Complex trait differentiation between host-populations of the pea aphid Acyrthosiphon pisum (Harris): implications for the evolution of ecological specialisation

Variation in traits affecting preference for, and performance on, new habitats is a key factor in the initiation of ecological specialisation and adaptive speciation. However, habitat and resource use also involves other traits whose influence on ecological and genetic divergence remains poorly understood. In the present study, we investigated the extent of variation of life-history traits among sympatric populations of the pea aphid Acyrthosiphon pisum , which shows several host races that are specialised on various plants of the family Fabaceae plants and is an established model for ecological speciation. First, we assessed the community structure of microbial partners within host populations of the pea aphid. The effect of these microbes on host fitness is uncertain, although there is growing evidence that they may modulate various important adaptive traits of their host such as plant utilisation and resistance against natural enemies. Second, we performed a multivariate analysis on several ecologically relevant features of host populations recorded in the present and previous studies (including microbial composition, colour morph, reproductive mode, and male dispersal phenotype), enabling the identification of correlations between phenotypic traits. We discuss the ecological significance of these associations of traits in relation to the habitat characteristics of pea aphid populations, and their consequences for the evolution of ecological specialisation and sympatric speciation.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 718–727.     

Host-based divergence in populations of the pea aphid: insights from nuclear markers and the prevalence of facultative symbionts

In North America, the pea aphid Acyrthosiphon pisum encompasses ecologically and genetically distinct host races that offer an ideal biological system for studies on sympatric speciation. In addition to its obligate symbiont Buchnera, pea aphids harbour several facultative and phylogenetically distant symbionts. We explored the relationships between host races of A. pisum and their symbiotic microbiota to gain insights into the historical process of ecological specialization and symbiotic acquisition in this aphid. We used allozyme and microsatellite markers to analyse the extent of genetic differentiation between populations of A. pisum on pea, alfalfa and clover in France. In parallel, we examined: (i) the distribution of four facultative symbionts; and (ii) the genetic variation in the Buchnera genome across host-associated populations of A. pisum. Our study clearly demonstrates that populations of A. pisum on pea, clover and alfalfa in France are genetically divergent, which indicates that they constitute distinct host races. We also found a very strong association between host races of A. pisum and their symbiotic microbiota. We stress the need for phylogeographic studies to shed light on the process of host-race formation and acquisition of facultative symbionts in A. pisum. We also question the effects of these symbionts on aphid host fitness, including their role in adaptation to a host plant.     

Predation Determines Different Selective Pressure on Pea Aphid Host Races in a Complex Agricultural Mosaic

Field assessments were conducted to examine the interplay between host plant and predation in complex agricultural mosaic on pea aphid clover and alfalfa races. In one experiment, we examined the relative fitness on clover race (CR) and alfalfa race (AR) pea aphids on broad bean, red clover and alfalfa alone. But because clover is typically grown in a more complex agricultural mosaic with alfalfa and broad bean, a second experiment was conducted to assess the fitness consequences under predation in a more complex agricultural field setting that also included potential apparent competition with AR pea aphids. In a third experiment we tested for the effect of differential host race density on the fitness of the other host race mediated by a predator effect. CR pea aphids always had fitness losses when on broad bean (had lower fitness on broad bean relative to red clover) and fitness benefits when on red clover (higher fitness on red clover relative to broad bean), whether or not in apparent competition with alfalfa race aphids on bean and alfalfa. AR suffered fitness loss on both alfalfa and bean in apparent competition with CR on clover. Therefore we can conclude that the predation rate between host races was highly asymmetrical. The complexity of the agricultural mosaic thus can influence prey selection by predators on different host plants. These may have evolutionary consequences through context dependent fitness benefits on particular host plants.     

Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex

A major goal in evolutionary biology is to uncover the genetic basis of adaptation. Divergent selection exerted on ecological traits may result in adaptive population differentiation and reproductive isolation and affect differentially the level of genetic divergence along the genome. Genome‐wide scan of large sets of individuals from multiple populations is a powerful approach to identify loci or genomic regions under ecologically divergent selection. Here, we focused on the pea aphid, a species complex of divergent host races, to explore the organization of the genomic divergence associated with host plant adaptation and ecological speciation. We analysed 390 microsatellite markers located at variable distances from predicted genes in replicate samples of sympatric populations of the pea aphid collected on alfalfa, red clover and pea, which correspond to three common host‐adapted races reported in this species complex. Using a method that accounts for the hierarchical structure of our data set, we found a set of 11 outlier loci that show higher genetic differentiation between host races than expected under the null hypothesis of neutral evolution. Two of the outliers are close to olfactory receptor genes and three other nearby genes encoding salivary proteins. The remaining outliers are located in regions with genes of unknown functions, or which functions are unlikely to be involved in interactions with the host plant. This study reveals genetic signatures of divergent selection across the genome and provides an inventory of candidate genes responsible for plant specialization in the pea aphid, thereby setting the stage for future functional studies.     

Ecological specialization correlates with genotypic differentiation in sympatric host-populations of the pea aphid

The pea aphid, Acyrthosiphon pisum, encompasses distinct host races specialized on various Fabaceae species, but the extent of genetic divergence associated with ecological specialization varies greatly depending on plant and geographic origins of aphid populations. Here, we studied the genetic structure of French sympatric pea aphid populations collected on perennial (pea and faba bean) and annual (alfalfa and red clover) hosts using 14 microsatellite loci. Classical and Bayesian population genetics analyses consistently identified genetic clusters mostly related to plant origin: the pea/faba bean cluster was highly divergent from the red clover and the alfalfa ones, indicating they represent different stages along the continuum of genetic differentiation. Some genotypes were assigned to a cluster differing from the one expected from their plant origin while others exhibited intermediate genetic characteristics. These results suggest incomplete barriers to gene flow. However, this limited gene flow seems insufficient to prevent ecological specialization and genetic differentiation in sympatry.     

EVOLUTION OF AN APHID-PARASITOID INTERACTION: VARIATION IN RESISTANCE TO PARASITISM AMONG APHID POPULATIONS SPECIALIZED ON DIFFERENT PLANTS

The evolution of associations between herbivorous insects and their parasitoids is likely to be influenced by the relationship between the herbivore and its host plants. If populations of specialized herbivorous insects are structured by their host plants such that populations on different hosts are genetically differentiated, then the traits affecting insect-parasitoid interactions may exhibit an associated structure. The pea aphid (Acyrthosiphon pisum) is a herbivorous insect species comprised of genetically distinct groups that are specialized on different host plants (Via 1991a, 1994). Here, we examine how the genetic differentiation of pea aphid populations on different host plants affects their interaction with a parasitoid wasp, Aphidius ervi. We performed four experiments. (1) By exposing pea aphids from both alfalfa and clover to parasitoids from both crops, we demonstrate that pea aphid populations that are specialized on alfalfa are successfully parasitized less often than are populations specialized on clover. This difference in parasitism rate does not depend upon whether the wasps were collected from alfalfa or clover fields. (2) When we controlled for potential differences in aphid and parasitoid behavior between the two host plants and ensured that aphids were attacked, we found that pea aphids from alfalfa were still parasitized less often than pea aphids from clover. Thus, the difference in parasitism rates is not due to behavior of either aphids or wasps, but appears to be a physiologically based difference in resistance to parasitism. (3) Replicates of pea aphid clones reared on their own host plant and on a common host plant, fava bean, exhibited the same pattern of resistance as above. Thus, there do not appear to be nutritional or secondary chemical effects on the level of physiological resistance in the aphids due to feeding on clover or alfalfa, and therefore the difference in resistance on the two crops appears to be genetically based. (4) We assayed for genetic variation in resistance among individual pea aphid clones collected from clover fields and found no detectable genetic variation for resistance to parasitism within two populations sampled from clover. This is in contrast to Henter and Via's (1995) report of abundant genetic variation in resistance to this parasitoid within a pea aphid population on alfalfa. Low levels of genetic variation may be one factor that constrains the evolution of resistance to parasitism in the populations of pea aphids from clover, leading them to remain more susceptible than populations of the same species from alfalfa.     

