Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies

The role of sexual isolation during rapid ecological divergence: Evidence for a new dimension of isolation in Rhagoletis pomonella

The pace of divergence and likelihood of speciation often depends on how and when different types of reproductive barriers evolve. Questions remain about how reproductive isolation evolves after initial divergence. We tested for the presence of sexual isolation (reduced mating between populations due to divergent mating preferences and traits) in Rhagoletis pomonella flies, a model system for incipient ecological speciation. We measured the strength of sexual isolation between two very recently diverged (~170 generations) sympatric populations, adapted to different host fruits (hawthorn and apple). We found that flies from both populations were more likely to mate within than between populations. Thus, sexual isolation may play an important role in reducing gene flow allowed by early-acting ecological barriers. We also tested how warmer temperatures predicted under climate change could alter sexual isolation and found that sexual isolation was markedly asymmetric under warmer temperatures - apple males and hawthorn females mated randomly while apple females and hawthorn males mated more within populations than between. Our findings provide a window into the early speciation process and the role of sexual isolation after initial ecological divergence, in addition to examining how environmental conditions could shape the likelihood of further divergence.

Cold tolerance and diapause within and across trophic levels: Endoparasitic wasps and their fly host have similar phenotypes

Low temperatures associated with winter can limit the survival of organisms, especially ectotherms whose body temperature is similar to their environment. However, there is a gap in understanding how overwintering may vary among groups of species that interact closely, such as multiple parasitoid species that attack the same host insect. Here, we investigate cold tolerance and diapause phenotypes in three endoparasitoid wasps of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae): Utetes canaliculatus, Diachasma alloeum, and Diachasmimorpha mellea (Hymenoptera: Braconidae). Using a combination of respirometry and eclosion tracking, we found that all three wasp species exhibited the same three diapause duration phenotypes as the fly host. Weak (short duration) diapause was rare, with <5 % of all three wasp species prematurely terminating diapause at 21 °C. Most D.mellea (93 %) entered a more intense (longer duration) diapause that did not terminate within 100 d at this warm temperature. The majority of U.canaliculatus (92 %) and D. alloeum (72 %) averted diapause (non-diapause) at 21 °C. There was limited interspecific variation in acute cold tolerance among the three wasp species: wasps and flies had similarly high survival (>87 %) following exposure to extreme low temperatures (-20 °C) as long as their body fluids did not freeze. The three wasp species also displayed little interspecific variation in survival following prolonged exposure to mild chilling of 8 or more weeks at 4 °C. Our study thus documents a remarkable conservation of cold tolerance and diapause phenotypes within and across trophic levels.

Rapid adaptation in a fast-changing world: Emerging insights from insect genomics

Many researchers have questioned the ability of biota to adapt to rapid anthropogenic environmental shifts. Here, we synthesize emerging genomic evidence for rapid insect evolution in response to human pressure. These new data reveal diverse genomic mechanisms (single locus, polygenic, structural shifts; introgression) underpinning rapid adaptive responses to a variety of anthropogenic selective pressures. While the effects of some human impacts (e.g. pollution; pesticides) have been previously documented, here we highlight startling new evidence for rapid evolutionary responses to additional anthropogenic processes such as deforestation. These recent findings indicate that diverse insect assemblages can indeed respond dynamically to major anthropogenic evolutionary challenges. Our synthesis also emphasizes the critical roles of genomic architecture, standing variation and gene flow in maintaining future adaptive potential. Broadly, it is clear that genomic approaches are essential for predicting, monitoring and responding to ongoing anthropogenic biodiversity shifts in a fast-changing world.

Host association, environment, and geography underlie genomic differentiation in a major forest pest

