Browsing by Author "Egan, Scott P."
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Item A keeper of many crypts: a behaviour-manipulating parasite attacks a taxonomically diverse array of oak gall wasp species(The Royal Society of Publishing, 2019) Ward, Anna K.G.; Khodor, Omar S.; Egan, Scott P.; Weinersmith, Kelly L.; Forbes, Andrew A.Parasites of animals and plants can encounter trade-offs between their specificity to any single host and their fitness on alternative hosts. For parasites that manipulate their host's behaviour, the added complexity of that manipulation may further limit the parasite's host range. However, this is rarely tested. The recently described crypt-keeper wasp, Euderus set, changes the behaviour of the gall wasp Bassettia pallida such that B. pallida chews a significantly smaller exit hole in the side of its larval chamber and ‘plugs’ that hole with its head before dying. Euderus set benefits from this head plug, as it facilitates the escape of the parasitoid from the crypt after it completes development. Here, we find direct and indirect evidence that E. set attacks and manipulates the behaviour of at least six additional gall wasp species, and that these hosts are taxonomically diverse. Interestingly, each of E. set's hosts has converged upon similarities in their extended phenotypes: the galls they induce on oaks share characters that may make them vulnerable to attack by E. set. The specialization required to behaviourally manipulate hosts may be less important in determining the range of hosts in this parasitoid system than other dimensions of the host–parasitoid interaction, like the host's physical defences.Item Borders on the Rise: The Unintended Evolutionary Consequences of Border Barriers on Natural Populations(2018) Egan, Scott P.; Comerford, Mattheau; Hood, Glen R.; Zhang, Linyi; Weinersmith, Kelly L.; James A. Baker III Institute for Public PolicyItem Chromosomes of Belonocnema treatae Mayr, 1881 (Hymenoptera, Cynipidae)(Pensoft, 2015) Gokhman, Vladimir E.; Ott, James R.; Egan, Scott P.Chromosomes of the asexual and sexual generation of the gall wasp Belonocnema treatae Mayr, 1881 (Cynipidae) were analyzed. Females of both generations have 2n = 20, whereas males of the sexual generation have n = 10. Cyclical deuterotoky is therefore confirmed in this species. All chromosomes are acrocentric and form a continuous gradation in size. This karyotype structure is probably ancestral for many gall wasps and perhaps for the family Cynipidae in general. Chromosome no. 7 carries a characteristic achromatic gap that appears to represent a nucleolus organizing region.Item Cryptic diversity in the North American Dromochorus tiger beetles (Coleoptera: Carabidae: Cicindelinae): a congruence-based method for species discovery(Oxford University Press, 2019) Duran, Daniel P.; Herrmann, David P.; Roman, Stephen J.; Gwiazdowski, Rodger A.; Drummond, Jennifer A.; Hood, Glen R.; Egan, Scott P.A fundamental problem in biodiversity science is determining the number of species in any taxon, and there is a growing awareness that cryptic diversity contributes to this problem – even in well-studied groups. Discovering cryptic species requires several lines of evidence to elucidate congruent patterns across data-types, and distinguish unrecognized species. Tiger beetles are among the most well-studied insect groups; yet few new North American species have been described since the mid-20th century, suggesting that that the number of morphologically distinct species is reaching an asymptote. We explore the possibility that more species exist in the fauna as cryptic species, by analysing a broad geographic sample of all species in the genus Dromochorus. We employ a ‘taxonomic congruence’ approach, where we first generate species hypotheses from patterns of reciprocal monophyly across the mitochondrial and nuclear datasets, and test these hypotheses through congruence with population structure, morphological measures and ecological divergence. We find broad congruence that supports eight species of Dromochorus, more than doubling the known diversity. We also validate a previously ambiguous taxon, and re-describe previously named species. Lastly, we identify new diagnostic morphological characters, include an updated dichotomous key and provide updated natural history/ecological characteristics for the genus and individual species.Item Description of a new species of Chrysonotomyia Ashmead from Houston, Texas, USA (Hymenoptera, Chalcidoidea, Eulophidae)(Pensoft Publishers, 2024) O’Loughlin, Brendan; Brandão-Dias, Pedro