Population differentiation and genetic variation in host choice among pea aphids from eight host plant genera

Habitat choice plays a critical role in the processes of host range evolution, specialization, and ecological speciation. Pea aphid, Acyrthosiphon pisum, populations from alfalfa and red clover in eastern North America are known to be genetically differentiated and show genetic preferences for the appropriate host plant. This species feeds on many more hosts, and here we report a study of the genetic variation in host plant preference within and between pea aphid populations collected from eight genera of host plants in southeastern England. Most host-associated populations show a strong, genetically based preference for the host plant from which they were collected. Only in one case (populations from Vicia and Trifolium) was there little difference in the plant preference spectrum between populations. All populations showed a significant secondary preference for the plant on which all the aphid lines were reared: broad bean, Vicia faba, previously suggested to be a "universal host" for pea aphids. Of the total genetic variance in host preference within our sample, 61% could be attributed to preference for the collection host plant and a further 9% to systematic differences in secondary preferences with the residual representing within-population genetic variation between clones. We discuss how a combination of host plant preference and mating on the host plant may promote local adaptation and possibly ecological speciation, and whether a widely accepted host could oppose speciation by mediating gene flow between different populations.     

REPRODUCTIVE ISOLATION BETWEEN SYMPATRIC RACES OF PEA APHIDS. I. GENE FLOW RESTRICTION AND HABITAT CHOICE

Determining the extent and causes of barriers to gene flow between genetically divergent populations or races of single species is an important complement to post facto analyses of the causes of reproductive isolation between recognized species. Sympatric populations of pea aphids (Acyrthosiphon pisum Harris, Homoptera: Aphididae) on alfalfa and red clover are highly genetically divergent and locally adapted. Here, hierarchical estimates of population structure based on F_st suggest that gene exchange between closely adjacent aphid populations on the two hosts is highly restricted relative to that among fields of the same host plant. Although these host-associated races are presently considered to be the same subspecies, they appear to be significantly reproductively isolated, suggesting incipient speciation. Habitat (host) choice was investigated as the first in a temporal series of factors that could reduce gene exchange between these sympatric populations. Field studies of winged colonists to newly planted fields of each host suggest pronounced habitat fidelity. This result was verified using replicated observations of the host choice behavior of different aphid genotypes for which the relative demographic performance on each host was known. These laboratory observations of behavior revealed a strong genetic correlation between habitat choice (or acceptance) and the relative performance in each habitat. Because mating occurs on the host plant, habitat choice in this system leads to assortative mating and is therefore a major cause of reproductive isolation between the sympatric pea aphid populations on alfalfa and clover. However, the extent of dispersal between hosts estimated from the field study of winged colonists (9–11%) is too great to be consistent with the genetic divergence estimated between the races. This suggests that barriers to gene flow other than host choice also exist, such as selection against migrants or hybrids in the parental environments, hybrid sterility, or hybrid breakdown.     

Field estimation of variation in host plant use between local populations of pea aphids from two crops

Abstract. 1. In a reciprocal transplant experiment on pea aphids (Acyrthosiphon pisum (Harris)), the relative performance of clones collected from nearby alfalfa and red clover fields was tested by allowing clonal replicates to develop on both crops under field conditions.
2. Populations from alfalfa and red clover differed in relative survivorship and probabilities of reproduction on the two crops. Clones had significantly higher performance on the crop from which they were collected (the 'home' crop) than they did on the other crop.
3. Evidence is presented that previous experience on these host plants cannot account for the increased probability of reproduction observed on the 'home' crop. Thus, the differences between these two populations in their relative performance on alfalfa and clover are likely to be genetically based.
4. These results illustrate that local adaptation to different host plants can occur within small geographical areas, despite the high probability that migrants are exchanged between nearby fields of the two crops.
5. Experimental designs of the type described here permit estimation of patterns of genetic variation within and between insect populations. When applied to pest species, such designs will facilitate the study of evolution in agricultural systems.     