Diverse geographic, environmental, and ecological factors affect gene flow and adaptive genomic variation within species. With recent advances in landscape ecological modelling and high-throughput DNA sequencing, it is now possible to effectively quantify and partition their relative contributions. Here, we use landscape genomics to identify determinants of genomic differentiation in the forest tent caterpillar, Malacosoma disstria, a widespread and irruptive pest of numerous deciduous tree species in North America. We collected larvae from multiple populations across Eastern Canada, where the species experiences a diversity of environmental gradients and feeds on a number of different host tree species, including trembling aspen (Populus tremuloides), sugar maple (Acer saccharum), red oak (Quercus rubra), and white birch (Betula papyrifera). Using a combination of reciprocal causal modelling (RCM) and distance-based redundancy analyses (dbRDA), we show that differentiation of thousands of genome-wide single nucleotide polymorphisms (SNPs) among individuals is best explained by a combination of isolation by distance, isolation by environment (spatial variation in summer temperatures and length of the growing season), and differences in host association. Configuration of suitable habitat inferred from ecological niche models was not significantly related to genomic differentiation, suggesting that M. disstria dispersal is agnostic with respect to habitat quality. Although population structure was not discretely related to host association, our modelling framework provides the first molecular evidence of host-associated differentiation in M. disstria, congruent with previous documentation of reduced growth and survival of larvae moved between natal host species. We conclude that ecologically mediated selection is contributing to variation within M. disstria, and that divergent adaptation related to both environmental conditions and host association should be considered in ongoing research and management of this important forest pest.

Interactions With Plant Defences Isolate Sympatric Populations of an Herbivorous Mite

Host plant specialisation can promote evolutionary divergence between herbivore populations associated with different plant species. While the mechanisms by which specialist species exploit their hosts have been studied widely across taxa, less is known about the mechanisms that allow intraspecific variants to arise and to be maintained across spatial and temporal scales. To understand whether adaptations to plant defences against herbivory contribute to the co-existence of genetically distinct populations of an herbivore, we investigate the interaction between honeysuckle (Lonicera periclymenum) and sympatric specialist and generalist populations of the spider mite Tetranychus urticae. We found that mite folivory induces the production of sticky droplets on honeysuckle, which have a defensive role: they increase mite mortality directly, and potentially indirectly by increasing the arrestment of a predator. We show that droplet induction and the preference to feed on honeysuckle depend on mite genotype, where the generalist avoids this host and the specialist suppresses droplet production. These traits are heritable and dominant in F1 hybrids between generalists and specialists. Selection pressure from honeysuckle and differences in host preference likely reduce the opportunity of mating encounters on this host. We propose that the interplay between selection from host plant defences and ecological barriers to hybridisation contribute to the persistence of genetically distinct populations of a single species in sympatry.

Sensitivities to Chill Durations and No-Chill Temperatures Regulating Eclosion Responses Differ Between Rhagoletis zephyria (Diptera: Tephritidae) and its Braconid Parasitoids (Hymenoptera: Braconidae)

Seasonal temperatures select for eclosion timing of temperate insects and their parasitoids. In western North America, the fruit fly Rhagoletis zephyria Snow (Diptera: Tephritidae) is parasitized by the hymenopterous wasps Utetes lectoides (Gahan), an egg parasite, and Opius downesi Gahan, a larval parasite (both Braconidae). Eclosion of wasps should be timed with the presence of susceptible fly stages, but reports indicate U. lectoides ecloses in the absence of flies under no-chill conditions. Based on this, we tested the hypotheses that chill durations and no-chill temperatures both differentially regulate eclosion times of R. zephyria and its parasitic wasps. When fly puparia were chilled at ~3°C for 130-180 d, U. lectoides and O. downesi always eclosed on average later than flies. However, after 180-d chill, flies eclosed on average earlier than after 130- and 150-d chill, whereas eclosion times of U. lectoides and O. downesi were less or not affected by chill duration. When fly puparia were exposed to 20-22°C (no chill), U. lectoides eclosed before flies, with 88.9% of U. lectoides versus only 0.61% of flies eclosing. Taken together, findings show that eclosion times of flies are more sensitive to changes in chill duration than those of wasps. Flies are less sensitive than wasps to no-chill in that most flies do not respond by eclosing after no-chill while most wasps do. Our results suggest that shorter winters and longer summers due to climate change could cause mismatches in eclosion times of flies and wasps, with potentially significant evolutionary consequences.

