Evaluating gene flow using selected markers: a case study

Major SCP/TAPS protein expansion in Lucilia cuprina is associated with novel tandem array organisation and domain architecture

Background

Larvae of the Australian sheep blowfly, Lucilia cuprina, parasitise sheep by feeding on skin excretions, dermal tissue and blood, causing severe damage known as flystrike or myiasis. Recent advances in -omic technologies and bioinformatic data analyses have led to a greater understanding of blowfly biology and should allow the identification of protein families involved in host-parasite interactions and disease. Current literature suggests that proteins of the SCP (Sperm-Coating Protein)/TAPS (Tpx-1/Ag5/PR-1/Sc7) (SCP/TAPS) superfamily play key roles in immune modulation, cross-talk between parasite and host as well as developmental and reproductive processes in parasites.

Methods

Here, we employed a bioinformatics workflow to curate the SCP/TAPS protein gene family in L. cuprina. Protein sequence, the presence and number of conserved CAP-domains and phylogeny were used to group identified SCP/TAPS proteins; these were compared to those found in Drosophila melanogaster to make functional predictions. In addition, transcription levels of SCP/TAPS protein-encoding genes were explored in different developmental stages.

Results

A total of 27 genes were identified as belonging to the SCP/TAPS gene family: encoding 26 single-domain proteins each with a single CAP domain and a solitary double-domain protein containing two conserved cysteine-rich secretory protein/antigen 5/pathogenesis related-1 (CAP) domains. Surprisingly, 16 SCP/TAPS predicted proteins formed an extended tandem array spanning a 53 kb region of one genomic region, which was confirmed by MinION long-read sequencing. RNA-seq data indicated that these 16 genes are highly transcribed in all developmental stages (excluding the embryo).

Conclusions

Future work should assess the potential of selected SCP/TAPS proteins as novel targets for the control of L. cuprina and related parasitic flies of major socioeconomic importance.

Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations of Haemonchus contortus

The parasitic nematode Haemonchus contortus is one of the world's most important parasites of small ruminants that causes significant economic losses to the livestock sector. The population structure and selection in its various strains are poorly understood. No study so far compared its different populations using genome-wide data. Here, we focused on different geographic populations of H. contours from China (Tibet, TB; Hubei, HB; Inner Mongolia, IM; Sichuan, SC), UK and Australia (AS), using genome-wide population-genomic approaches, to explore genetic diversity, population structure and selection. We first performed next-generation high-throughput 2b RAD pool sequencing using Illumina technology, and identified single-nucleotide polymorphisms (SNPs) in all the strains. We identified 75,187 SNPs for TB, 82,271 for HB, 82,420 for IM, 79,803 for SC, 83,504 for AS and 78,747 for UK strain. The SNPs revealed low-nucleotide diversity (pi= 0.0092-0.0133) within each strain, and a significant differentiation level (average F_st = 0.34264) among them. Chinese populations TB and SC, along with the UK strain, were more divergent populations. Chinese populations IM and HB showed affinities to the Australian strain. We then analysed signature of selection and detected 44 (UK) and 03 (AS) private selective sweeps containing 49 and 05 genes, respectively. Finally, we performed the functional annotation of selective sweeps and proposed biological significance to signature of selection. Our data suggest that 2b-RAD pool sequencing can be used to assess the signature of selection in H. contortus.

Adaptive deletion in resistance gene duplications in the malaria vector Anopheles gambiae

While gene copy-number variations play major roles in long-term evolution, their early dynamics remains largely unknown. However, examples of their role in short-term adaptation are accumulating: identical repetitions of a locus (homogeneous duplications) can provide a quantitative advantage, while the association of differing alleles (heterogeneous duplications) allows carrying two functions simultaneously. Such duplications often result from rearrangements of sometimes relatively large chromosome fragments, and even when adaptive, they can be associated with deleterious side effects that should, however, be reduced by subsequent evolution. Here, we took advantage of the unique model provided by the malaria mosquito Anopheles gambiae s.l. to investigate the early evolution of several duplications, heterogeneous and homogeneous, segregating in natural populations from West Africa. These duplications encompass ~200 kb and 11 genes, including the adaptive insecticide resistance ace-1 locus. Through the survey of several populations from three countries over 3-4 years, we showed that an internal deletion of all coamplified genes except ace-1 is currently spreading in West Africa and introgressing from An. gambiae s.s. to An. coluzzii. Both observations provide evidences of its selection, most likely due to reducing the gene-dosage disturbances caused by the excessive copies of the nonadaptive genes. Our study thus provides a unique example of the early adaptive trajectory of duplications and underlines the role of the environmental conditions (insecticide treatment practices and species ecology). It also emphasizes the striking diversity of adaptive responses in these mosquitoes and reveals a worrisome process of resistance/cost trade-off evolution that could impact the control of malaria vectors in Africa.

Putting evolution in elimination: Winning our ongoing battle with evolving malaria mosquitoes and parasites

Since 2000, the world has made significant progress in reducing malaria morbidity and mortality, and several countries in Africa, South America and South-East Asia are working hard to eliminate the disease. These elimination efforts continue to rely heavily on antimalarial drugs and insecticide-based interventions, which remain the cornerstones of malaria treatment and prevention. However, resistance has emerged against nearly every antimalarial drug and insecticide that is available. In this review we discuss the evolutionary consequences of the way we currently implement antimalarial interventions, which is leading to resistance and may ultimately lead to control failure, but also how evolutionary principles can be applied to extend the lifespan of current and novel interventions. A greater understanding of the general evolutionary principles that are at the core of emerging resistance is urgently needed if we are to develop improved resistance management strategies with the ultimate goal to achieve a malaria-free world.

