Biology subjects

Egan, S. P.

Publications and source records attributed to Egan, S. P..

13 recordsLinked to original sources

bioRxiv2025

A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes (ACTG) program. Originating from a clone of Auburn Universitys historic "Toomers Oak," this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.

genomics↗

bioRxiv2025

Measuring the Strength of Spatial Sorting

Empirical work suggests that spatial sorting--a mechanism of evolutionary change fueled by spatial assortment of phenotypes--may lead to phenotypic shifts on ecological timescales. However, we currently lack theoretical tools to measure the strength of spatial sorting, as we do to measure the strength of natural selection. To address this gap, we present a quantitative genetics model and identify an evolutionary parameter in the model to measure the strength of spatial sorting. This parameter, the standardized sorting gradient, is structurally akin to the standardized selection gradient, commonly used to measure the strength of natural selection. To show the utility of our approach, we analyzed wing-morphology data of soapberry bugs (Jadera haematoloma) recolonizing flooded habitats extirpated by a hurricane. We found that the estimated strength of spatial sorting ranked in the top ten percentile of standardized selection gradients documented in the scientific literature. Our results underscore that, like natural selection, spatial sorting, too, can yield rapid evolution after extreme events.

evolutionary biology↗

bioRxiv2023

A genomic test of subspecies in the Eunota togata species group (Coleoptera: Cicindelidae): Morphology masks evolutionary relationships and taxonomy

Most of the worlds biodiversity is described primarily or exclusively using morphological traits that may not always reflect the true evolutionary units. Accurate taxonomy is critical for conservation efforts and re-evaluation of traditional taxonomy may often be warranted since species and subspecies are frequently the focus of conservation and faunistic studies. Here, we test comprehensive taxonomic hypotheses of morphologically defined subspecies in the tiger beetle, Eunota togata (LaFerte-Senectere, 1841). The four recognized subspecies were delineated based mainly on the dorsal coloration and extent of white markings termed maculations. We combine inferences from mtDNA genealogies and genome-wide multilocus data to elucidate the evolutionary relationships within the group and assess the taxonomic implications. Three of the four subspecific taxa delineated by morphology were not supported by the genomic or mtDNA data. In fact, the species-level diversity in this group was underestimated, as E. togata was found to represent three well-supported distinct species in all genetic analyses. Emerging from these analyses, we also document an intriguing example of convergent evolution in lighter colored E. togata adapting to similar white sand backgrounds. Our collective work underscores the importance of integrating molecular methods with morphology for species and subspecies delimitation and conservation.

evolutionary biology↗

bioRxiv2022

The arthropod associates of 155 North American cynipid oak galls

The identities of most arthropod associates of cynipid-induced oak galls in the western Palearctic are generally known. However, a comprehensive accounting of associates has been performed for only a small number of the galls induced by the estimated 700 species of cynipid gall wasp in the Nearctic. This gap in knowledge stymies many potential studies of diversity, coevolution, and community ecology, for which oak gall systems are otherwise ideal models. We report rearing records of insects and other arthropods from more than 527,306 individual galls representing 201 different oak gall types collected from 32 oak tree species in North America. Of the 201 gall types collected, 155 produced one or more animals. A total of 151,075 animals were found in association with these 155 gall types, and of these 61,044 (40.4%) were gall wasps while 90,031 (59.6%) were other arthropods. We identified all animals to superfamily, family, or, where possible, to genus. We provide raw numbers and summaries of collections, alongside notes on natural history, ecology, and previously published associations for each taxon. For eight common gall-associated genera (Synergus, Ceroptres, Euceroptres, Ormyrus, Torymus, Eurytoma, Sycophila, and Euderus), we also connect rearing records to gall wasp phylogeny, geography, and ecology - including host tree and gall location (host organ), and their co-occurrence with other insect genera. Though the diversity of gall wasps and the large size of these communities is such that many Nearctic oak gall-associated insects still remain undescribed, this large collection and identification effort should facilitate the testing of new and varied ecological and evolutionary hypotheses in Nearctic oak galls.

zoology↗

bioRxiv2022

Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both.

Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ~1000 species of phytophagous insects that induce gall formation on various organs of trees in the family Fagacae, -- primarily the oaks (genus Quercus; ~435 sp). The association of oak gall wasps with oaks is ancient (~50 my), and most oak species are galled by one or more gall wasp species. Despite the diversity of both gall wasp species and their plant associations, previous phylogenetic work has not identified a strong signal of host plant shifting among oak gall wasps. However, most emphasis has been on the Western Palearctic and not the Nearctic where both oaks and oak gall wasps are considerably more species rich and where oaks are more phylogenetically diverse. We collected 86 species of Nearctic oak gall wasps from 10 of the 14 major clades of Nearctic oaks and sequenced >1000 Ultra Conserved Elements (UCEs) and flanking sequences to infer wasp phylogenies. We assessed the relationships of Nearctic gall wasps to one another and, by leveraging previously published UCE data, to the Palearctic fauna. We then used phylogenies to infer historical patterns of shifts among host tree species and tree organs. Our results indicate that oak gall wasps have moved between the Palearctic and Nearctic at least four times, that some Palearctic clades have their proximate origin in the Nearctic, and that gall wasps have shifted within and between oak tree sections, subsections, and organs considerably more often than the analysis of previous data have suggested. Given that host shifts have been demonstrated to drive reproductive isolation between host-associated populations in other phytophagous insects, our analyses of Nearctic gall wasps suggest that host shifts are key drivers of speciation in this clade, especially in hotspots of oak diversity. Though formal assessment of this hypothesis requires further study, two putatively oligophagous gall wasp species in our dataset show signals of host-associated genetic differentiation unconfounded by geographic distance, suggestive of barriers to gene flow associated with the use of alternative host plants.

evolutionary biology↗

bioRxiv2022

Asymmetric habitat isolation and sexual isolation predicted by the cost of migration and hybridization generate novel signatures of reinforcing selection

While ecology and geography can play important roles in the evolution of reproductive isolation across the speciation continuum, the few studies to date examining their relative contributions have largely focused on the early stages of speciation. Studies exploring the evolution of multiple reproductive barriers among divergent lineages, where speciation is nearly complete, are also needed to gain a fuller understanding of the mechanisms promoting and constraining the speciation process. We examine the later stage of speciation by comparing the strength of habitat isolation and sexual isolation among closely related species of gall-forming wasps in the genus Belonocnema experiencing divergent ecologies due to different hos plant use and variable rates of migration due to geography. We found that the strength of both habitat isolation and sexual isolation is lowest among allopatric species pairs with the same host plant association, followed by allopatric species with different host plant association, and highest between sympatric species with different host-plant associations. This pattern strongly suggests that both ecology due to divergent host use, and geography contribute to the evolution of these two reproductive barriers. Notably, reproductive character displacement contributes to nearly half of the strength of both habitat isolation and sexual isolation in sympatry.

evolutionary biology↗

bioRxiv2021

Ormyrus labotus Walker (Hymenoptera: Ormyridae): another generalist that should not be a generalist is not a generalist

Several recent reappraisals of supposed generalist parasite species have revealed hidden complexes of species, each with considerably narrower host ranges. Parasitic wasps that attack gall-forming insects on plants have life history strategies that are thought to promote specialization, and though many species are indeed highly specialized, others have been described as generalist parasites. Ormyrus labotus Walker (Hymenoptera: Ormyridae) is one such apparent generalist, with rearing records spanning more than 65 host galls associated with a diverse set of oak tree species and plant tissues. We pair a molecular approach with morphology, host ecology, and phenological data from across a wide geographic sample to test the hypothesis that this supposed generalist is actually a complex of several more specialized species. We find 16-18 putative species within the morphological species O. labotus, each reared from only 1-6 host gall types, though we identify no single unifying axis of specialization. We also find cryptic habitat specialists within two other named Ormyrus species. Our study suggests that caution should be applied when considering host ranges of parasitic insects described solely by morphological traits, particularly given their importance as biocontrol organisms and their role in biodiversity and evolutionary studies.