Partial Ribosomal Nontranscribed Spacer Sequences Distinguish Rhagoletis zephyria (Diptera: Tephritidae) From the Apple Maggot, R. pomonella

The apple maggot, Rhagoletis pomonella (Walsh), was introduced into the apple-growing regions of the Pacific Northwest in the U.S.A. during the past 60-100 yr. Apple maggot (larvae, puparia, and adults) is difficult to distinguish from its morphologically similar sister species, Rhagoletis zephyria Snow, which is native and abundant in the Pacific Northwest. While morphological identifications are common practice, a simple, inexpensive assay based on genetic differences would be very useful when morphological traits are unclear. Here we report nucleotide substitution and insertion-deletion mutations in the nontranscribed spacer (NTS) of the ribosomal RNA gene cistron of R. pomonella and R. zephyria that appear to be diagnostic for these two fly species. Insertion-deletion variation is substantial and results in a 49 base-pair difference in PCR amplicon size between R. zephyria and R. pomonella that can be scored using agarose gel electrophoresis. PCR amplification and DNA sequencing of 766 bp of the NTS region from 38 R. pomonella individuals and 35 R. zephyria individuals from across their geographic ranges led to the expected PCR fragments of approx. 840 bp and 790 bp, respectively, as did amplification and sequencing of a smaller set of 26 R. pomonella and 16 R. zephyria flies from a sympatric site in Washington State. Conversely, 633 bp mitochondrial COI barcode sequences from this set of flies were polyphyletic with respect to R. pomonella and R. zephyria. Thus, differences in NTS PCR products on agarose gels potentially provide a simple way to distinguish between R. pomonella and R. zephyria.

The Build-Up of Population Genetic Divergence along the Speciation Continuum during a Recent Adaptive Radiation of Rhagoletis Flies

New species form through the evolution of genetic barriers to gene flow between previously interbreeding populations. The understanding of how speciation proceeds is hampered by our inability to follow cases of incipient speciation through time. Comparative approaches examining different diverging taxa may offer limited inferences, unless they fulfill criteria that make the comparisons relevant. Here, we test for those criteria in a recent adaptive radiation of the Rhagoletis pomonella species group (RPSG) hypothesized to have diverged in sympatry via adaptation to different host fruits. We use a large-scale population genetic survey of 1568 flies across 33 populations to: (1) detect on-going hybridization, (2) determine whether the RPSG is derived from the same proximate ancestor, and (3) examine patterns of clustering and differentiation among sympatric populations. We find that divergence of each in-group RPSG taxon is occurring under current gene flow, that the derived members are nested within the large pool of genetic variation present in hawthorn-infesting populations of R. pomonella, and that sympatric population pairs differ markedly in their degree of genotypic clustering and differentiation across loci. We conclude that the RPSG provides a particularly robust opportunity to make direct comparisons to test hypotheses about how ecological speciation proceeds despite on-going gene flow.

Tolerances of Apple Maggot (Diptera: Tephritidae) Larvae and Different Age Puparia to Water Flotation and Immersion

Tolerance of terrestrial insects in temperate regions to water immersion and hypoxia has rarely been studied but can be an important adaptation to moist environments, with implications for insect dispersal through waterways. In the Pacific Northwest of the United States, apple maggot fly, Rhagoletis pomonella (Walsh) (Diptera: Tephritidae), can be found in riparian habitats subject to flooding. Here, survival of R. pomonella larvae and different age puparia after flotation or immersion in 13.3°C or 21.1°C water for 1-12 d was determined. Larvae sank in water and when submerged for 1 or 2 d suffered greater mortality than control larvae. Fewer young (1-2 d old) than older puparia (13-15 d old) floated in water. When immersed in water for 1-12 d, young puparia suffered greater mortality than older puparia, which were not affected by water immersion. Consequently, fewer adult flies eclosed from puparia that had been water treated when young than older. Adult flies from pre-chill and post-chill puparia that had been water treated eclosed later than control flies, but treatment flies survived about 60 d and reproduced. Although newly-formed puparia are susceptible to hypoxic water conditions, increased buoyancy and water tolerance occur rapidly after formation, perhaps making survival possible and allowing water-borne dispersal of older puparia.