Lack of evidence for reproductive isolation among ecologically specialised lycaenid butterflies

Abstract 1. The evolution of reproductive isolation between recently diverged or incipient species is a critical component of speciation and a major focus of speciation models. In phytophagous insects, host plant fidelity (the habit of mating and ovipositing on a single host species) can contribute to assortative mating and reproductive isolation between populations adapting to alternative hosts. The potential role of host plant fidelity in the evolution of reproductive isolation was examined in a pair of North American blue butterfly species, Lycaeides idas and L. melissa .
2. These species are morphologically distinct and populations of each species utilise different host plants; however they share 410 bp haplotypes of the mitochondrial cytochrome oxidase subunit I (COI) gene, indicating recent divergence.
3. Some populations using native hosts exhibited strong fidelity for their natal host plant over the hosts used by nearby populations. Because these butterflies mate on or near the host plant, the development of strong host fidelity may create reproductive isolation among populations on different hosts and restrict gene flow.
4. Tests of population differentiation using allozyme allele frequency data did not provide convincing evidence of restricted gene flow among populations. Based on morphological differences, observed ecological specialisation, and the sharing of genetic markers, these butterflies appear to be undergoing adaptive radiation driven at least partially by host shifts. Neutral genetic markers may fail to detect the effects of very recent host shifts in these populations due to gene flow and/or the recency of divergence and shared ancestral polymorphism.     

Reproductive isolation between divergent races of pea aphids on two hosts. II. Selection against migrants and hybrids in the parental environments

Sympatric races of pea aphids on alfalfa and red clover are highly ecologically specialized and significantly reproductively isolated. Much of the restriction of gene flow between the specialized populations is due to habitat choice behavior of the winged colonizers (Via 1999). Here, we document additional pre- and postmating reproductive isolation through selection against migrants and hybrids in the parental environments. First, a group of randomly chosen genotypes from each race that were experimentally migrated between hosts had very low survival and reproduction on the alternate host relative to genotypes originating from that host (natives). Such selection against cross-host migrants forms a premating barrier to gene flow because it is likely to reduce migrant frequencies before the sexual forms are induced in the fall. Our reciprocal transplant experiment also shows that natural selection acts directly on individual migrants between the crops to favor host choice behavior: genotypes from each host suffered large losses of fitness when forced to migrate to the alternate host plant relative to the fitness they would have enjoyed had they been able to choose their native host. In a companion field study, sequential sampling throughout the summer in newly colonized fields of both alfalfa and clover revealed a decrease in the frequency of host-specific marker alleles characteristic of the alternate crop. These field data further support the hypothesis that selection disfavors migrants that cross between crops. Second, when two sets of F1 hybrids between the races were reciprocally tested on alfalfa and clover, both sets had significantly lower average fitness than the specialized parent in each of the two environments. This demographic selection against hybrids in the parental environments is a source of postmating reproductive isolation between the specialized races. Finally, significant genetic variation in fitness traits was seen among F1 hybrid genotypes from both crosses between alfalfa and clover specialists. Although this variation suggests that a generalized pea aphid could evolve, such generalists are not seen in field collections of these populations.     

Differences in host plant selection among three Athalia sawflies feeding on crucifers in Japan

Abstract 1. The ways of using host plants were compared among the three Athalia sawflies [ A. japonica (Klug), A. rosae ruficornis Jakovlev, and A. infumata (Marlatt)] feeding on crucifers in Japan to determine whether host specialisation can explain the difference in their life-history traits. The occurrence of their larvae was examined on each crucifer species in the field, and the suitability of each crucifer species for the three successive steps of host use by the sawflies was evaluated: microhabitat selection by adult females, female oviposition, and larval growth.
2. There were 11 species of crucifer in the study area, and A. japonica , A. rosae , and A. infumata used nine, seven, and eight species respectively. Thus, sawfly host ranges overlapped.
3. Adult females of A. japonica , A. rosae , and A. infumata preferred shady clumps of crucifers, sunny clumps of crucifers, and disturbed areas respectively.
4. Unsuitable hosts for larval performance such as Brassica oleracea and Arabis plants were eliminated from the host ranges of the three sawflies.
5. Once they chose microhabitats, the suitability of each host plant for female oviposition and larval growth was similar.
6. Because of the divergent preferences for microhabitats, the host plants that were suitable for all the three steps were restricted to different sets of plants among the sawflies: Cardamine for A. japonica , cultivated crucifers ( Raphanus and Brassica ) for A. rosae , and Rorippa for A. infumata . These plants could be recognised as the respective primary host plants.
7. The spatio-temporal distributions of primary hosts were consistent with and explained the pattern of diapause and migration of each sawfly, suggesting that host specialisation caused their life-history traits to differentiate.     