F. P.; Gates, Michael W.; Egan, Scott P.A new species of the genus Chrysonotomyia Ashmead, Chrysonotomyia susbelli sp. nov., is described from the Rice University campus in Houston, Texas, USA. The species is a parasitoid emerging from Neuroterus nr. bussae galls in leaves of the southern live oak (Quercus virginiana). This represents the 6th species described from North America north of Mexico and the first in the world known to parasitize cynipid gall wasps. This discovery hints at an entire undiscovered niche between Chrysonotomyia parasitoids, cynipid gall wasps, and oaks in the Nearctic, which is a global biodiversity hotspot for oaks and cynipids. This new species description is complemented by mtDNA-COI-barcode data and information on the natural history of this species. We record host association, phenology, and report a leaf-scanning behavior performed by females, presumably to search for host galls. Modifications to the key of New World members of the genus (Hansson 2004) are included to integrate this new species.Item Development and field validation of an environmental DNA (eDNA) assay for invasive clams of the genus Corbicula(REABIC, 2018) Cowart, Dominique A.; Renshaw, Mark A.; Gantz, Crysta A.; Umek, John; Chandra, Sudeep; Egan, Scott P.; Lodge, David M.; Larson, Eric R.Early detection is imperative for successful control or eradication of invasive species, but many organisms are difficult to detect at the low abundances characteristic of recently introduced populations. Environmental DNA (eDNA) has emerged as a promising invasive species surveillance tool for freshwaters, owing to its high sensitivity to detect aquatic species even when scarce. We report here a new eDNA assay for the globally invasive Asian clam Corbicula fluminea (Müller, 1774), with field validation in large lakes of western North America. We identified a candidate primer pair for the Cytochrome c oxidase subunit 1 (COI) gene for C. fluminea. We tested it for specificity via qPCR assay against genomic DNA of the target species C. fluminea, and synthetic DNA gBlocks for other non-target species within and outside of the genus Corbicula. Our best identified primer amplifies a 208-bp fragment for C. fluminea and several closely related species within the genus, but was specific for these non-native Asian clams relative to native mollusks of western North America. We further evaluated this assay in application to eDNA water samples for the detection of C. fluminea from four lakes in California and Nevada, United States, where the species is known to occur (including Lake Tahoe) relative to seven lakes where it has never been observed. Our assay successfully detected C. fluminea in all four lakes with historic records for this species, and did not detect C. fluminea from the seven lakes without known populations. Further, the distribution of eDNA detections within Lake Tahoe generally matched the known, restricted distribution of C. fluminea in this large lake. We conclude from this successful field validation that our eDNA assay for C. fluminea will be useful for researchers and managers seeking to detect new introductions and potentially monitor population trends of this major freshwater invader and other closely related members of its genus.Item Development of a Synthetic Toolkit for the Exploration of All-Hydrocarbon α-Helical Stapled Peptide Chemical Space via DNA-Encoded Chemical Libraries(2020-04-23) Monty, Olivier Brian Cyril; Young, Damian W; Ball, Zachary T; Hartgerink, Jeffrey D.; Egan, Scott P.The recognized attrition of drug discovery has been the central motivation behind the work described in the following chapters. Such decline in the rate of discovery has been partially blamed on the exhaustive exploration of part of chemical space by largely flat, sp2-rich chemotypes, which, until recently, made up most screening libraries. The exploration of new chemical space through the incorporation of three-dimensional chemotypes has been adopted as a potential solution, which has proven effective as evidenced by the recent surge in three-dimensional molecular probes and therapeutics. All-hydrocarbon α-helical stapled peptides represent a class of such three-dimensional chemotypes that have proven capable of targeting the challenging intracellular protein-protein interactions (~80% of the proteome). Those cell-permeable mini-proteins have promoted peptide drug discovery to the main stage and the work described in this document is intended to buttress and exploit this rise to prominence. Because the chemical space of stapled peptides is relatively underexplored