Genomically correlated trait combinations and antagonistic selection contributing to counterintuitive genetic patterns of adaptive diapause divergence in Rhagoletis flies

Adaptation to novel environments can result in unanticipated genomic responses to selection. Here, we illustrate how multifarious, correlational selection helps explain a counterintuitive pattern of genetic divergence between the recently derived apple- and ancestral hawthorn-infesting host races of Rhagoletis pomonella (Diptera: Tephritidae). The apple host race terminates diapause and emerges as adults earlier in the season than the hawthorn host race, to coincide with the earlier fruiting phenology of their apple hosts. However, alleles at many loci associated with later emergence paradoxically occur at higher frequencies in sympatric populations of the apple compared to the hawthorn race. We present genomic evidence that historical selection over geographically varying environmental gradients across North America generated genetic correlations between two life history traits, diapause intensity and diapause termination, in the hawthorn host race. Moreover, the loci associated with these life history traits are concentrated in genomic regions in high linkage disequilibrium (LD). These genetic correlations are antagonistic to contemporary selection on local apple host race populations that favours increased initial diapause depth and earlier, not later, diapause termination. Thus, the paradox of apple flies appears due, in part, to pleiotropy or linkage of alleles associated with later adult emergence and increased initial diapause intensity, the latter trait strongly selected for by the earlier phenology of apples. Our results demonstrate how understanding of multivariate trait combinations and the correlative nature of selective forces acting on them can improve predictions concerning adaptive evolution and help explain seemingly counterintuitive patterns of genetic diversity in nature.

Contrast in Post-Chill Eclosion Time Strategies Between Two Specialist Braconid Wasps (Hymenoptera: Braconidae) Attacking Rhagoletis Flies (Diptera: Tephritidae) in Western North America

Parasitoids comprise a speciose insect group, displaying a wide array of life history strategies. In the Pacific Northwest of the United States, the tephritid fruit flies Rhagoletis tabellaria (Fitch) and Rhagoletis indifferens Curran infest red osier dogwood, Cornus sericea L. (Cornaceae), and bitter cherry, Prunus emarginata (Douglas ex Hooker) Eaton (Rosaceae), respectively. The flies are parasitized by different braconid wasps at different life stages; Utetes tabellariae (Fischer) oviposits into R. tabellaria eggs, whereas Diachasma muliebre (Muesebeck) oviposits into R. indifferens larvae feeding in cherries. Because Rhagoletis only have one major generation a year and the wasps attack temporally distinct fly life stages, we predicted that eclosion times of U. tabellariae should more closely follow that of its host than the larval-attacking D. muliebre. As predicted, U. tabellariae eclosed on average 6.0-12.5 d later than R. tabellaria, whereas D. muliebre eclosed on average 32.1 d after R. indifferens. Unexpectedly, however, longer chill duration differentially affected the systems; longer overwinters minimally influenced eclosion times of R. tabellaria and U. tabellariae but caused earlier eclosion of both R. indifferens and D. muliebre. Results imply that in temperate regions, diapause timing in braconid wasps evolves in response to both host life stage attacked and fly eclosion characteristics, possibly reflecting differential effects of winter on host plant fruiting phenology. Differences in phenological sensitivity of the lower host plant trophic level to variation in environmental conditions may have cascading effects, sequentially and differentially affecting eclosion times in higher frugivore (fly) and parasitoid (wasp) trophic levels.

Adaptive divergence and post-zygotic barriers to gene flow between sympatric populations of a herbivorous mite

Plant-herbivore interactions promote the generation and maintenance of both plant and herbivore biodiversity. The antagonistic interactions between plants and herbivores lead to host race formation: the evolution of herbivore types specializing on different plant species, with restricted gene flow between them. Understanding how ecological specialization promotes host race formation usually depends on artificial approaches, using laboratory experiments on populations associated with agricultural crops. However, evidence on how host races are formed and maintained in a natural setting remains scarce. Here, we take a multidisciplinary approach to understand whether populations of the generalist spider mite Tetranychus urticae form host races in nature. We demonstrate that a host race co-occurs among generalist conspecifics in the dune ecosystem of The Netherlands. Extensive field sampling and genotyping of individuals over three consecutive years showed a clear pattern of host associations. Genome-wide differences between the host race and generalist conspecifics were found using a dense set of SNPs on field-derived iso-female lines and previously sequenced genomes of T. urticae. Hybridization between lines of the host race and sympatric generalist lines is restricted by post-zygotic breakdown, and selection negatively impacts the survival of generalists on the native host of the host race. Our description of a host race among conspecifics with a larger diet breadth shows how ecological and reproductive isolation aid in maintaining intra-specific variation in sympatry, despite the opportunity for homogenization through gene flow. Our findings highlight the importance of explicitly considering the spatial and temporal scale on which plant-herbivore interactions occur in order to identify herbivore populations associated with different plant species in nature. This system can be used to study the underlying genetic architecture and mechanisms that facilitate the use of a large range of host plant taxa by extreme generalist herbivores. In addition, it offers the chance to investigate the prevalence and mechanisms of ecological specialization in nature.