Quantitative genetics of feeding behavior in two ecological races of the pea aphid, Acyrthosiphon pisum

Much of the diversity of herbivorous insects stems from the adaptive divergence of populations onto different host plants. This often involves the evolution of specialized patterns of host acceptance that in turn lead to assortative mating for insects that mate exclusively on their hosts. Here, we explore the genetic architecture of feeding behavior in a herbivorous insect that has become a model for the study of incipient speciation, the pea aphid (Acyrthosiphon pisum). We use crosses between individuals specialized to either alfalfa or red clover in order to perform both a biometrical analysis and a quantitative trait locus (QTL) analysis of key feeding behaviors. For each character in each environment, Castle-Wright's estimator for the number of effective factors segregating ranged from 0.11 to 2.54. Similarly, between 0 and 3 QTLs were detected. In one case, a single QTL explained over 50% of the variance in the F2, suggesting that at least one gene (or a complex of tightly linked genes) has a major effect on feeding behavior in the pea aphid. However, the identified QTL explain only 23-73% of the genetic variance for these characters thus additional genes of minor effect are also involved. We found a variety of modes of gene action, including several cases of non-additive gene action. Our results suggest that feeding behavior in pea aphids is neither simple nor highly polygenic. The oligogenetic basis of variation in feeding behavior may facilitate host shifts, providing one explanation for the frequent divergence and speciation of herbivorous insects.     

Does variation in host plant association and symbiont infection of pea aphid populations induce genetic and behaviour differentiation of its main parasitoid, Aphidius ervi?

The host-associated differentiation (HAD) hypothesis states that higher trophic levels in parasitic associations should exhibit similar divergence in case of host sympatric speciation. We tested HAD on populations of Aphidius ervi the main parasitoid of the pea aphid Acyrthosiphon pisum, emerging from host populations specialized on either alfalfa or red clover. Host and parasitoid populations were assessed for genetic variation and structure, while considering geography, host plant and host aphid protective symbionts Regiella insecticola and Hamiltonella defensa as potential covariables. Cluster and hierarchical analyses were used to assess the contribution of these variables to population structure, based on genotyping pea aphids and associated A. ervi with microsatellites, and host aphid facultative symbionts with 16S rDNA markers. Pea aphid genotypes were clearly distributed in two groups closely corresponding with their plant origins, confirming strong plant associated differentiation of this aphid in North America. Overall parasitism by A. ervi averaged 21.5 % across samples, and many parasitized aphids producing a wasp hosted defensive bacteria, indicating partial or ineffective protective efficacy of these symbionts in the field. The A. ervi population genetic data failed to support differentiation according to the host plant association of their pea aphid host. Potential for parasitoid specialization was also explored in experiments where wasps from alfalfa and clover aphids were reciprocally transplanted on alternate hosts, the hypothesis being that wasp behaviour and parasitic stages should be most adapted to their host of origin. Results revealed higher probability of oviposition on the alfalfa aphids, but higher adult emergence success on red clover aphids, with no interaction as expected under HAD. We conclude that our study provides no support for the HAD in this system. We discuss factors that might impair A. ervi specialization on its divergent aphid hosts on alfalfa and clover.     

Host selection by winged colonisers within the Myzus persicae group: a contribution towards understanding host specialisation

Abstract.  1.  Myzus persicae sensu lato demonstrates considerable genetic variation in respect to adaptation to host plants. The subspecies M. persicae nicotianae shows a preference for tobacco, while M. persicae sensu stricto ( s. str. ) for other herbaceous plants. Given that winged colonisers of several aphid species play an important role in selecting host plants, here their role in the host specialisation observed in M. persicae was examined in choice and no-choice tests conducted outdoors, in performance studies, and in DC Electrical Penetration Graph (DC-EPG) studies.
2. In outdoor choice tests, 77% of spring migrants of M. persicae nicotianae chose tobacco, whereas equal proportions of M. persicae s. str. selected tobacco and pepper. In no-choice tests, spring migrants settled more quickly after alighting on host rather than on non host plants, and significantly more alate M. persicae s. str. (27%) than M. persicae nicotianae (2%) left tobacco after walking briefly on the leaf surface, whilst no significant differences were found on pepper. Cross-host transfers significantly reduced the fecundity of both summer and spring migrants of the two subspecies. Finally, the results of no-choice tests and DC-EPG studies showed that winged aphids distinguished their host through cues located on the plant surface or in subcutaneous tissues perceived prior to the initiation of feeding.
3. This study demonstrates the important role of winged colonisers in the evolution of host specialisation in M. persicae . The multifarious divergent selection that the two host forms experience, i.e. the selection against cross-migrants and their subsequent generations, is a crucial factor involved in the development and maintenance of host specialisation and promotes the parallel evolution of improved host-recognition ability.     