Two-locus clines on the real line with a step environment

The shape of allele-frequency clines maintained by migration-selection balance depends not only on the properties of migration and selection, but also on the dominance relations among alleles and on linkage to other loci under selection. We investigate a two-locus model in which two diallelic, recombining loci are subject to selection caused by an abrupt environmental change. The habitat is one-dimensional and unbounded, selection at each locus is modeled by step functions such that in one region one allele at each locus is advantageous and in the other deleterious. We admit an environmentally independent, intermediate degree of dominance at both loci, including complete dominance. First, we derive an explicit expression for the single-locus cline with dominance, thus generalizing classical results by Haldane (1948). We show that the slope of the cline in the center (at the step) or, equivalently, the width of the cline, is independent of the degree of dominance. Second, under the assumption of strong recombination relative to selection and migration, the first-order approximations of the allele-frequency clines at each of the loci and of the linkage disequilibrium are derived. This may be interpreted as the quasi-linkage-equilibrium approximation of the two-locus cline. Explicit asymptotic expressions for the clines are deduced as x→±∞. For equivalent loci, explicit expressions for the whole clines are derived. The influence of dominance and of linkage on the slope of the cline in the center and on a global measure of steepness are investigated. This global measure reflects the influence of dominance. Finally, the accuracy of the approximations and the dependence of the shape of the two-locus cline on the full range of recombination rates is explored by numerical integration of the underlying system of partial differential equations.

Fungal adaptation to contemporary fungicide applications: the case of Botrytis cinerea populations from Champagne vineyards (France)

In addition to being one of the most acute problems impeding chemical control of fungal diseases, the evolution of fungicide resistance is an emblematic case of local adaptation to spatially heterogeneous and temporally variable selection pressures. Here we dissected the adaptation of Botrytis cinerea (the causal agent of grey mould) populations on grapes to several fungicides. We carried out a 2-year survey (four collection dates) on three treated/untreated pairs of plots from vineyards in Champagne (France) and monitored the frequency of four resistant phenotypes that are unambiguously associated with four distinct genotypes. For two loci under selection by currently used fungicides (MDR1 and MDR2), the frequencies of resistant mutations at vintage were greater in treated plots compared to untreated plots, showing that the effect of selection is detectable even at the plot scale. This effect was not detectable for two other loci under selection by previously used fungicides (BenR1 and ImiR1). We also found that treatment with currently used fungicides reduced B. cinerea effective population size, leading to a significant decrease in genic diversity and allelic richness in treated vs. untreated plots. We further highlight that even under ample drift and migration, fungal populations can present an efficient response to selection. Finally, for the four studied loci, the costs of fungicide resistance were estimated by modelling the decrease in the frequency of resistant mutations in the absence of treatment. We discuss the importance of these estimates for defining strategies for limiting or counteracting the local adaptation of pests to fungicides.

Identifying patterns of dispersal, connectivity and selection in the sea scallop, Placopecten magellanicus, using RADseq-derived SNPs

Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used restriction-site-associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. Based on 245 individuals sampled rangewide at 12 locations from Newfoundland to the Mid-Atlantic Bight, we identified and genotyped 7163 single nucleotide polymorphisms; 112 (1.6%) were identified as outliers potentially under directional selection. Bayesian clustering revealed a discontinuity between northern and southern samples, and latitudinal clines in allele frequencies were observed in 42.9% of the outlier loci and in 24.6% of neutral loci. Dispersal estimates derived using these clines and estimates of linkage disequilibrium imply limited dispersal; 373.1 ± 407.0 km (mean ± SD) for outlier loci and 641.0 ± 544.6 km (mean ± SD) for neutral loci. Our analysis suggests restricted dispersal compared to the species range (>2000 km) and that dispersal and effective connectivity differ. These observations support the hypothesis that limited effective dispersal structures scallop populations along eastern North America. These findings can help refine the appropriate scale of management and conservation in this commercially valuable species.

Relating fitness to long-term environmental variations in natura

Quantifying links between ecological processes and adaptation dynamics in natura remains a crucial challenge. Many studies have documented the strength, form and direction of selection, and its variations in space and time, but only a few managed to link these variations to their proximal causes. This step is, however, crucial, if we are to understand how the variation in selective pressure affects adaptive allele dynamics in natural settings. We used data from a long-term survey (about 30 years) monitoring the adaptation to insecticides of Culex pipiens mosquitoes in Montpellier area (France), focusing on three resistance alleles of the Ester locus. We used a population genetics model taking temporal and spatial variations in selective pressure into account, to assess the quantitative relationships between variations in the proximal agent of selection (amounts of insecticide sprayed) and the fitness of resistance alleles. The response to variations in selective pressure was fast, and the alleles displayed different fitness-to-environment relationships: the analyses revealed that even slight changes in insecticide doses could induce changes in the strength and direction of selection, thus changing the fitness ranking of the adaptive alleles. They also revealed that selective pressures other than the insecticides used for mosquito control affected the resistance allele dynamics. These fitness-to-environment relationships, fast responses and continuous evolution limit our ability to predict the outcome of adaptive allele dynamics in a changing environment, but they clearly contribute to the maintenance of polymorphism in natural populations. Our study also emphasizes the necessity of long-term surveys in evolutionary ecology.