The Eclosion of Rhagoletis pomonella (Diptera: Tephritidae) Under Different Chill Durations and Simulated Temperate and Tropical Conditions

The apple maggot fly, Rhagoletis pomonella (Walsh) (Diptera: Tephritidae), is a serious pest of apple in North America that is subject to quarantine measures to prevent its spread to currently pest-free regions, including the tropics. How the fly may survive in warmer climates is unclear. Here, we studied the effects of exposing postchill puparia to simulated temperate and tropical environmental conditions on eclosion of R. pomonella from Washington State, U.S.A. Puparia were chilled for 0-30 wk at 3°C and then held under four postchill conditions: A = 23°C, 16:8 L:D, 40% RH; B = 26°C, 12:12 L:D, 80% RH; C = 26°C, 16:8 L:D, 80% RH; and D = 23°C, 12:12 L:D, 40% RH, with B and D representing tropical conditions and A and C temperate conditions. Within each chill duration, total numbers of flies eclosed were equally high in tropical treatment B and temperate treatment C, while they were lower in treatments A and D. Mean weeks of the first eclosion in treatments B and C were earlier than in treatment D; mean week of peak eclosion and 50% eclosion in treatments A, B, and C were earlier than in treatment D. Eclosion spans in treatments A, B, and D were generally shorter than in treatment C. Results suggest that if introduced into a humid tropical country, R. pomonella puparia from Washington State could produce adult flies, regardless of chill duration or lack of chilling during the pupal stage, but whether flies could establish there would require further study.

The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes

Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave vs. surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark-pigmented "reed" and light-pigmented "stonewort" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a quantitative trait locus (QTL) mapping study using a laboratory bred F₂ and F₄ cave × surface intercross. We identified genomic regions associated with body pigmentation, antennae length and body size. Furthermore, we compared genome-wide differentiation between natural populations and found several genes potentially associated with these habitats. The assessment of the cave QTL regions in the light-dark comparison of lake populations suggests that the regions associated with cave adaptation are also involved with genomic differentiation in the lake ecotypes. These demonstrate how troglomorphic adaptations can be used as a model for related ecotype formation.

Divergent diapause life history timing drives both allochronic speciation and reticulate hybridization in an adaptive radiation of Rhagoletis flies

Divergent adaptation to new ecological opportunities can be an important factor initiating speciation. However, as niches are filled during adaptive radiations, trait divergence driving reproductive isolation between sister taxa may also result in trait convergence with more distantly related taxa, increasing the potential for reticulated gene flow across the radiation. Here, we demonstrate such a scenario in a recent adaptive radiation of Rhagoletis fruit flies, specialized on different host plants. Throughout this radiation, shifts to novel hosts are associated with changes in diapause life history timing, which act as "magic traits" generating allochronic reproductive isolation and facilitating speciation-with-gene-flow. Evidence from laboratory rearing experiments measuring adult emergence timing and genome-wide DNA-sequencing surveys supported allochronic speciation between summer-fruiting Vaccinium spp.-infesting Rhagoletis mendax and its hypothesized and undescribed sister taxon infesting autumn-fruiting sparkleberries. The sparkleberry fly and R. mendax were shown to be genetically discrete sister taxa, exhibiting no detectable gene flow and allochronically isolated by a 2-month average difference in emergence time corresponding to host availability. At sympatric sites across the southern USA, the later fruiting phenology of sparkleberries overlaps with that of flowering dogwood, the host of another more distantly related and undescribed Rhagoletis taxon. Laboratory emergence data confirmed broadly overlapping life history timing and genomic evidence supported on-going gene flow between sparkleberry and flowering dogwood flies. Thus, divergent phenological adaptation can drive the initiation of reproductive isolation, while also enhancing genetic exchange across broader adaptive radiations, potentially serving as a source of novel genotypic variation and accentuating further diversification.