and due to the pressing need for new therapeutics in the face of global issues such as drug resistance, fast and deep exploration via the large numbers and diversity attainable in DNA-encoded chemistry is desirable. To do so, however, one needs a DNA-compatible synthetic toolkit to generate all-hydrocarbon staples on DNA-chemical conjugates and to perform peptide synthesis on DNA. Chapters 1 and 2 describe the development of such a toolkit. ii Chapter 3 finally discusses how the latter could be used for the exploration of the α-helical stapled peptide chemical space via DNA-encoded chemical libraries.Item Diversity and distribution ofﾠWolbachiaﾠin relation to geography, host plant affiliation and life cycle of a heterogonic gall wasp(Springer Nature, 2018) Schuler, Hannes; Egan, Scott P.; Hood, Glen Ray; Busbee, Robert W.; Driscoe, Amanda L.; Ott, James R.Background: The maternally inherited endosymbiont Wolbachia is widespread in arthropods and nematodes and can play an important role in the ecology and evolution of its host through reproductive manipulation. Here, we survey Wolbachia in Belonocnema treatae, a widely distributed North American cynipid gall forming wasp that exhibits regional host specialization on three species of oaks and alternation of sexually and asexually reproducing generations. We investigated whether patterns of Wolbachia infection and diversity in B. treatae are associated with the insect’s geographic distribution, host plant association, life cycle, and mitochondrial evolutionary history. Results: Screening of 463 individuals from 23 populations including sexual and asexual generations from all three host plants across the southern U.S. showed an average infection rate of 56% with three common Wolbachia strains: wTre1–3 and an additional rare variant wTre4. Phylogenetic analysis based on wsp showed that these strains are unrelated and likely independently inherited. We found no difference in Wolbachia infection frequency among host plant associated populations or between the asexual and sexual generations, or between males and females of the sexual generation. Partially incomplete Wolbachia transmission rates might explain the occurrence of uninfected individuals. A parallel analysis of the mitochondrial cytochrome oxidase I gene in B. treatae showed high mtDNA haplotype diversity in both infected and uninfected populations suggesting an ancestral infection by Wolbachia as well as a clear split between eastern and western B. treatae mtDNA clades with a sequence divergence of > 6%. The strain wTre1 was present almost exclusively in the western clade while wTre2 and wTre3 occur almost exclusively in eastern populations. In contrast, the same strains co-occur as double-infections in Georgia and triple-infections in two populations in central Florida. Conclusions: The diversity of Wolbachia across geographically and genetically distinct populations of B. treatae and the co-occurrence of the same strains within three populations highlights the complex infection dynamics in this system. Moreover, the association of distinct Wolbachia strains with mitochondrial haplotypes of its host in populations infected by different Wolbachia strains suggests a potential role of the endosymbiont in reproductive isolation in B. treatae.Item Diversity Metrics Are Robust to Differences in Sampling Location and Depth for Environmental DNA of Plants in Small Temperate Lakes(Frontiers Media S.A., 2021) Drummond, Jennifer A.; Larson, Eric R.; Li, Yiyuan; Lodge, David M.; Gantz, Crysta A.; Pfrender, Michael E.; Renshaw, Mark A.; Correa, Adrienne M.S.; Egan, Scott P.Environmental DNA (eDNA) analysis methods permit broad yet detailed biodiversity sampling to be performed with minimal field effort. However, considerable uncertainty remains regarding the spatial resolution necessary for effective sampling, especially in aquatic environments. Also, contemporary plant communities are under-investigated with eDNA methods relative to animals and microbes. We analyzed eDNA samples from six small temperate lakes to elucidate spatial patterns in the distributions of algae and aquatic and terrestrial plants, using metabarcoding of the Internal Transcribed Spacer-1 (ITS1) genomic region. Sampling locations were varied across horizontal and vertical space: sites in each lake included a mixture of nearshore and offshore positions, each of which was stratified into surface (shallow) and benthic (deep) samples. We detected the expected community variation (beta diversity) from lake to lake, but only small effects of offshore distance and sampling depth. Taxon richness (alpha diversity) was slightly elevated in nearshore samples, but displayed no other significant spatial effects. These diversity metrics imply that plant eDNA is more evenly distributed than its generating organisms in these small lake environments. Read abundances were heavily weighted toward aquatic macrophytes, though taxon richness was greatest in the algae and other nonvascular plants. We also identified representatives of many phylogenetically and ecologically varied plant taxa, including terrestrial species from surrounding areas. We conclude that freshwater plant eDNA surveys successfully capture differences among lake communities, and that easily-accessible, shore-based sampling may be a reliable technique for informing research and management in similar ecosystems.Item Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs(Elsevier, 2017) Trebitz, Anett S.; Hoffman, Joel C.; Darling, John A.; Pilgrim, Erik M.; Kelly, John R.; Brown, Emily A.; Chadderton, W.Lindsay; Egan, Scott P.; Grey, Erin K.; Hashsham, Syed A.; Klymus, Katy E.; Mahon, Andrew R.; Ram, Jeffrey L.; Schultz, Martin T.; Stepien, Carol A.; Schardt, James C.Following decades of ecologic and economic impacts from a growing list of nonindigenous and invasive species, government and management entities are committing to systematic early- detection monitoring (EDM). This has reinvigorated investment in the science underpinning such monitoring, as well as the need to convey that science in practical terms to those tasked with EDM implementation. Using the context of nonindigenous species in the North American Great Lakes, this article summarizes the current scientific tools and knowledge – including limitations, research needs, and likely future developments – relevant to various aspects of planning and conducting comprehensive EDM. We begin with the scope of the effort, contrasting target-species with broad-spectrum monitoring, reviewing information to support prioritization based on species and locations, and exploring the challenge of moving beyond individual surveys towards a coordinated monitoring network. Next, we discuss survey design, including effort to expend and its allocation over space and time. A section on sample collection and analysis overviews the merits of collecting actual organisms versus shed DNA, reviews the capabilities and limitations of identification by morphology, DNA target markers, or DNA barcoding, and examines best practices for sample handling and data verification. We end with a section addressing the analysis of monitoring data, including methods to evaluate survey performance and characterize and communicate uncertainty. Although the body of science supporting EDM implementation is already substantial, research and information needs (many already actively being addressed) include: better data to support risk assessments that guide choice of taxa and locations to monitor; improved understanding of spatiotemporal scales for sample collection; further development of DNA target markers, reference barcodes, genomic workflows, and synergies between DNA-based and morphology-based taxonomy; and tools and information management systems for better evaluating and communicating survey outcomes and uncertainty.Item Environment and shipping drive environmental DNA beta-diversity among commercial ports(Wiley, 2023) Andrés, Jose; Czechowski, Paul; Grey, Erin; Saebi, Mandana; Andres, Kara; Brown, Christopher; Chawla, Nitesh; Corbett, James J.; Brys, Rein; Cassey, Phillip; Correa, Nancy; Deveney, Marty R.; Egan, Scott P.; Fisher, Joshua P.; vanden Hooff, Rian; Knapp, Charles R.; Leong, Sandric Chee Yew; Neilson, Brian J.; Paolucci, Esteban M.; Pfrender, Michael E.; Pochardt, Meredith R.; Prowse, Thomas A. A.; Rumrill, Steven S.; Scianni, Chris; Sylvester, Francisco; Tamburri, Mario N.; Therriault, Thomas W.; Yeo, Darren C. J.; Lodge, David M.The spread of nonindigenous species by shipping is a large and growing global problem that harms coastal ecosystems and economies and may blur coastal biogeographical patterns. This study coupled eukaryotic environmental DNA (eDNA) metabarcoding with dissimilarity regression to test the hypothesis that ship-borne species spread homogenizes port communities. We first collected and metabarcoded water samples from ports in Europe, Asia, Australia and the Americas. We then calculated community dissimilarities between port pairs and tested for effects of environmental dissimilarity, biogeographical region and four alternative measures of ship-borne species transport risk. We predicted that higher shipping between ports would decrease community dissimilarity, that the effect of shipping would be small compared to that of environment dissimilarity and shared biogeography, and that more complex shipping risk metrics (which account for ballast water and stepping-stone spread) would perform better. Consistent with our hypotheses, community dissimilarities increased significantly with environmental dissimilarity and, to a lesser extent, decreased with ship-borne species transport risks, particularly if the ports had similar environments and stepping-stone risks were considered. Unexpectedly, we found no clear effect of shared biogeography, and that risk metrics incorporating estimates of ballast discharge did not offer more explanatory power than simpler traffic-based risks. Overall, we found that shipping homogenizes eukaryotic communities between ports in predictable ways, which could inform improvements in invasive species policy and management. We demonstrated the usefulness of eDNA metabarcoding and dissimilarity regression for disentangling the drivers of large-scale biodiversity patterns. We conclude by outlining logistical considerations and recommendations for future studies using this approach.Item Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America(Springer, 2017) Larson, Eric R.; Renshaw, Mark A.; Gantz, Crysta A.; Umek, John; Chandra, Sudeep; Lodge, David M.; Egan, Scott P.We report results of a study that made reciprocal comparisons of environmental DNA (eDNA) assays for two major invasive crayfishes between their disparate invasive ranges in North America. Specifically, we tested for range expansions of the signal crayfish Pacifastacus leniusculus (Dana, 1852) into the Laurentian Great Lakes region known to be invaded by the rusty crayfish Orconectes rusticus (Girard, 1852), as well as for the invasion of O. rusticus into large lakes of California and Nevada, US known to be invaded by P. leniusculus. We compared eDNA detections to historic localities for O. rusticus within the Great Lakes, and to recent sampling for presence/absence and relative abundance of P. leniusculus in California and Nevada via overnight sets of baited traps. We successfully detected O. rusticus eDNA at six sites from the Great Lakes and P. leniusculus from six of seven lakes where it was known to occur in California and Nevada, but did not detect any range expansions by either species across the North American continent. eDNA appears suitable to detect benthic arthropods from exceptionally large lakes, and will likely be useful in applications for monitoring of new biological invasions into these and other freshwater and marine habitats.Item Environmental DNA (eDNA) detects the invasive crayfishesﾠOrconectes rusticusﾠandﾠPacifastacus leniusculusﾠin large lakes of North America(Springer, 2017) Larson, Eric R.; Renshaw, Mark A.; Gantz, Crysta A.; Umek, John; Chandra, Sudeep; Lodge, David M.; Egan, Scott P.We report results of a study that made reciprocal comparisons of environmental DNA (eDNA) assays for two major invasive crayfishes between their disparate invasive ranges in North America. Specifically, we tested for range expansions of the signal crayfishﾠPacifastacus leniusculusﾠ(Dana, 1852) into the Laurentian Great Lakes region known to be invaded by the rusty crayfishﾠOrconectes rusticusﾠ(Girard, 1852), as well as for the invasion ofﾠO. rusticusﾠinto large lakes of California and Nevada, US known to be invaded byﾠP. leniusculus.ﾠWe compared eDNA detections to historic localities forﾠO. rusticusﾠwithin the Great Lakes, and to recent sampling for presence/absence and relative abundance ofﾠP. leniusculusﾠin California and Nevada via overnight sets of baited traps. We successfully detectedﾠO. rusticusﾠeDNA at six sites from the Great Lakes andﾠP. leniusculusﾠfrom six of seven lakes where it was known to occur in California and Nevada, but did not detect any range expansions by either species across the North American continent. eDNA appears suitable to detect benthic arthropods from exceptionally large lakes, and will likely be useful in applications for monitoring of new biological invasions into these and other freshwater and marine habitats.Item Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances(Wiley, 2016) Dougherty, Matthew M.; Larson, Eric R.; Renshaw, Mark A.; Gantz, Crysta A.; Egan, Scott P.; Erickson, Daniel M.; Lodge, David M.1. Early detection is invaluable for the cost-effective control and eradication of invasive species, yet many traditional sampling techniques are ineffective at the low population abundances found at the onset of the invasion process. Environmental DNA (eDNA) is a promising and sensitive tool for early detection of some invasive species, but its efficacy has not yet been evaluated for many taxonomic groups and habitat types. 2. We evaluated the ability of eDNA to detect the invasive rusty crayfish Orconectes rusticus and to reflect patterns of its relative abundance, in upper Midwest, USA, inland lakes. We paired conventional baited trapping as a measure of crayfish relative abundance with water samples for eDNA, which were analysed in the laboratory with a qPCR assay. We modelled detection probability for O. rusticus eDNA using relative abundance and site characteristics as covariates and also tested the relationship between eDNA copy number and O. rusticus relative abundance. 3. We detected O. rusticus eDNA in all lakes where this species was collected by trapping, down to low relative abundances, as well as in two lakes where trap catch was zero. Detection probability of O. rusticus eDNA was well predicted by relative abundance of this species and lake water clarity. However, there was poor correspondence between eDNA copy number and O. rusticus relative abundance estimated by trap catches. 4. Synthesis and applications. Our study demonstrates a field and laboratory protocol for eDNA monitoring of crayfish invasions, with results of statistical models that provide guidance of sampling effort and detection probabilities for researchers in other regions and systems. We propose eDNA be included as a tool in surveillance for invasive or imperiled crayfishes and other benthic arthropods.Item Evidence for spatial clines and mixed geographic modes of speciation for North American cherry‐infesting Rhagoletis (Diptera: Tephritidae) flies(Wiley, 2020) Doellman, Meredith M.; Jean, Gilbert Saint; Egan, Scott P.; Powell, Thomas H.Q.; Hood, Glen Ray; Schuler, Hannes; Bruzzese, Daniel J.; Glover, Mary M.; Smith, James J.; Yee, Wee L.; Goughnour, Robert B.; Rull, Juan; Aluja, Martin; Feder, Jeffrey L.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.Item Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow(Wiley, 2015) Egan, Scott P.; Ragland, Gregory J.; Assour, Lauren; Powell, Thomas H.Q.; Hood, Glen Ray; Emrich, Scott; Nosil, Patrik; Feder, Jeffrey L.Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple host races of Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary speciation-with-gene-flow. Allele frequency shifts of 32ﾠ455 SNPs induced in a selection experiment based on host phenology were genome wide and highly concordant with genetic divergence between co-occurring apple and hawthorn flies in nature. This striking genome-wide similarity between experimental and natural populations of R. pomonella underscores the importance of ecological selection at early stages of divergence and calls for further integration of studies of eco-evolutionary dynamics and genome divergence.Item Genomic Differentiation during Speciation-with-Gene-Flow: Comparing Geographic and Host-Related Variation in Divergent Life History Adaptation in Rhagoletis pomonella(MDPI, 2018) Doellman, Meredith M.; Ragland, Gregory J.; Hood, Glen Ray; Meyers, Peter J.; Egan, Scott P.; Powell, Thomas H.Q.; Lazorchak, Peter; Glover, Mary M.; Tait, Cheyenne; Schuler, Hannes; Hahn, Daniel A.; Berlocher, Stewart H.; Smith, James J.; Nosil, Patrik; Feder, Jeffrey L.A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a geographic survey of genomic variation across four sites where apple and hawthorn flies co-occur from north to south in the Midwestern USA. The results demonstrated that the majority of the genome showing significant geographic and host-related variation can be accounted for by initial diapause intensity and eclosion time. Local genomic differences between sympatric apple and hawthorn flies were subsumed within broader geographic clines; allele frequency differences within the races across the Midwest were two to three-fold greater than those between the races in sympatry. As a result, sympatric apple and hawthorn populations displayed more limited genomic clustering compared to geographic populations within the races. The findings suggest that with reduced gene flow and increased selection on diapause equivalent to that seen between geographic sites, the host races may be recognized as different genotypic entities in sympatry, and perhaps species, a hypothesis requiring future genomic analysis of related sibling species to R. pomonella to test. Our findings concerning the way selection and geography interplay could be of broad significance for many cases of earlier stages of divergence-with-gene flow, including (1) where only modest increases in geographic isolation and the strength of selection may greatly impact genetic coupling and (2) the dynamics of how spatial and temporal standing variation is extracted by selection to generate differences between new and discrete units of biodiversity.Item Geographic and Ecological Dimensions of Host Plant-Associated Genetic Differentiation and Speciation in theﾠRhagoletis cingulataﾠ(Diptera: Tephritidae) Sibling Species Group(MDPI, 2019) Doellman, Meredith M.; Schuler, Hannes; Jean Saint, Gilbert; Hood, Glen R.; Egan, Scott P.; Powell, Thomas H.Q.; Glover, Mary M.; Bruzzese, Daniel J.; Smith, James J.; Yee, Wee L.; Goughnour, Robert B.; Rull, Juan; Aluja, Martin; Feder, Jeffrey L.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.Item Hybridization and the spread of the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), in the northwestern United States(Wiley, 2015) Arcella, Tracy; Hood, Glen Ray; Powell, Thomas H.Q.; Sim, Sheina B.; Yee, Wee L.; Schwarz, Dietmar; Egan, Scott P.; Goughnour, Robert B.; Smith, James J.; Feder, Jeffrey L.Hybridization may be an important process interjecting variation into insect populations enabling host plant shifts and the origin of new economic pests. Here, we examine whether hybridization between the native snowberry-infesting fruit fly Rhagoletis zephyria (Snow) and the introduced quarantine pest R. pomonella (Walsh) is occurring and may aid the spread of the latter into more arid commercial apple-growing regions of central Washington state, USA. Results for 19 microsatellites implied hybridization occurring at a rate of 1.44% per generation between the species. However, there was no evidence for increased hybridization in central Washington. Allele frequencies for seven microsatellites in R. pomonella were more ‘R. zephyria-like’ in central Washington, suggesting that genes conferring resistance to desiccation may be adaptively introgressing from R. zephyria. However, in only one case was the putatively introgressing allele from R. zephyria not found in R. pomonella in the eastern USA. Thus, many of the alleles changing in frequency may have been prestanding in the introduced R. pomonella population. The dynamics of hybridization are therefore complex and nuanced for R. pomonella, with various causes and factors, including introgression for a portion, but not all of the genome, potentially contributing to the pest insect's spread.Item Impact of a natural disturbance on the performance and microbial communities in a full-scale constructed wetland for industrial wastewater treatment(Frontiers Media S.A., 2023) Hollstein, Marielle; Comerford, Mattheau; Uhl, Michael; Abel, Michael; Egan, Scott P.; Stadler, Lauren B.Constructed Wetlands (CWs) are a cost-effective, versatile and sustainable choice for wastewater treatment. In these environments, microbial communities play a significant role in pollutant removal. However, little is known about how microbial communities in full-scale CWs contribute to maintaining water quality or how their dynamics change in response to pulse disturbances such as fire or freezes. Furthermore, few studies have examined the relationship between CW microbial community structure and performance in full-scale industrial operations. We characterized the water-column and leaf-litter layer microbial communities in a 110-acre free water surface CW that provides tertiary wastewater treatment to a plastics manufacturing plant. The CW’s sampling campaign was conducted over a 12-month period that included Winter Storm Uri, a 100-year freeze event. Analysis of 16S rRNA gene amplicon sequences revealed that the bacterial communities experienced a temporal shift. There was also a shift in microbial community structure between the influent and the first segment of the CW. However, no differences in microbial community structure were observed in the second segment of the CW. There was a negative association between microbial community diversity and chlorophyll a, as well as microbial community diversity and total suspended solids (TSS); demonstrating an increase in microbial biodiversity as water quality improved throughout the CW. Six months after the freeze, CW performance in terms of removal of water quality constituents began to return to former removal trends. Yet, there was still a significant difference in microbial community structure within the CW relative to the previous year. This suggests CW functional resilience despite a shift in microbial community structure in the wetland.