Insecticide resistance alleles in wetland and residential populations of the West Nile virus vector Culex pipiens in New Jersey

BACKGROUND

In spite of the extensive use of insecticides to control Culex pipiens in the aftermath of West Nile virus, knowledge of the spatial distribution and frequency of insecticide resistance in this species is poorly understood in the United States. This paper reports on the occurrence of upregulated esterases that detoxify organophosphates (OPs) and mutations conferring resistance to pyrethroid insecticides in natural and developed areas of New Jersey.

RESULTS

We report the first observations of the OP resistance alleles Ester(B1) and Ester(2) and the classical knockdown resistance (kdr) mutation L1014F in New Jersey Cx. pipiens. Upregulated Ester(B1) peaked at 23% (mean ± SE = 12 ± 2.3%) and Ester(2) at 14% (8 ± 1.8%), and both were widely distributed. L1014F, which confers strong resistance to pyrethroids when homozygous, was also widely distributed and ranged in frequency from 2 to 19% (5.1% heterozygous individuals and 1.4% homozygous).

CONCLUSION

We have demonstrated that OP resistance is common and broadly distributed in New Jersey Cx. pipiens, and that homozygous individuals resistant to pyrethroids are present. Further, we have detected double mutants at Ester and kdr, a condition that may annul the purging effects of insecticide rotations. Our results therefore indicate the need for continued monitoring of insecticide resistance in order to achieve effective mosquito control.

Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era

Estimating the rate of exchange of individuals among populations is a central concern to evolutionary ecology and its applications to conservation and management. For instance, the efficiency of protected areas in sustaining locally endangered populations and ecosystems depends on reserve network connectivity. The population genetics theory offers a powerful framework for estimating dispersal distances and migration rates from molecular data. In the marine realm, however, decades of molecular studies have met limited success in inferring genetic connectivity, due to the frequent lack of spatial genetic structure in species exhibiting high fecundity and dispersal capabilities. This is especially true within biogeographic regions bounded by well-known hotspots of genetic differentiation. Here, we provide an overview of the current methods for estimating genetic connectivity using molecular markers and propose several directions for improving existing approaches using large population genomic datasets. We highlight several issues that limit the effectiveness of methods based on neutral markers when there is virtually no genetic differentiation among samples. We then focus on alternative methods based on markers influenced by selection. Although some of these methodologies are still underexplored, our aim was to stimulate new research to test how broadly they are applicable to nonmodel marine species. We argue that the increased ability to apply the concepts of cline analyses will improve dispersal inferences across physical and ecological barriers that reduce connectivity locally. We finally present how neutral markers hitchhiking with selected loci can also provide information about connectivity patterns within apparently well-mixed biogeographic regions. We contend that one of the most promising applications of population genomics is the use of outlier loci to delineate relevant conservation units and related eco-geographic features across which connectivity can be measured.

Behavioral cost & overdominance in Anopheles gambiae

In response to the widespread use of control strategies such as Insecticide Treated Nets (ITN), Anopheles mosquitoes have evolved various resistance mechanisms. Kdr is a mutation that provides physiological resistance to the pyrethroid insecticides family (PYR). In the present study, we investigated the effect of the Kdr mutation on the ability of female An. gambiae to locate and penetrate a 1cm-diameter hole in a piece of netting, either treated with insecticide or untreated, to reach a bait in a wind tunnel. Kdr homozygous, PYR-resistant mosquitoes were the least efficient at penetrating an untreated damaged net, with about 51% [39-63] success rate compared to 80% [70-90] and 78% [65-91] for homozygous susceptible and heterozygous respectively. This reduced efficiency, likely due to reduced host-seeking activity, as revealed by mosquito video-tracking, is evidence of a recessive behavioral cost of the mutation. Kdr heterozygous mosquitoes were the most efficient at penetrating nets treated with PYR insecticide, thus providing evidence for overdominance, the rarely-described case of heterozygote advantage conveyed by a single locus. The study also highlights the remarkable capacity of female mosquitoes, whether PYR-resistant or not, to locate holes in bed-nets.

Genetic Characterization of Esterase Activity Variants Associated with an Esterase Gene Amplification in a Strain of Culex pipiens from California

In the Culex pipiens complex, a common mechanism of insecticide resistance is amplification of esterase genes leading to overproduction of detoxifying esterase enzymes. A number of electrophoretic esterase alleles have been identified, and in field populations individuals with the same esterase electromorph can exhibit a wide range of esterase enzyme activities. We isolated and characterized esterase activity variants associated with the esterase B1 electromorph from a field strain. A mating scheme was used to isolate chromosomes with esterase genes from the strain into 45 families. Twenty-six of the families received esterase genes from the field strain that conferred elevated esterase activity. Mean esterase activities in these families ranged from 43 to 695 nmoles α-naphthyl acetate hydrolyzed/min/mg protein. Variance components indicated that genetic variance (i.e., genetic differences among families) accounted for 77% of the total variation in esterase activity. A comparison of mean esterase activities indicated that there were at least 11 different esterase activity variants contributing to the observed genetic variation in esterase activity among the 26 families. The relevance of these results to understanding the dynamics of amplified esterase genes in populations is discussed.