Distinct Adult Eclosion Traits of Sibling Species Rhagoletis pomonella and Rhagoletis zephyria (Diptera: Tephritidae) Under Laboratory Conditions

Closely related phytophagous insects that specialize on different host plants may have divergent responses to environmental factors. Rhagoletis pomonella (Walsh) and Rhagoletis zephyria Snow (Diptera: Tephritidae) are sibling, sympatric fly species found in western North America that attack and mate on plants of Rosaceae (~60 taxa) and Caprifoliaceae (three taxa), respectively, likely contributing to partial reproductive isolation. Rhagoletis zephyria evolved from R. pomonella and is native to western North America, whereas R. pomonella was introduced there. Given that key features of the flies' ecology, breeding compatibility, and evolution differ, we predicted that adult eclosion patterns of the two flies from Washington State, USA are also distinct. When puparia were chilled, eclosion of apple- and black hawthorn-origin R. pomonella was significantly more dispersed, with less pronounced peaks, than of snowberry-origin R. zephyria within sympatric and nonsympatric site comparisons. Percentages of chilled puparia that produced adults were ≥67% for both species. However, when puparia were not chilled, from 13.5 to 21.9% of apple-origin R. pomonella versus only 1.2% to 1.9% of R. zephyria eclosed. The distinct differences in eclosion traits of R. pomonella and R. zephyria could be due to greater genetic variation in R. pomonella, associated with its use of a wider range of host plants than R. zephyria.

Genome-wide variation and transcriptional changes in diverse developmental processes underlie the rapid evolution of seasonal adaptation

Many organisms enter a dormant state in their life cycle to deal with predictable changes in environments over the course of a year. The timing of dormancy is therefore a key seasonal adaptation, and it evolves rapidly with changing environments. We tested the hypothesis that differences in the timing of seasonal activity are driven by differences in the rate of development during diapause in Rhagoletis pomonella, a fly specialized to feed on fruits of seasonally limited host plants. Transcriptomes from the central nervous system across a time series during diapause show consistent and progressive changes in transcripts participating in diverse developmental processes, despite a lack of gross morphological change. Moreover, population genomic analyses suggested that many genes of small effect enriched in developmental functional categories underlie variation in dormancy timing and overlap with gene sets associated with development rate in Drosophila melanogaster Our transcriptional data also suggested that a recent evolutionary shift from a seasonally late to a seasonally early host plant drove more rapid development during diapause in the early fly population. Moreover, genetic variants that diverged during the evolutionary shift were also enriched in putative cis regulatory regions of genes differentially expressed during diapause development. Overall, our data suggest polygenic variation in the rate of developmental progression during diapause contributes to the evolution of seasonality in R. pomonella We further discuss patterns that suggest hourglass-like developmental divergence early and late in diapause development and an important role for hub genes in the evolution of transcriptional divergence.

Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis

Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether and how host-related selection on diapause timing associates with genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of Rhagoletis pomonella to their sibling species Rhagoletis mendax that attacks blueberries. The associations of 57 857 single nucleotide polymorphisms in a diapause genome-wide-association study (GWAS) on the hawthorn race strongly predicted the direction and magnitude of genomic divergence among the three fly populations at a field site in Fennville, MI, USA. The apple race and R. mendax show parallel changes in the frequencies of putative inversions on three chromosomes associated with the earlier fruiting times of apples and blueberries compared to hawthorns. A diapause GWAS on R. mendax revealed compensatory changes throughout the genome accounting for the earlier eclosion of blueberry, but not apple flies. Thus, a degree of predictability, although not complete, exists in the genomics of diapause across the ecological speciation continuum in Rhagoletis. The generality of this result is placed in the context of other similar systems. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Comparing Adaptive Radiations Across Space, Time, and Taxa

Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, the concept has provoked strong and differing opinions concerning its definition and nature among researchers studying a wide diversity of systems. Here, we take a broad view of what constitutes an adaptive radiation, and seek to find commonalities among disparate examples, ranging from plants to invertebrate and vertebrate animals, and remote islands to lakes and continents, to better understand processes shared across adaptive radiations. We surveyed many groups to evaluate factors considered important in a large variety of species radiations. In each of these studies, ecological opportunity of some form is identified as a prerequisite for adaptive radiation. However, evolvability, which can be enhanced by hybridization between distantly related species, may play a role in seeding entire radiations. Within radiations, the processes that lead to speciation depend largely on (1) whether the primary drivers of ecological shifts are (a) external to the membership of the radiation itself (mostly divergent or disruptive ecological selection) or (b) due to competition within the radiation membership (interactions among members) subsequent to reproductive isolation in similar environments, and (2) the extent and timing of admixture. These differences translate into different patterns of species accumulation and subsequent patterns of diversity across an adaptive radiation. Adaptive radiations occur in an extraordinary diversity of different ways, and continue to provide rich data for a better understanding of the diversification of life.

Rapid host-plant adaptation in the herbivorous spider mite Tetranychus urticae occurs at low cost

The herbivorous spider mite Tetranychus urticae is a generalist world crop pest. Early evidence for host races, its fully sequenced genome resolved to the chromosome level, and the development of other molecular tools in this species suggest that this arthropod can be a good model to address host plant adaptation and early stages of speciation. Here, we evaluate this possibility by reviewing recent studies of host-plant adaptation in T. urticae. We find that evidence for costs of adaptation are relatively scarce and that studies involving molecular-genetics and genomics are mostly disconnected from those with phenotypic tests. Still, with the ongoing development of genetic and genomic tools for this species, T. urticae is becoming an attractive model to understand the molecular basis of host-plant adaptation.

Rapid and repeatable host plant shifts drive reproductive isolation following a recent human-mediated introduction of the apple maggot fly, Rhagoletis pomonella

Ecological speciation via host-shifting is often invoked as a mechanism for insect diversification, but the relative importance of this process is poorly understood. The shift of Rhagoletis pomonella in the 1850s from the native downy hawthorn, Crataegus mollis, to introduced apple, Malus pumila, is a classic example of sympatric host race formation, a hypothesized early stage of ecological speciation. The accidental human-mediated introduction of R. pomonella into the Pacific Northwest (PNW) in the late 1970s allows us to investigate how novel ecological opportunities may trigger divergent adaptation and host race formation on a rapid timescale. Since the introduction, the fly has spread in the PNW, where in addition to apple, it now infests native black hawthorn, Crataegus douglasii, and introduced ornamental hawthorn, Crataegus monogyna. We use this "natural experiment" to test for genetic differentiation among apple, black, and ornamental hawthorn flies co-occurring at three sympatric sites. We report evidence that populations of all three host-associations are genetically differentiated at the local level, indicating that partial reproductive isolation has evolved in this novel habitat. Our results suggest that conditions suitable for initiating host-associated divergence may be common in nature, allowing for the rapid evolution of new host races when ecological opportunity arises.

Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi

Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher F_ST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.

Geographic and Ecological Dimensions of Host Plant-Associated Genetic Differentiation and Speciation in the Rhagoletis cingulata (Diptera: Tephritidae) Sibling Species Group

Ascertaining the causes of adaptive radiation is central to understanding how new species arise and come to vary with their resources. The ecological theory posits adaptive radiation via divergent natural selection associated with novel resource use; an alternative suggests character displacement following speciation in allopatry and then secondary contact of reproductively isolated but ecologically similar species. Discriminating between hypotheses, therefore, requires the establishment of a key role for ecological diversification in initiating speciation versus a secondary role in facilitating co-existence. Here, we characterize patterns of genetic variation and postzygotic reproductive isolation for tephritid fruit flies in the Rhagoletis cingulata sibling species group to assess the significance of ecology, geography, and non-adaptive processes for their divergence. Our results support the ecological theory: no evidence for intrinsic postzygotic reproductive isolation was found between two populations of allopatric species, while nuclear-encoded microsatellites implied strong ecologically based reproductive isolation among sympatric species infesting different host plants. Analysis of mitochondrial DNA suggested, however, that cytoplasmic-related reproductive isolation may also exist between two geographically isolated populations within R cingulata. Thus, ecology associated with sympatric host shifts and cytoplasmic effects possibly associated with an endosymbiont may be the key initial drivers of the radiation of the R. cingulata group.