation of fitness costs is even less straightforward because all fitness components can be influenced during both larval and adult stages. For example, larval development time, fecundity, susceptibility to parasites or predators, ability to blood feed, etc., can be modified by the presence of resistance genes (e.g., ![]()
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0.11 and 0.06 for Ace.1 and Ester, respectively).
Conditions for the maintenance of Ace.1 and Ester clines:
Both clines maintain each other. Their concomitant presence makes the conditions for their maintenance less strict than if they were alone. However, this effect concerns mainly the least selected locus, Ester. We computed that the frequencies of Ester0 and Ace.1S in coastal populations would be 0.074 and 0.013 higher, respectively, if each locus was considered independently from the other. Using the estimates of migration and selection provided by model E (codominance at both loci), the Ester cline would disappear if the width of the treated area (L) was reduced to 11 km. Similarly, the Ace.1 cline is not maintained when L < 7 km. In an infinite and uniform environment, the minimum size of a potential adaptive pocket would therefore be ~15 km for codominance at both loci.
Estimating gene flow from selected loci:
When estimating gene flow from selected loci, the selection pressure is taken explicitly into account. This situation presents different advantages. First, there is no need to formulate ad hoc hypotheses concerning neutrality of markers; second, few markers are needed; and third, predictable frequency patterns are expected and can be tested. However, this method requires that some genes be identified that are subjected to clear selection pressures and that some conclusion be made a priori concerning these selection pressures. Additionally, this method permits working at a restricted scale in time and space where assumptions of constant population sizes and homogeneity of space are the most reliable. In particular, it is possible to take explicitly into account specific features of the environment (e.g., presence of geographic barriers), if needed. The drawback is that such estimates can hardly be representative of other environmental conditions because they are not averaged over a long period of time and over large geographic areas. However, they provide an "instantaneous" measure of dispersal that is the most pertinent for the area, the period, and the scale considered, especially in the case of recent local adaptation. In this respect, these measures may be comparable to mark-recapture estimates. However, direct measures of dispersal do not provide estimates of effective gene flow and may miss long-distance migrants because individuals are often trapped at the limit of the trapping grid.
We have estimated gene flow using two selected genetic markers. This estimation is an essential step in understanding the dynamics of selected genes when selection pressures vary in space and time. We have focused on the selection-migration equilibrium on a local scale, considering gene flow as a "constraining force" reducing the potential for local adaptation. However, on a much wider scale, gene flow is also responsible for the spread of resistance alleles across the species range mainly by passive migration (![]()
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| FOOTNOTES |
|---|
1 Present address: Station de Recherche de lutte biologique, INRA La Minière, 78285 Guyancourt Cedex, France. ![]()
| ACKNOWLEDGMENTS |
|---|
We are very grateful to C. CHEVILLON, N. PASTEUR, F. ROUSSET and J. BRITTON-DAVIDIAN for their helpful comments and discussion about the manuscript. This work was financed by Groupement de Recherche 1105 du programme Environnement, Vie et Sociétés du Centre National de la Recherche Scientifique, the Région Languedoc-Roussillon (no. 963223) and ACC SV3 (no. 9503037). T.L. was supported by an ASC from Institut National de la Recherche Agronomique. Contribution 98.062 of the Institut des Sciences de l'Evolution de Montpellier (UMR CNRS 5554).
Manuscript received September 16, 1997; Accepted for publication March 9, 1998.
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