GENE-dosage effects on fitness in recent adaptive duplications: ace-1 in the mosquito Culex pipiens

Gene duplications have long been advocated to contribute to the evolution of new functions. The role of selection in their early spread is more controversial. Unless duplications are favored for a direct benefit of increased expression, they are likely detrimental. In this article, we investigated the case of duplications favored because they combine already functionally divergent alleles. Their gene-dosage/fitness relations are poorly known because selection may operate on both overall expression and duplicates relative dosage. Using the well-documented case of Culex pipiens resistance to insecticides, we compared strains with various ace-1 allele combinations, including two duplicated alleles carrying both susceptible and resistant copies. The overall protein activity was nearly additive, but, surprisingly, fitness correlated better with the relative proportion of susceptible and resistant copies rather than any absolute measure of activity. Gene dosage is thus crucial, duplications stabilizing a "heterozygote" phenotype. It corroborates the view that these were favored because they fix a permanent heterosis, thereby solving the irreducible trade-off between resistance and synaptic transmission. Moreover, we showed that the contrasted successes of the two duplicated alleles in natural populations depend on genetic changes unrelated to ace-1, confirming the probable implication of recessive sublethal mutations linked to structural rearrangements in some duplications.

Multiple insecticide resistances in the disease vector Culex p. quinquefasciatus from Western Indian Ocean

Several mosquito-borne diseases affect the Western Indian Ocean islands. Culex pipiens quinquefasciatus is one of these vectors and transmits filariasis, Rift Valley and West Nile viruses and the Japanese encephalitis. To limit the impact of these diseases on public health, considerable vector control efforts have been implemented since the 50s, mainly through the use of neurotoxic insecticides belonging to Organochlorines (OC), Organophosphates (OP) and pyrethroids (PYR) families. However, mosquito control failures have been reported on site, and they were probably due to the selection of resistant individuals in response to insecticide exposure. In this study, we used different approaches to establish a first regional assessment of the levels and mechanisms of resistance to various insecticides. Bioassays were used to evaluate resistance to various insecticides, enzyme activity was measured to assess the presence of metabolic resistances through elevated detoxification, and molecular identification of known resistance alleles was investigated to determine the frequency of target-site mutations. These complementary approaches showed that resistance to the most used insecticides families (OC, OP and PYR) is widespread at a regional scale. However, the distribution of the different resistance genes is quite heterogeneous among the islands, some being found at high frequencies everywhere, others being frequent in some islands and absent in others. Moreover, two resistance alleles displayed clinal distributions in Mayotte and La Réunion, probably as a result of a heterogeneous selection due to local treatment practices. These widespread and diverse resistance mechanisms reduce the capacity of resistance management through classical strategies (e.g. insecticide rotation). In case of a disease outbreak, it could undermine the efforts of the vector control services, as only few compounds could be used. It thus becomes urgent to find alternatives to control populations of Cx. p. quinquefasciatus in the Indian Ocean.

Estimation of the dispersal of a major pest of maize by cline analysis of a temporary contact zone between two invasive outbreaks

Dispersal is a key factor in invasion and in the persistence and evolution of species. Despite the importance of estimates of dispersal distance, dispersal measurement remains a real methodological challenge. In this study, we characterized dispersal by exploiting a specific case of biological invasion, in which multiple introductions in disconnected areas lead to secondary contact between two differentiated expanding outbreaks. By applying cline theory to this ecological setting, we estimated σ, the standard deviation of the parent-offspring distance distribution, of the western corn rootworm, Diabrotica virgifera virgifera, one of the most destructive pests of maize. This species is currently invading Europe, and the two largest invasive outbreaks, in northern Italy and Central Europe, have recently formed a secondary contact zone in northern Italy. We identified vanishing clines at 12 microsatellite loci throughout the contact zone. By analysing both the rate of change of cline slope and the spatial variation of linkage disequilibrium at these markers, we obtained two σ estimates of about 20 km/generation(1/2). Simulations indicated that these estimates were robust to changes in dispersal kernels and differences in population density between the two outbreaks, despite a systematic weak bias. These estimates are consistent with the results of direct methods for measuring dispersal applied to the same species. We conclude that secondary contact resulting from multiple introductions is very useful for the inference of dispersal parameters and should be more widely used in other species.

Using neutral cline decay to estimate contemporary dispersal: a generic tool and its application to a major crop pathogen

Dispersal is a key parameter of adaptation, invasion and persistence. Yet standard population genetics inference methods hardly distinguish it from drift and many species cannot be studied by direct mark-recapture methods. Here, we introduce a method using rates of change in cline shapes for neutral markers to estimate contemporary dispersal. We apply it to the devastating banana pest Mycosphaerella fijiensis, a wind-dispersed fungus for which a secondary contact zone had previously been detected using landscape genetics tools. By tracking the spatio-temporal frequency change of 15 microsatellite markers, we find that σ, the standard deviation of parent–offspring dispersal distances, is 1.2 km/generation^1/2. The analysis is further shown robust to a large range of dispersal kernels. We conclude that combining landscape genetics approaches to detect breaks in allelic frequencies with analyses of changes in neutral genetic clines offers a powerful way to obtain ecologically relevant estimates of dispersal in many species.

Outlier loci highlight the direction of introgression in oaks

Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Quercus petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and nonoutlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late-successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with nonoutlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species' contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized.

Identification of resistant carboxylesterase alleles in Culex pipiens complex via PCR-RFLP

BACKGROUND

Carboxylesterase overproduction is a frequently observed resistance mechanism of insects to organophosphate insecticides. As a major transmitter of human diseases, mosquitoes in the Culex pipiens complex have evolved 13 carboxylesterase alleles (Ester) that confer organophosphate resistance. Six alleles, Ester(B1), Ester², Ester⁸, Ester⁹, Ester(B10), and Ester¹¹, have been observed in field populations in China, sometimes co-existing in one population. To differentiate the carboxylesterase alleles found in these field populations, PCR-RFLP was designed for use in resistance monitoring.

RESULTS

Based on the DNA sequences of resistant and nonresistant carboxylesterase alleles, Ester B alleles were first amplified with PCR-specific primers and then digested with the restriction enzyme DraI. In this step, Ester² and Ester¹¹ were differentiated from the other Ester alleles. When the other Ester B alleles were digested with the restriction enzyme XbaI, Ester(B1) and the susceptible C. p. pallens Ester were screened out. Ester⁸ and Ester⁹ were differentiated from Ester(B10) and the susceptible C. p. quinquefasciatus esterase allele, respectively, by amplifying and digesting the Ester A alleles with the restriction enzyme ApaLI. The effectiveness of the custom-designed PCR-RFLP was verified in two field mosquito populations.

CONCLUSIONS

A PCR-RFLP based approach was developed to differentiate carboxylesterase alleles in Culex pipiens complex mosquitoes. These processes may be useful in monitoring the evolutionary dynamics of known carboxylesterase alleles as well as in the identification of new alleles in field populations.

From Local Adaptation to Speciation: Specialization and Reinforcement

Local adaptation is the first step in the process of ecological speciation. It is, however, an unstable and dynamic situation. It can be strengthened by the occurrence of alleles more specialized to the different habitats or vanish if generalist alleles arise by mutations and increase in frequency. This process can have complicated dynamics as specialist alleles may be much more common and may maintain local adaptation for a long time. Thus, even in the absence of an absolute fitness tradeoff between habitats, local adaptation may persist a long time before vanishing. Furthermore, several feedback loops can help to maintain it (the reinforcement, demographic, and recombination loops). This reinforcement can occur by modifying one of the three fundamental steps in a sexual life cycle (dispersal, syngamy, meiosis), which promotes genetic clustering by causing specific genetic associations. Distinguishing these mechanisms complements the one- versus two-allele classification. Overall, the relative rates of the two processes (specialization and reinforcement) dictate whether ecological speciation will occur.

Molecular spandrels: tests of adaptation at the genetic level

Although much progress has been made in identifying the genes (and, in rare cases, mutations) that contribute to phenotypic variation, less is known about the effects that these genes have on fitness. Nonetheless, genes are commonly labelled as 'adaptive' if an allele has been shown to affect a phenotype with known or suspected functional importance or if patterns of nucleotide variation at the locus are consistent with positive selection. In these cases, the 'adaptive' designation may be premature and may lead to incorrect conclusions about the relationships between gene function and fitness. Experiments to test targets and agents of natural selection within a genomic context are necessary for identifying the adaptive consequences of individual alleles.

High incidence of ace-1 duplicated haplotypes in resistant Culex pipiens mosquitoes from Algeria

The status of genes conferring resistance to organophosphate and carbamate insecticides has been examined in Culex pipiens pipiens mosquitoes sampled in Algeria. Presence of overproduced esterases was sporadic, but acetylcholinesterase-1 resistant alleles were observed in almost all samples. We focused our study on the AChE1 G119S substitution characterized in almost all samples, mostly at the heterozygous state. A genetic test revealed the presence of ace-1 duplication associating a susceptible and a resistant ace-1 copy. Molecular characterization showed a high occurrence of ace-1 duplication with six distinct duplicated alleles out of four samples. The inferred frequency of duplicated allele suggests that it is replacing the single resistant G119S allele. Finally, we discuss the mechanism at the origin of these duplicated haplotypes and their consequences on the management of insecticide resistance.

Tandemly arrayed genes in vertebrate genomes

Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72-94%) have parallel transcription orientation (i.e., they are encoded on the same strand) in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation.

The skill and style to model the evolution of resistance to pesticides and drugs

Resistance to pesticides and drugs led to the development of theoretical models aimed at identifying the main factors of resistance evolution and predicting the efficiency of resistance management strategies. We investigated the various ways in which the evolution of resistance has been modelled over the last three decades, by reviewing 187 articles published on models of the evolution of resistance to all major classes of pesticides and drugs. We found that (i) the technical properties of the model were most strongly influenced by the class of pesticide or drug and the target organism, (ii) the resistance management strategies studied were quite similar for the different classes of pesticides or drugs, except that the refuge strategy was mostly used in models of the evolution of resistance to insecticidal proteins, (iii) economic criteria were rarely used to evaluate the evolution of resistance and (iv) the influence of mutation, migration and drift on the speed of resistance development has been poorly investigated. We propose guidelines for the future development of theoretical models of the evolution of resistance. For instance, we stress the potential need to give more emphasis to the three evolutionary forces migration, mutation and genetic drift rather than simply selection.

Genes conferring resistance to organophosphorus insecticides in Culex pipiens (Diptera: Culicidae) from Tunisia

In Tunisia, the mosquito Culex pipiens shows various organophosphate resistance alleles at Ester and ace-1 loci. The characterization and the distribution pattern of these alleles were studied among 20 populations sampled from north to center of Tunisia. At the Ester locus, Ester4, Ester5, and Ester(B12) were present. A new esterase characterized by the same electrophoretic migration as esterase A1 was identified: A13, encoded by Ester(A13) allele. At the ace-1 locus, the presence of the ace-1(R), ace-1(D), and F290V mutated alleles was also detected. A large heterogeneity in allelic frequencies at Ester and ace-1 loci was observed among samples, with a high significant genotypic differentiation considering both loci (F, = 0.077, P < 10(-5)), depicting variations of insecticide treatment intensity between areas. A comparison between populations collected in 1996 and 2005 showed an absence of significant resistance evolution. However, the high frequencies of resistance alleles in 2005 populations suggested that the selection pressures are still important in Tunisia. Strategies for resistance management are discussed in the context of the current knowledge of the Tunisian situation.

Resistance Gene Replacement in the mosquito Culex pipiens: fitness estimation from long-term cline series

How adaptation appears and is later refined by natural selection has been the object of intense theoretical work. However, the testing of these theories is limited by our ability to estimate the strength of natural selection in nature. Using a long-term cline series, we estimate the selection coefficients acting on different alleles at the same locus to analyze the allele replacement observed in the insecticide resistance gene Ester in the mosquito Culex pipiens in the Montpellier area, southern France. Our method allows us to accurately account for the resistance allele replacement observed in this area since 1986. A first resistance allele appeared early, which was replaced by a second resistance allele providing the same advantage but at a lower cost, itself being replaced by a third resistance allele with both higher advantage and cost. It shows that amelioration of the adaptation (here resistance to insecticide) through allele replacement was successively achieved by selection of first a generalist allele (i.e., with a low fitness variance across environments) and later a specialist allele (i.e., with a large fitness variance across environments). More generally, we discuss how precise estimates of the strength of selection obtained from field data help us understand the process of amelioration of adaptation.

Forty years of erratic insecticide resistance evolution in the mosquito Culex pipiens

One view of adaptation is that it proceeds by the slow and steady accumulation of beneficial mutations with small effects. It is difficult to test this model, since in most cases the genetic basis of adaptation can only be studied a posteriori with traits that have evolved for a long period of time through an unknown sequence of steps. In this paper, we show how ace-1, a gene involved in resistance to organophosphorous insecticide in the mosquito Culex pipiens, has evolved during 40 years of an insecticide control program. Initially, a major resistance allele with strong deleterious side effects spread through the population. Later, a duplication combining a susceptible and a resistance ace-1 allele began to spread but did not replace the original resistance allele, as it is sublethal when homozygous. Last, a second duplication, (also sublethal when homozygous) began to spread because heterozygotes for the two duplications do not exhibit deleterious pleiotropic effects. Double overdominance now maintains these four alleles across treated and nontreated areas. Thus, ace-1 evolution does not proceed via the steady accumulation of beneficial mutations. Instead, resistance evolution has been an erratic combination of mutation, positive selection, and the rearrangement of existing variation leading to complex genetic architecture.

Adaptation is not always a straightforward process, and often results from natural selection tinkering with available variation. We present in this study just such a tortuous natural selection pathway, which allows the mosquito Culex pipiens to resist organophosphorous insecticides. In the Montpellier area, following the use of insecticide to control mosquito populations, a high-resistance allele of the insecticide target enzyme appeared. But this allele also displayed strong deleterious side effects. Recently, several duplicated haplotypes began to spread in natural population that put in tandem a susceptible and a resistant allele. We show that the duplicated haplotypes actually display reduced side effects compared to the resistant allele when in the heterozygous state, but also new and strong costs in the homozygote. This pattern leads to an unexpected equilibrium between four different alleles across treated and nontreated areas. The story of resistance in C. pipiens is indeed far from a slow progression toward a “perfect” adaptation. Rather, selection for resistance to insecticide is a long process of trial and error leading to an uncommon genetic architecture.

Characterization of novel esterases in insecticide-resistant mosquitoes

In the mosquito Culex pipiens complex (Diptera: Culicidae), the amplification of carboxylesterase genes is an important mechanism providing resistance to organophosphate insecticides. Various amplified alleles at the Ester locus have been identified over the world. In this study, two newly detected Ester alleles, Ester(B10) and Ester(11) (including associated Ester(A11) and Ester(B11)), coding for esterases B10 and A11-B11, respectively, are characterized qualitatively and quantitatively. A high molecular identity is observed both at the nucleotide level and at the deduced amino acid level among the known Ester alleles. Real-time quantitative PCR results suggest 2.5-fold amplification of the Ester(B10) allele, 36.5-fold amplification of the Ester(A11) allele, and 19.1-fold amplification of the Ester(B11) allele. The ca. 2-fold difference in amplification level between Ester(A11) and Ester(B11) may indicate a new model for the esterase amplification. Bioassays show that these two resistant Ester alleles only can confer moderate or low resistance to the tested organophosphate insecticides.

Genetic differentiation of Culex pipiens (Diptera: Culicidae) in China

The population genetic structures of Culex pipiens Linnaeus were evaluated in China over a 2000 km transect that encompasses the two subspecies, C. p. pallens and C. p. quinquefasciatus. Four polymorphic allozyme loci were investigated in 1376 mosquitoes sampled from 20 populations across four provinces. These loci were not statistically dependent with no apparent heterozygote deficit or excess. On a regional scale (intra-province), a low (Fst=0.007-0.016) and significant genetic differentiation was found, with no clear geographical pattern. On a wider scale (inter-province), the genetic differentiation was higher (Fst=0.059), and an isolation by distance emerged. The results are compared with previous population genetic surveys of this mosquito species in different geographic areas over the world. The overall pattern suggests that Culex pipiens requires considerable distance (500-1000 km) to show isolation by distance, irrespective of the subspecies (C. p. pipiens, C. p. quinquefasciatus and C. p. pallens) or the geographic location.

Acetylcholinesterase genes within the Diptera: takeover and loss in true flies

It has recently been reported that the synaptic acetylcholinesterase (AChE) in mosquitoes is encoded by the ace-1 gene, distinct and divergent from the ace-2 gene, which performs this function in Drosophila. This is an unprecedented situation within the Diptera order because both ace genes derive from an old duplication and are present in most insects and arthropods. Nevertheless, Drosophila possesses only the ace-2 gene. Thus, a secondary loss occurred during the evolution of Diptera, implying a vital function switch from one gene (ace-1) to the other (ace-2). We sampled 78 species, representing 50 families (27% of the Dipteran families) spread over all major subdivisions of the Diptera, and looked for ace-1 and ace-2 by systematic PCR screening to determine which taxonomic groups within the Diptera have this gene change. We show that this loss probably extends to all true flies (or Cyclorrhapha), a large monophyletic group of the Diptera. We also show that ace-2 plays a non-detectable role in the synaptic AChE in a lower Diptera species, suggesting that it has non-synaptic functions. A relative molecular evolution rate test showed that the intensity of purifying selection on ace-2 sequences is constant across the Diptera, irrespective of the presence or absence of ace-1, confirming the evolutionary importance of non-synaptic functions for this gene. We discuss the evolutionary scenarios for the takeover of ace-2 and the loss of ace-1, taking into account our limited knowledge of non-synaptic functions of ace genes and some specific adaptations of true flies.

The use of genetic clines to estimate dispersal distances of marine larvae

Many unresolved issues in the ecology and evolution of marine populations center on how far planktonic larvae disperse away from their parents. Genetic tools provide a promising way to define the spatial spread of larvae, yet their accurate interpretation depends on the extent to which genetic loci are under selection. Genetic clines, geographic zones in which genetically differentiated populations interbreed, provide opportunities to explicitly and simultaneously quantify the relative roles of selection and dispersal. Here, we review the theory and analysis of genetic clines and apply these techniques to published studies of multilocus clines in the sea. The geographic width of a stable genetic cline is determined by a balance between the homogenizing effects of dispersal and the diversifying effects of selection. For marine researchers, the power of genetic clines is that, if selection and clinal width are quantified, then the average geographic distances that larvae move can be inferred. Measuring selection or dispersal through laboratory or field-based experimentation is possible, though logistically difficult, for pelagically dispersed organisms. Instead, dispersal may be more robustly quantified from the degree of linkage disequilibrium between two or more loci, because linkage disequilibrium integrates selection across multiple life stages and generations. It is also relatively insensitive to whether exogenous or endogenous selection operates. Even without quantifying linkage disequilibrium, the theory of genetic clines indicates that the average dispersal distance of larvae is a fraction (i.e., generally <35%) of the clinal width. Because cline theory is based on several underlying assumptions, including near-equilibrium between selection and migration, the dispersal distances inferred from empirical data should be of the correct order but may not be precise. Even so, such estimates of larval dispersal are valuable, as they can be utilized to design appropriate scales for future investigations and provide some guidance to conservation efforts.

The use of genetic clines to estimate dispersal distances of marine larvae

Many unresolved issues in the ecology and evolution of marine populations center on how far planktonic larvae disperse away from their parents. Genetic tools provide a promising way to define the spatial spread of larvae, yet their accurate interpretation depends on the extent to which genetic loci are under selection. Genetic clines, geographic zones in which genetically differentiated populations interbreed, provide opportunities to explicitly and simultaneously quantify the relative roles of selection and dispersal. Here, we review the theory and analysis of genetic clines and apply these techniques to published studies of multilocus clines in the sea. The geographic width of a stable genetic cline is determined by a balance between the homogenizing effects of dispersal and the diversifying effects of selection. For marine researchers, the power of genetic clines is that, if selection and clinal width are quantified, then the average geographic distances that larvae move can be inferred. Measuring selection or dispersal through laboratory or field-based experimentation is possible, though logistically difficult, for pelagically dispersed organisms. Instead, dispersal may be more robustly quantified from the degree of linkage disequilibrium between two or more loci, because linkage disequilibrium integrates selection across multiple life stages and generations. It is also relatively insensitive to whether exogenous or endogenous selection operates. Even without quantifying linkage disequilibrium, the theory of genetic clines indicates that the average dispersal distance of larvae is a fraction (i.e., generally <35%) of the clinal width. Because cline theory is based on several underlying assumptions, including near-equilibrium between selection and migration, the dispersal distances inferred from empirical data should be of the correct order but may not be precise. Even so, such estimates of larval dispersal are valuable, as they can be utilized to design appropriate scales for future investigations and provide some guidance to conservation efforts.

On the worldwide spread of an insecticide resistance gene: a role for local selection

Adaptation occurs by gene replacement (or transient balanced polymorphism). Replacement may be caused by selection (local or global) and/or genetic drift among alleles. In addition, historical events may blur the respective effects of selection and drift during the course of replacement. We address the relative importance of these processes in the evolution of insecticide resistance genes in the mosquito Culex pipiens. The resistance allele, Ester2, has a broad geographic distribution compared to the other resistance alleles. To distinguish between the different processes explaining this distribution, we reviewed the literature and analysed updated data from the Montpellier area of southern France. Overall, our data indicate that Ester2 prevails over other Ester resistance alleles in moderately treated areas. Such conditions are common and favour the hypothesis of selection acting at a local level. This places an emphasis on the importance of ecological conditions during the evolution of resistance. Finally, we highlight that historical events have contributed to its spread in some areas.

Male-specific insecticide resistance and mosquito transgene dispersal

There is a need to develop methods to spread disease-blocking transgenes through mosquito populations. This article discusses the possibility of linking transgenes to insecticide-resistant alleles engineered to be expressed only in males. The resulting increase in mean longevity of males carrying the construct under insecticide treatment could easily outweigh any fitness costs in females, so that the construct would spread rapidly. It should be possible to produce constructs where any potential risk of loss of male-specific expression would be negligible.

Estimates of gene flow from rare alleles in natural populations of medfly Ceratitis capitata (Diptera: Tephritidae)

Gene flow based on the spatial distribution of rare alleles at 25 gene loci was estimated in 15 populations of Ceratitis capitata (Wiedemann) from different parts of the world. Estimates of Nm, the number of migrants exchanged per generation among populations in different regions of the world, appeared to be quite similar, ranging from 3.36 in tropical Africa to 2.94 in the New World and 2.72 in Mediterranean basin populations. This suggests that gene flow among neighbouring populations of medfly is quite extensive. The genetic differentiation in American, Mediterranean and African populations was related to major climatic differences between North and South. These differences arise mainly from five loci that showed gene frequency patterns suggestive of latitudinal clines in allele frequencies. The clinal variation was such that tropical-subtropical populations were more heterozygous than temperate populations. It was concluded that gene flow, counteracting the forces of natural selection and genetic drift, determines the extent to which geographical populations of C. capitata are differentiated.

Locus-specific genetic differentiation at Rw among warfarin-resistant rat (Rattus norvegicus) populations

Populations may diverge at fitness-related genes as a result of adaptation to local conditions. The ability to detect this divergence by marker-based genomic scans depends on the relative magnitudes of selection, recombination, and migration. We survey rat (Rattus norvegicus) populations to assess the effect that local selection with anticoagulant rodenticides has had on microsatellite marker variation and differentiation at the warfarin resistance gene (Rw) relative to the effect on the genomic background. Initially, using a small sample of 16 rats, we demonstrate tight linkage of microsatellite D1Rat219 to Rw by association mapping of genotypes expressing an anticoagulant-rodenticide-insensitive vitamin K 2,3-epoxide reductase (VKOR). Then, using allele frequencies at D1Rat219, we show that predicted and observed resistance levels in 27 populations correspond, suggesting intense and recent selection for resistance. A contrast of F(ST) values between D1Rat219 and the genomic background revealed that rodenticide selection has overwhelmed drift-mediated population structure only at Rw. A case-controlled design distinguished these locus-specific effects of selection at Rw from background levels of differentiation more effectively than a population-controlled approach. Our results support the notion that an analysis of locus-specific population genetic structure may assist the discovery and mapping of novel candidate loci that are the object of selection or may provide supporting evidence for previously identified loci.

Population structure and dispersal of the freshwater mosquitoes Culex annulirostris and Culex palpalis (Diptera: Culicidae) in Papua New Guinea and northern Australia

In 1995 and 1998, outbreaks of Japanese encephalitis (JE) virus occurred for the first time in Australia. Virus isolation from pools of mosquitoes indicated Culex annulirostris Skuse was the most likely vector. It was hypothesized that wind-blown mosquitoes introduced JE from Papua New Guinea to the Torres Strait and Cape York, northern Australia. This study used levels of genetic differentiation, as indirect evidence of dispersal of mosquitoes between the two continents. The results have demonstrated that in the region incorporating Western Province in PNG, the Torres Strait and Cape York Peninsula, Cx. annulirostris is represented by a panmictic population, indicating frequent widespread dispersal throughout the region of investigation. The closely related Cx. Palpalis Taylor was also present at some locations but the population structure of this species is uncertain. This supports the hypothesis that wind-blown Cx. annulirostris and possibly Cx. Palpalis could be a possible mechanism for introduction of JE virus into Australia.

Natural selection and the genetic differentiation of coastal and Arctic populations of the Atlantic cod in northern Norway: a test involving nucleotide sequence variation at the pantophysin (PanI) locus

To examine the role of contemporary selection in maintaining significant allele frequency differences at the pantophysin (PanI) locus among populations of the Atlantic cod, Gadus morhua, in northern Norway, we sequenced 127 PanIA alleles sampled from six coastal and two Barents Sea populations. The distributions of variable sites segregating within the PanIA allelic class were then compared among the populations. Significant differences were detected in the overall frequencies of PanIA alleles among populations within coastal and Arctic regions that was similar in magnitude to heterogeneity in the distributions of polymorphic sites segregating within the PanIA allelic class. The differentiation observed at silent sites in the PanIA allelic class contradicts the predicted effects of widescale gene flow and suggests that postsettlement selection acting on cohorts cannot be responsible for the genetic differences described between coastal and Arctic populations. Our results suggest that the marked differences observed between coastal and Arctic populations of G. morhua in northern Norway at the PanI locus reflect the action of recent diversifying selection and that populations throughout the region may be more independent than suggested by previous studies.