The ‘mother knows best’ principle: should soil insects be included in the preference–performance debate?

Abstract.  1. Few entomological studies include soil-dwelling insects in mainstream ecological theory, for example the preference–performance debate. The preference–performance hypothesis predicts that when insect herbivores have offspring with limited capacity to relocate in relation to a host plant, there is a strong selection pressure for the adult to oviposit on plants that will maximise offspring performance.
2. This paper discusses the proposition that insect herbivores that live above ground, but have soil-dwelling offspring, should be included in the preference–performance debate. Twelve relevant studies were reviewed to assess the potential for including soil insects in this framework, before presenting a preliminary case study using the clover root weevil ( Sitona lepidus ) and its host plant, white clover ( Trifolium repens ).
3. Maternal S. lepidus preferentially oviposited on T. repens plants that had rhizobial root nodules (which enhance offspring performance) rather than T. repens plants without nodules, despite plants having similar foliar nutritional quality. This suggests that adult behaviour above ground was influenced by below-ground host-plant quality.
4. A conceptual model is presented to describe how information about the suitability for offspring below ground could underpin oviposition behaviour of parental insects living above ground, via plant- and soil-mediated semiochemicals. These interactions between genetically related, but spatially separated, insect herbivores raise important evolutionary questions such as how induced plant responses above ground affect offspring living below ground and vice versa.     

Facultative symbionts are associated with host plant specialization in pea aphid populations

The pea aphid, Acyrthosiphon pisum, shows significant reproductive isolation and host plant specialization between populations on alfalfa and clover in New York. We examine whether specialization is seen in pea aphids in California, and whether fitness on alternative host plants is associated with the presence of bacterial symbionts. We measured the fitness of alfalfa- and clover-derived aphids on both types of plants and found no evidence for specialization when all aphid lineages were considered simultaneously. We then screened all aphids for the presence of four facultative bacterial symbionts: PAR, PASS, PABS and PAUS. Aphids with PAUS were host-plant specialized, having twice as many offspring as other aphids on clover, and dying on alfalfa. Other aphids showed no evidence of specialization. Additionally, aphids with PABS had 50% more offspring than aphids with PASS when on alfalfa. Thus, specialist and generalist aphid lineages coexist, and specialization is symbiont associated. Further work will resolve whether PAUS is directly responsible for this variation in fitness or whether PAUS is incidentally associated with host-plant specialized aphid lineages.     

Evolutionary dynamics of specialisation in herbivorous stick insects

Understanding the evolutionary dynamics underlying herbivorous insect mega‐diversity requires investigating the ability of insects to shift and adapt to different host plants. Feeding experiments with nine related stick insect species revealed that insects retain the ability to use ancestral host plants after shifting to novel hosts, with host plant shifts generating fundamental feeding niche expansions. These expansions were, however, not accompanied by expansions of the realised feeding niches, as species on novel hosts are generally ecologically specialised. For shifts from angiosperm to chemically challenging conifer hosts, generalist fundamental feeding niches even evolved jointly with strong host plant specialisation, indicating that host plant specialisation is not driven by constraints imposed by plant chemistry. By coupling analyses of plant chemical compounds, fundamental and ecological feeding niches in multiple insect species, we provide novel insights into the evolutionary dynamics of host range expansion and contraction in herbivorous insects.     

Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races

Identifying the genomic bases of adaptation to novel environments is a long‐term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant‐specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model‐based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population‐specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host–plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host–plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes.