Allopatric genetic origins for sympatric host-plant shifts and race formation in Rhagoletis

Genetics and the Evolution of Prezygotic Isolation

The significance of prezygotic isolation for speciation has been recognized at least since the Modern Synthesis. However, fundamental questions remain. For example, how are genetic associations between traits that contribute to prezygotic isolation maintained? What is the source of genetic variation underlying the evolution of these traits? And how do prezygotic barriers affect patterns of gene flow? We address these questions by reviewing genetic features shared across plants and animals that influence prezygotic isolation. Emerging technologies increasingly enable the identification and functional characterization of the genes involved, allowing us to test established theoretical expectations. Embedding these genes in their developmental context will allow further predictions about what constrains the evolution of prezygotic isolation. Ongoing improvements in statistical and computational tools will reveal how pre- and postzygotic isolation may differ in how they influence gene flow across the genome. Finally, we highlight opportunities for progress by combining theory with appropriate data.

Anthropogenic Change and the Process of Speciation

Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging lineages. Human-caused environmental changes produce new ecological niches, altering selection in diverse ways that can drive diversification; but changes also often remove niches and cause extirpations. Human impacts that alter selection regimes are widespread and strong in magnitude, ranging from local changes in biotic and abiotic conditions to direct harvesting to global climate change. Altered selection, and evolutionary responses to it, impacts early-stage divergence of lineages, but does not necessarily lead toward speciation and persistence of separate species. Altogether, humans both promote and hinder speciation, although new species would form very slowly relative to anthropogenic hybridization, which can be nearly instantaneous. Speculating about the future of speciation, we highlight two key conclusions: (1) Humans will have a large influence on extinction and "despeciation" dynamics in the short term and on early-stage lineage divergence, and thus potentially speciation in the longer term, and (2) long-term monitoring combined with easily dated anthropogenic changes will improve our understanding of the processes of speciation. We can use this knowledge to preserve and restore ecosystems in ways that promote (re-)diversification, increasing future opportunities of speciation and enhancing biodiversity.

Hybridization and Transgressive Evolution Generate Diversity in an Adaptive Radiation of Anolis Lizards

Interspecific hybridization may act as a major force contributing to the evolution of biodiversity. Although generally thought to reduce or constrain divergence between 2 species, hybridization can, paradoxically, promote divergence by increasing genetic variation or providing novel combinations of alleles that selection can act upon to move lineages toward new adaptive peaks. Hybridization may, then, play a key role in adaptive radiation by allowing lineages to diversify into new ecological space. Here, we test for signatures of historical hybridization in the Anolis lizards of Puerto Rico and evaluate 2 hypotheses for the role of hybridization in facilitating adaptive radiation-the hybrid swarm origins hypothesis and the syngameon hypothesis. Using whole genome sequences from all 10 species of Puerto Rican anoles, we calculated D and f-statistics (from ABBA-BABA tests) to test for introgression across the radiation and employed multispecies network coalescent methods to reconstruct phylogenetic networks that allow for hybridization. We then analyzed morphological data for these species to test for patterns consistent with transgressive evolution, a phenomenon in which the trait of a hybrid lineage is found outside of the range of its 2 parents. Our analyses uncovered strong evidence for introgression at multiple stages of the radiation, including support for an ancient hybrid origin of a clade comprising half of the extant Puerto Rican anole species. Moreover, we detected significant signals of transgressive evolution for 2 ecologically important traits, head length and toepad width, the latter of which has been described as a key innovation in Anolis. [Adaptive radiation; introgression; multispecies network coalescent; phenotypic evolution; phylogenetic network; reticulation; syngameon; transgressive segregation.].

Potential Contribution of Ancient Introgression to the Evolution of a Derived Reproductive Strategy in Ricefishes

Transitions from no parental care to extensive care are costly and involve major changes in life history, behavior, and morphology. Nevertheless, in Sulawesi ricefishes, pelvic brooding evolved from transfer brooding in two distantly related lineages within the genera Adrianichthys and Oryzias, respectively. Females of pelvic brooding species carry their eggs attached to their belly until the fry hatches. Despite their phylogenetic distance, both pelvic brooding lineages share a set of external morphological traits. A recent study found no direct gene flow between pelvic brooding lineages, suggesting independent evolution of the derived reproductive strategy. Convergent evolution can, however, also rely on repeated sorting of preexisting variation of an admixed ancestral population, especially when subjected to similar external selection pressures. We thus used a multispecies coalescent model and D-statistics to identify gene-tree-species-tree incongruencies, to evaluate the evolution of pelvic brooding with respect to interspecific gene flow not only between pelvic brooding lineages but also between pelvic brooding lineages and other Sulawesi ricefish lineages. We found a general network-like evolution in Sulawesi ricefishes, and as previously reported, we detected no gene flow between the pelvic brooding lineages. Instead, we found hybridization between the ancestor of pelvic brooding Oryzias and the common ancestor of the Oryzias species from the Lake Poso area. We further detected signs of introgression within the confidence interval of a quantitative trait locus associated with pelvic brooding in O. eversi. Our results hint toward a contribution of ancient standing genetic variation to the evolution of pelvic brooding in Oryzias.

Crowd-sourced observations of a polyphagous moth reveal evidence of allochronic speciation varying along a latitudinal gradient

Allochronic speciation, where reproductive isolation between populations of a species is facilitated by a difference in reproductive timing, depends on abiotic factors such as seasonality and biotic factors such as diapause intensity. These factors are strongly influenced by latitudinal trends in climate, so we hypothesized that there is a relationship between latitude and divergence among populations separated by life history timing. Hyphantria cunea (the fall webworm), a lepidopteran defoliator with red and black colour morphs, is hypothesized to be experiencing an incipient allochronic speciation. However, given their broad geographic range, the strength of allochronic speciation may vary across latitude. We annotated >11,000 crowd-sourced observations of fall webworm to model geographic distribution, phenology, and differences in colour phenotype between morphs across North America. We found that red and black morph life history timing differs across North America, and the phenology of morphs diverges more in warmer climates at lower latitudes. We also found some evidence that the colour phenotype of morphs also diverges at lower latitudes, suggesting reduced gene flow between colour morphs. Our results demonstrate that seasonality in lower latitudes may increase the strength of allochronic speciation in insects, and that the strength of sympatric speciation can vary along a latitudinal gradient. This has implications for our understanding of broad-scale speciation events and trends in global biodiversity.

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.

A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of Populus davidiana

Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the Populus davidiana southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of P. davidiana in the Yunnan-Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 P. davidiana samples from three regions across the species range. Our results showed that the uplift of the Qinghai-Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of P. davidiana. Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of P. davidiana adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region.

Population genomic evidence of selection on structural variants in a natural hybrid zone

Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson Hole Lycaeides) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviated from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average than SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess ancestry from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might disproportionately affect hybrid fitness and thus contribute to reproductive isolation.

Three problems in the genetics of speciation by selection

Speciation is the process by which barriers to gene flow evolve between populations. Although we now know that speciation is largely driven by natural selection, knowledge of the agents of selection and the genetic and genomic mechanisms that facilitate divergence is required for a satisfactory theory of speciation. In this essay, we highlight three advances/problems in our understanding of speciation that have arisen from studies of the genes and genomic regions that underlie the evolution of reproductive isolation. First, we describe how the identification of “speciation” genes makes it possible to identify the agents of selection causing the evolution of reproductive isolation, while also noting that the link between the genetics of phenotypic divergence and intrinsic postzygotic reproductive barriers remains tenuous. Second, we discuss the important role of recombination suppressors in facilitating speciation with gene flow, but point out that the means and timing by which reproductive barriers become associated with recombination cold spots remains uncertain. Third, we establish the importance of ancient genetic variation in speciation, although we argue that the focus of speciation studies on evolutionarily young groups may bias conclusions in favor of ancient variation relative to new mutations.

Sympatric speciation by allochrony?

Sympatric speciation was once thought most improbable, but careful study of some systems, particularly the apple maggot (Rhagoletis pomonella) and related Rhagoletis species, has led to its reinstatement as a likely mode of speciation in some cases. Different species and host races in this clade of flies often have highly specialized host preference, and along with frequent evolutionary shifts to different fruit species between sister taxa, there is a likely effect of the timing of adult emergence that follows host fruiting phenology. This is known as “allochronic” isolation (from the Greek meaning “different timing”). This overview covers recent discoveries by Inskeep et al. (Molecular Ecology, 2021) showing how allochrony is a major factor in preventing gene flow between a pair of sister species of Rhagoletis on different host fruits. Although the authors do not claim to prove sympatric speciation, it does seem very likely, and the work clearly underscores how readily host shifts via allochrony can aid sympatric speciation.

Genomic changes underlying repeated niche shifts in an adaptive radiation

In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, that is, the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by resequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment, and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.

Ecological speciation by sympatric host shifts in a clade of herbivorous sea slugs, with introgression and localized mitochondrial capture between species

Host shifting in insect-plant systems was historically important to the development of ecological speciation theory, yet surprisingly few studies have examined whether host shifting drives diversification of marine herbivores. When small-bodied consumers feed and also mate on a preferred host, disruptive selection can split a population into host races despite gene flow. Support for host shifts is notably lacking for invertebrates associated with macroalgae, where the scale of dispersal by planktonic larvae often far exceeds the grain of host patchiness, and adults are typically less specialized than terrestrial herbivores. Here, we present a candidate example of ecological speciation in a clade of sea slugs that primarily consume green algae in the genus Caulerpa, including highly invasive species. Ancestral character state reconstructions supported 'sea grapes' (C. racemosa, C. lentillifera) as the ancestral host for a tropical radiation of 12 Elysia spp., with one shift onto alternative Caulerpa spp. in the Indo-Pacific. A Caribbean radiation of three species included symaptric host shifts to Rhipocephalus brevicaulis in the ancestor of E. pratensis Ortea & Espinosa, 1996, and to C. prolifera in E. hamanni Krug, Vendetti & Valdes 2016, plus a niche expansion to a range of Caulerpa spp. in E. subornata Verrill, 1901. All three species are broadly sympatric across the Caribbean but are host-partitioned at a fine grain, and distinct by morphology and at nuclear loci. However, non-recombining mtDNA revealed a history of gene flow between E. pratensis and E. subornata: COI haplotypes from E. subornata were 10.4% divergent from E. pratensis haplotypes from four sites, but closely related to all E. pratensis haplotypes sampled from six Bahamian islands, indicating historical introgression and localized "mitochondrial capture." Disruptive selective likely fueled divergence and adaptation to distinct host environments, indicating ecological speciation may be an under-appreciated driver of diversification for marine herbivores as well as epibionts and other resource specialists.

Genetical, Morphological, Behavioral, and Ecological Traits Support the Existence of Three Brazilian Species of the Anastrepha fraterculus Complex of Cryptic Species

Within the Neotropical genus Anastrepha, the nominal species Anastrepha fraterculus is widely distributed from Mexico through northern Argentina. Currently it is believed to comprises a complex of at least eight cryptic species—known as the Anastrepha fraterculus complex (AF complex)—three of which occur in Brazil: A. sp.1 aff. fraterculus, A. sp.2 aff. fraterculus, and A. sp.3 aff. fraterculus. In this study, we present the results of a broad integrated analysis of multiple biological attributes in samples of the three species collected in sympatric areas. Analyses of the mitotic chromosomes confirm that all of them differ in sex chromosomes, and that the relative frequency of the distinct karyotypes is associated with variation in altitude. In these sympatric areas, a single female hybrid karyotype was detected within a significant sample of individuals. Population samples were analyzed for the ribosomal transcribed spacer ITS1, confirming that the three species have specific sequence types. Observations of reproductive behavior under laboratory conditions revealed that A. sp.1 and A. sp.2 mate early in the morning, while A. sp.3 mates in the middle of the day. A bimodal distribution of mating time was observed in the laboratory for hybrids, obtained between A. sp.1 and A. sp.3. In a mating choice experiment, most of the mating pairs were homospecific. In addition, through a list of the most frequent hosts associated with geographical occurrence, a bioclimatic model of their potential distribution was generated. The set of data allowed for the construction of explanatory hypothesis about the observed geographical pattern and the differential use of host fruits. Morphometric analyses of wings clearly demonstrated differences among the three species, for both males and females. Based on a wing image of the A. fraterculus (Wiedemann, 1830) type specimen, the morphometric analysis indicated that the type specimen would correspond to a male of A. sp.2 aff. fraterculus. The information provided by this report is not only useful for taxonomic purposes, but also reveals aspects to be considered in any reconstruction of an evolutionary scenario of the Anastrepha fraterculus complex.

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.

Population genetic structure of the carrot weevil ( Listronotus oregonensis ) in North America

Population genetic studies of insect pests enhance our ability to anticipate problems in agroecosystems, such as pest outbreaks, insecticide resistance, or expansions of the host range. This study focuses on geographic distance and host plant selection as potential determinants of genetic differentiation of the carrot weevil Listronotus oregonensis, a major pest of several apiaceous crops in North America. To undertake genetic studies on this species, we assembled the first complete genome sequence for L. oregonensis. Then, we used both haplotype discrimination with mitochondrial DNA (mtDNA) and a genotyping‐by‐sequencing (GBS) approach to characterize the genetic population structure. A total of 220 individuals were sampled from 17 localities in the provinces of Québec, Ontario, Nova Scotia (Canada), and the state of Ohio (USA). Our results showed significant genetic differences between distant populations across North America, indicating that geographic distance represents an important factor of differentiation for the carrot weevil. Furthermore, the GBS analysis revealed more different clusters than COI analysis between Québec and Nova Scotia populations, suggesting a recent differentiation in the latter province. In contrast, we found no clear evidence of population structure associated with the four cultivated apiaceous plants tested (carrot, parsley, celery, and celeriac) using populations from Québec. This first characterization of the genetic structure of the carrot weevil contributes to a better understanding of the gene flow of the species and helps to adapt local pest management measures to better control this agricultural pest.

Genotype diversity promotes the persistence of Daphnia populations exposed to severe copper stress

When environmental stressors of high intensity are sustained for long periods of time, populations face high probabilities of being extirpated. However, depending on the intensity of the stressor, large populations with sufficient genetic diversity may persist. We report the results of an experiment that tracked the persistence of Daphnia populations exposed to copper contamination. We assessed whether genotypic diversity reduced the risk of extinction. We created monoclonal and multiclonal populations and monitored their population sizes during a 32-week experiment. Cu was applied at a sub-lethal concentration and then increased every week until the population sizes dropped to about 10% of the carrying capacity (Cu at 180 μg/L). The concentration was then increased up to 186 μg/L and held stable until the end of the experiment. A survival analysis showed that clonal diversity extended the persistence of Daphnia populations, but copper contamination caused a substantial genetic erosion followed by population extirpation. However, some Cu-treated populations, mostly multiclonal, showed U-shaped patterns of growth consistent with evolutionary rescue but these did not lead to lasting population recovery. These results highlight the importance of genetic variation for population persistence, but they also show how quickly it can be lost in contaminated environments.

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.

Hybridization, Behavioral Patterns, and Pre- and Postzygotic Isolation Between Two Recently Derived Species of Walnut-Infesting Rhagoletis Fruit Flies in the Highlands of Mexico

Episodes of isolation and secondary contact among populations of insects of Nearctic origin during Pleistocene glacial/postglacial climatic cycles had a strong evolutionary influence on the diversity of flies in the genus Rhagoletis in mountainous areas of Mexico. As a series of experiments undertaken to gather support for phylogenetic hypotheses on the origin of three walnut-infesting species in the suavis group, we examined pre- and postzygotic isolation between Rhagoletis completa Cresson, 1929 and R. ramosae Hernández-Ortiz, 1985. Despite morphological, biological, and behavioral differences, these two species were found to be capable of hybridization. Mating experiments in large enclosures revealed asymmetric sexual isolation. There were notable differences in male sexual behavior. While R. ramosae males mated exclusively on host fruit, R. completa males used fruit and alternative mating locations. During fruit-guarding and male-male contests, R. completa and R. ramosae males adopted markedly different wing postures. R. completa females were more reluctant to copulate with heterospecific males than R. ramosae females. During no choice crosses in small enclosures, there was a reduction of egg hatch for the hybrid cross of R. completa males × R. ramosae females. Our results and previous studies on reproductive isolation between other species pairs in the suavis group support a clade in which R. ramosae, R. zoqui Bush, 1966, and R. completa are close relatives all still capable of hybridizing.

Phylogenomic approach reveals strong signatures of introgression in the rapid diversification of neotropical true fruit flies (Anastrepha: Tephritidae)

New sequencing techniques have allowed us to explore the variation on thousands of genes and elucidate evolutionary relationships of lineages even in complex scenarios, such as when there is rapid diversification. That seems to be the case of species in the genus Anastrepha, which shows great species diversity that has been divided into 21 species groups, several of which show wide geographical distribution. The fraterculus group has several economically important species and it is also an outstanding model for speciation studies, since it includes several lineages that have diverged recently possibly in the presence of interspecific gene flow. Our main goal is to test whether we can infer phylogenetic relationships of recently diverged taxa with gene flow, such as what is expected for the fraterculus group and determine whether certain genes remain informative even in this complex scenario. An analysis of thousands of orthologous genes derived from transcriptome datasets of 10 different lineages across the genus, including some of the economically most important pests, revealed signals of incomplete lineage sorting, vestiges of ancestral introgression between more distant lineages and ongoing gene flow between closely related lineages. Though these patterns affect the phylogenetic signal, the phylogenomic inferences consistently show that the morphologically identified species here investigated are in different evolutionary lineages, with the sole exception involving Brazilian lineages of A. fraterculus, which has been suggested to be a complex assembly of cryptic species. A tree space analysis suggested that genes with greater phylogenetic resolution have evolved under similar selection pressures and are more resilient to intraspecific gene flow, which would make it more likely that these genomic regions may be useful for identifying fraterculus group lineages. Our findings help establish relationships among the most important Anastrepha species groups, as well as bring further data to indicate that the diversification of fraterculus group lineages, and even other lineages in the genus Anastrepha, has been strongly influenced by interspecific gene flow.

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.

Speciation across the Tree of Life

Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.

Biological and biochemical diversity in different biotypes of spotted stem borer, Chilo partellus (Swinhoe) in India

Because of variation in incidence and severity of damage by Chilo partellus (Swinhoe) in different geographical regions, it is difficult to identify stable sources of resistance against this pest. Therefore, the present studies were undertaken on biological attributes (damage in resistant and susceptible genotypes, survival and development) and biochemical profiles (amino acids and lipophilic compound) of C. partellus populations from eight geographical regions to understand it's population structure in India. There was a significant variation in biological attributes and biochemical profiles of C. partellus populations from different geographical regions. Based on virulence and biological attributes, similarity index placed the C. partellus populations in five groups. Likewise, lipophilic and amino acid profiling also placed the C. partellus populations in five groups. However, the different clusters based on biological and biochemical attributes did not include populations from the same regions. Similarity index based on virulence, biological attributes, and amino acids and lipophilic profiles placed the C. partellus populations in six groups. The C. partellus populations from Hisar, Hyderabad, Parbhani and Coimbatore were distinct from each other, indicating that there are four biotypes of C. partellus in India. The results suggested that sorghum and maize genotypes need to be tested against these four populations to identify stable sources of resistance. However, there is a need for further studies to establish the restriction in gene flow through molecular approaches across geographical regions to establish the distinctiveness of different biotypes of C. partellus in India.

Fitness maps to a large-effect locus in introduced stickleback populations

Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A quantitative trait locus map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980s. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 y, yielding a similar estimate of selection, s = 0.49 ± 0.05, but a different degree of dominance. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.

The genetic differentiation of a cricket (Velarifictorus micado) with two modes of life cycle in East Asia after the middle Pleistocene and the invasion origin of the United States of America

The cricket Velarifictorus micado is widely distributed in East Asia and colonized the United States of America (the USA) in 1959. It has two life cycles: egg and nymph diapause. We aimed to investigate the biogeographic boundary between them and determine when and why V. micado diverged. Mitochondrial fragments including COI and CytB were used for haplotype network, demographic analysis, and divergence time estimation in individuals of East Asia. We selected several samples from the USA to find out the colonization origin. The haplotype network indicated there were three lineages based on COI, NE lineage (the egg diapause and mainly distributed in the northern regions), SE lineage (the egg diapause and mainly distributed in the southern regions), and SN lineage (the nymph diapause and mainly distributed in the southern regions). The molecular chronograms indicated that the first divergence of V. micado into two main lineages, NE and southern lineages (SE and SN), was essentially bounded by the Yangtze River. It occurred around ~0.79 Ma (95% HPD: 1.13-0.46 Ma) in the Middle Pleistocene Transition. This was followed by the divergence of the southern lineage into two sublineages, SE and SN lineage, occurred around ~0.50 Ma (95% HPD: 0.71-0.25 Ma), corresponding to the time of development of glaciers in various parts of the Qinghai-Tibet Plateau (QTP) (0.73-0.46 Ma). SE lineage might originate from southwestern China based on the comparison between the haplotype network based on COI and CytB. Our study suggested that divergences of lineages have twice co-occurred with tendency of cooling climatic in Asia after the Mid-Pleistocene, and the life-history strategy may play an important role in lineage diversification. Additionally, our results indicated that the USA populations were revealed at least twice separate Asian invasions. These both belonged to the egg diapause, which might provide a new perspective for invasion control.

Evidence for spatial clines and mixed geographic modes of speciation for North American cherry-infesting Rhagoletis (Diptera: Tephritidae) flies

An important criterion for understanding speciation is the geographic context of population divergence. Three major modes of allopatric, parapatric, and sympatric speciation define the extent of spatial overlap and gene flow between diverging populations. However, mixed modes of speciation are also possible, whereby populations experience periods of allopatry, parapatry, and/or sympatry at different times as they diverge. Here, we report clinal patterns of variation for 21 nuclear-encoded microsatellites and a wing spot phenotype for cherry-infesting Rhagoletis (Diptera: Tephritidae) across North America consistent with these flies having initially diverged in parapatry followed by a period of allopatric differentiation in the early Holocene. However, mitochondrial DNA (mtDNA) displays a different pattern; cherry flies at the ends of the clines in the eastern USA and Pacific Northwest share identical haplotypes, while centrally located populations in the southwestern USA and Mexico possess a different haplotype. We hypothesize that the mitochondrial difference could be due to lineage sorting but more likely reflects a selective sweep of a favorable mtDNA variant or the spread of an endosymbiont. The estimated divergence time for mtDNA suggests possible past allopatry, secondary contact, and subsequent isolation between USA and Mexican fly populations initiated before the Wisconsin glaciation. Thus, the current genetics of cherry flies may involve different mixed modes of divergence occurring in different portions of the fly's range. We discuss the need for additional DNA sequencing and quantification of prezygotic and postzygotic reproductive isolation to verify the multiple mixed-mode hypothesis for cherry flies and draw parallels from other systems to assess the generality that speciation may commonly involve complex biogeographies of varying combinations of allopatric, parapatric, and sympatric divergence.

Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence

Nonrecombining sex chromosomes are widely found to be more differentiated than autosomes among closely related species, due to smaller effective population size and/or to a disproportionally large-X effect in reproductive isolation. Although fungal mating-type chromosomes can also display large nonrecombining regions, their levels of differentiation compared with autosomes have been little studied. Anther-smut fungi from the Microbotryum genus are castrating pathogens of Caryophyllaceae plants with largely nonrecombining mating-type chromosomes. Using whole genome sequences of 40 fungal strains, we quantified genetic differentiation among strains isolated from the geographically overlapping North American species and subspecies of Silene virginica and S. caroliniana. We inferred that gene flow likely occurred at the early stages of divergence and then completely stopped. We identified large autosomal genomic regions with chromosomal inversions, with higher genetic divergence than the rest of the genomes and highly enriched in selective sweeps, supporting a role of rearrangements in preventing gene flow in genomic regions involved in ecological divergence. Unexpectedly, the nonrecombining mating-type chromosomes showed lower divergence than autosomes due to higher gene flow, which may be promoted by adaptive introgressions of less degenerated mating-type chromosomes. The fact that both mating-type chromosomes are always heterozygous and nonrecombining may explain such patterns that oppose to those found for XY or ZW sex chromosomes. The specific features of mating-type chromosomes may also apply to the UV sex chromosomes determining sexes at the haploid stage in algae and bryophytes and may help test general hypotheses on the evolutionary specificities of sex-related chromosomes.

Model-Based Inference of Punctuated Molecular Evolution

In standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a rate that can vary (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary timescale. Here, we develop a model, which we call the Relaxed Clock with Spikes model, combining basal, clock-like molecular substitutions with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) cooccurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular substitutions and from variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.

Digest: The interplay between imprinting, mimicry, and multimodal signaling can lead to sympatric speciation†

Mimicry can directly affect the evolutionary history of models, mimics, and signal receivers. Mimics often use multimodal signaling to deceive receivers. Jamie et al. showed that brood parasitic birds display multimodal signaling of mimetic traits triggered by sexual and filial imprinting on host species. These resulting adaptations can interact with premating isolation barriers to strengthen reproductive isolation and potentially drive sympatric speciation.

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.

The tree and the table: Darwin, Mendeleev and the meaning of 'theory'

Darwin and Mendeleev revolutionized their respective disciplines by organizing diverse facts into simple, pictorial representations-a tree and a table. Each representation provides a foundation for a scientific theory for two reasons. First, a successful theory unites diverse phenomena under a single explanatory framework. Second, it does so in a way that defines paths for future inquiry that extends its reach and tests its limits. For Mendeleev, this meant creating a table that accommodated the current understanding of the elements but also contained blanks that predicted the discovery of previously unknown elements. More importantly, the structure of the table helped shape future research to define the structure of matter. For Darwin, envisioning life as a tree meant defining the rules that govern the origin of adaptations, species and shape the constantly shifting diversity of life. At the same time, his theory inspired research into the laws of inheritance and created diverse new areas of research, like behaviour, sexual selection and biogeography. The shared property of Darwin and Mendeleev's contributions was to provide a unifying rational explanation for natural phenomena. This article is part of the theme issue 'Mendeleev and the periodic table'.

Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.

Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.

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.

Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish

Genomic architecture and standing variation can play a key role in ecological adaptation and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behavior in regional analyses. However, the degree of parallelism, the extent of independent inheritance, and functional distinctiveness of these rearrangements remain poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangements with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures, has likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.

Speciation Post Synthesis: 1960-2000

Speciation-the origin of new species-has been one of the most active areas of research in evolutionary biology, both during, and since the Modern Synthesis. While the Modern Synthesis certainly shaped research on speciation in significant ways, providing a core framework, and set of categories and methods to work with, the history of work on speciation since the mid-twentieth century is a history of divergence and diversification. This piece traces this divergence, through both theoretical advances, and empirical insights into how different lineages, with different genetics and ecological conditions, are shaped by very different modes of diversification.

What Can Integrated Analysis of Morphological and Genetic Data Still Reveal about the Anastrepha fraterculus (Diptera: Tephritidae) Cryptic Species Complex?

The South American fruit fly Anastrepha fraterculus (Wiedemann) is a complex of cryptic species, the so-called “Anastrepha fraterculus complex”, for which eight morphotypes are currently recognized. A previous analysis of ITS1 in samples of the Anastrepha fraterculus complex, while revealing high distinctiveness among samples from different localities of South America, Central America, and Mexico, no direct association was made between sequence type and morphotype. In the present report, a correlated analysis of morphometry and ITS1 data involved individuals belonging to the same population samples. Although showing a low level of intra-populational nucleotide variability, the ITS1 analysis indicated numerous inter-population sequence type variants. Morphotypes identified by morphometric analysis based on female wing shape were highly concordant with ITS1 genetic data. The correlation of genetic divergence and morphological differences among the tested samples gives strong evidence of a robust dataset, thereby indicating the existence of various taxonomic species within the A. fraterculus complex. However, the data revealed genetic and morphological variations in some regions, suggesting that further analysis is still required for some geographic regions.

The paradox behind the pattern of rapid adaptive radiation: how can the speciation process sustain itself through an early burst?

Rapid adaptive radiation poses a distinct question apart from speciation and adaptation: what happens after one speciation event? That is, how are some lineages able to continue speciating through a rapid burst? This question connects global macroevolutionary patterns to microevolutionary processes. Here we review major features of rapid radiations in nature and their mismatch with theoretical models and what is currently known about speciation mechanisms. Rapid radiations occur on three major diversification axes - species richness, phenotypic disparity, and ecological diversity - with exceptional outliers on each axis. The paradox is that the hallmark early stage of adaptive radiation, a rapid burst of speciation and niche diversification, is contradicted by most existing speciation models which instead predict continuously decelerating speciation rates and niche subdivision through time. Furthermore, while speciation mechanisms such as magic traits, phenotype matching, and physical linkage of co-adapted alleles promote speciation, it is often not discussed how these mechanisms could promote multiple speciation events in rapid succession. Additional mechanisms beyond ecological opportunity are needed to understand how rapid radiations occur. We review the evidence for five emerging theories: 1) the 'transporter' hypothesis: introgression and the ancient origins of adaptive alleles, 2) the 'signal complexity' hypothesis: the dimensionality of sexual traits, 3) the connectivity of fitness landscapes, 4) 'diversity begets diversity', and 5) flexible stem/'plasticity first'. We propose new questions and predictions to guide future work on the mechanisms underlying the rare origins of rapid radiation.

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.

Differential Response to Photoperiod by Diverging Rhagoletis pomonella (Diptera: Tephritidae) Populations Exploiting Host Plants with Different Fruiting Phenology

Photoperiod has been found to influence the proportion of non-dormant individuals and the duration of dormancy among North American populations of Rhagoletis pomonella (Walsh) (Diptera: Tephritidae). In particular, long days combined with high temperatures can produce a 100% non-dormant generation. There are several genetically distinct populations of R. pomonella in the highlands of Mexico, two of which occur at the same latitude, at different elevations, that exploit hawthorn plants with different fruiting phenology (early (summer-fall) and late (winter)). Flies exploiting such hosts might use day length in different ways as a cue to match adult emergence with fruit availability. Here, we compared responses of pupae from two Mexican populations of R. pomonella to a 12/12 L/D photoperiod, a long-day photoperiod 17/7 L/D, and continuous illumination. Experiments were performed under warm conditions (27°C). Day length had no effect on the proportion of adults emerged from the early-fruiting hawthorn population, while pupae extracted from late-fruiting hawthorns and exposed to long days emerged as adults in lower proportions and engaged in prolonged dormancy in greater proportions than those exposed to a short day. Photoperiod had no effect on the proportion from both Mexican populations foregoing dormancy. Dormancy duration was affected by photoperiod and was longer than previous reports for North American populations. Host plant fruiting phenology may be the driver of these differences. These findings, coupled with previous reports of genetic and biological differences, suggest that the Eje Volcanico Trans-Mexicano R. pomonella population may actually be a distinct species.

The Effect of Seasonal Humidity on Survival and Duration of Dormancy on Diverging Mexican Rhagoletis pomonella (Diptera: Tephritidae) Populations Inhabiting Different Environments

Phytophagous insects synchronize emergence with plant phenology by engaging in dormancy during periods of host scarcity and environmental stress. Regulation of dormancy is achieved through response to seasonal cues. While temperature and photoperiod are important cues in temperate latitudes, seasonal humidity, such as the onset of rains, can be a reliable cue to for synchronization of emergence and affects survival of overwintering insects. We compared response of Mexican Rhagoletis pomonella (Walsh) (Diptera: Tephritidae) populations inhabiting subtropical environments differing in humidity patterns, to seasonal humidity regimes. Both populations emerged as adults in high proportions and suffered lower mortality under humidity regimes ending with a humid summer, but the effect was more pronounced for the Eje Volcanico Trans Mexicano (EVTM) population, which inhabits a dryer environment and undergoes longer dormancy. While there were no differences among pupae from the Sierra Madre Oriental (SMO) in percent of non-emerged pupae surviving and engaging in prolonged dormancy after a year, EVTM pupae exposed to an initial humid period engaged in prolonged dormancy in higher proportions than those exposed to other regimes. Seasonal humidity had little effect on the duration of dormancy, but EVTM pupae exposed to consecutive dry periods took longer to emerge than those exposed to other regimes. Our results suggest that rather than being used as a token stimulus, humidity affected survival of overwintering R. pomonella, especially at the end of dormancy when energy reserves are depleted and there is an increase in metabolic rate that renders EVTM pupae more susceptible to desiccation.

Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback

Ecological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation.

Ecological speciation can proceed rapidly, but the origin of genetic variation facilitating it has remained elusive. Here, the authors show that secondary contact and introgression between deeply diverged lineages of stickleback fish facilitated rapid ecological speciation into lake and stream ecotypes in Lake Constance.

Admixture between ancient lineages, selection, and the formation of sympatric stickleback species-pairs

Ecological speciation has become a popular model for the development and maintenance of reproductive isolation in closely related sympatric pairs of species or ecotypes. An implicit assumption has been that such pairs originate (possibly with gene flow) from a recent, genetically homogeneous ancestor. However, recent genomic data has revealed that currently sympatric taxa are often a result of secondary contact between ancestrally allopatric lineages. This has sparked an interest in the importance of initial hybridization upon secondary contact, with genomic re-analysis of classic examples of ecological speciation often implicating admixture in speciation. We describe a novel occurrence of unusually well-developed reproductive isolation in a model system for ecological speciation: the three-spined stickleback (Gasterosteus aculeatus), breeding sympatrically in multiple lagoons on the Scottish island of North Uist. Using morphological data, targeted genotyping and genome-wide single nucleotide polymorphism (SNP) data we show that lagoon resident and anadromous ecotypes are strongly reproductively isolated with an estimated hybridization rate of only ∼1%. We use palaeoecological and genetic data to test three hypotheses to explain the existence of these species-pairs. Our results suggest that recent, purely ecological speciation from a genetically homogeneous ancestor is probably not solely responsible for the evolution of species-pairs. Instead we reveal a complex colonisation history with multiple ancestral lineages contributing to the genetic composition of species-pairs, alongside strong disruptive selection. Our results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.

Searching for Sympatric Speciation in the Genomic Era

Sympatric speciation illustrates how natural and sexual selection may create new species in isolation without geographic barriers. However, recent genomic reanalyses of classic examples of sympatric speciation reveal complex histories of secondary gene flow from outgroups into the radiation. In contrast, the rich theoretical literature on this process distinguishes among a diverse range of models based on simple genetic histories and different types of reproductive isolating barriers. Thus, there is a need to revisit how to connect theoretical models of sympatric speciation and their predictions to empirical case studies in the face of widespread gene flow. Here, theoretical differences among different types of sympatric speciation and speciation-with-gene-flow models are reviewed and summarized, and genomic analyses are proposed for distinguishing which models apply to case studies based on the timing and function of adaptive introgression. Investigating whether secondary gene flow contributed to reproductive isolation is necessary to test whether predictions of theory are ultimately borne out in nature.