evolutionary biology↗

bioRxiv2021

Global port survey quantifies commercial shippings effect on biodiversity

Spread of nonindigenous organisms by shipping is one of the largest threats to coastal ecosystems. Limited monitoring and understanding of this phenomenon currently hinder development of effective prevention policies. Surveying ports in North America, South America, Europe, Southeast Asia, and Australia we explored environmental DNA community profiles evident of ship-born species spread. We found that community similarities between ports increased with the number of ship voyages, particularly if the ports had similar environments, and when indirect stepping-stone connections were considered. We also found 57 known non-indigenous taxa, some in hitherto unreported locations. We demonstrate the usefulness of eDNA-based tools for global biodiversity surveys, and highlight that shipping homogenizes biodiversity in predictable that could inform policy and management.

ecology↗

bioRxiv2021

Is energetics or competition a stronger driver of male smallmouth bass seasonal reproductive timing?

Intraspecific competitive ability is often associated with body size and has been shown to influence reproductive timing in many species. However, energetic constraints provide an alternative explanation for size-related differences of reproductive timing. In temperate fishes that experience a winter starvation period, for instance, a negative allometric relationship between body size and winter energy loss might explain why larger males spawn earlier in a season than smaller males, especially in fishes that exhibit paternal care, which is energetically costly and limits parental foraging opportunities. Male smallmouth bass, Micropterus dolomieu, defend nesting territories in which they care for offspring over an extended period. In northern populations, males rely on energy reserves over a winter starvation period and in spring must recoup energy losses before initiating reproduction, making them ideal systems in which to study contributions of competition and energetic allometry on differences of reproductive timing. Here, we harness data on parental male M. dolomieu from a 10-year study and show that larger males required fewer degree days-a measure of thermal energy experienced-in spring before they spawned each year and that the time of peak seasonal reproduction in the population was negatively related to the number of degree days accumulated before reproduction started. Furthermore, we found that growth of individual males between seasons better predicted changes in timing of reproduction than changes in size relative to competitors. Together, these results suggest that timing of reproduction in this population is more strongly influenced by energetic constraints than size-based competition amongst males.

animal behavior and cognition↗

bioRxiv2020

The genomics of trait combinations and their influence on adaptive divergence

Understanding rapid adaptation requires quantifying natural selection on traits and elucidating the genotype-phenotype relationship for those traits. However, recent studies have often failed to predict the direction of adaptive allelic variation in natural populations from laboratory studies. Here, we test for genomic signatures of genetic correlations to illustrate how multifarious, correlational selection may drive counterintuitive patterns of population divergence in the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae). Apple-infesting populations with relatively early emerging adults have recently evolved from hawthorn-infesting populations consisting of relatively later emerging adults. Multiple studies have reported a paradoxical relationship between population differentiation and seasonal timing, as determined by the timing of diapause termination; alleles associated with late termination occur at higher frequencies in the earlier emerging apple-infesting populations compared to hawthorn-infesting populations. We present evidence that historical selection on diapause termination and another trait, initial diapause intensity, over geographic gradients generated genetic correlations between the traits in a direction antagonistic to contemporary selection on apple-infesting populations. Single nucleotide polymorphism in genomic regions of high linkage disequilibrium associated strongly with diapause termination and intensity, population divergence, geography, and evolutionary responses in laboratory selection experiments. These associations were consistent with geographically variable selection and with correlated evolutionary responses driving higher frequencies of late-associated alleles in the early emerging apple race. In contrast, loci associated only with diapause termination showed the expected pattern (more early-associated alleles in the apple race) in half of the population pairs. Our results suggest that selection on loci demonstrating antagonistic pleiotropy may often shape genomic footprints of rapid adaptation.

evolutionary biology↗

bioRxiv2020

Invertebrate Community Associated with the Asexual Generation of Bassettia pallida Ashmead (Hymenoptera: Cynipidae)

Cynipid gall wasps play an important role in structuring oak invertebrate communities. Wasps in the Cynipini tribe typically lay their eggs in oaks (Quercus L.), and induce the formation of a "gall", which is a tumor-like growth of plant material that surrounds the developing wasp. As the wasp develops, the cynipid and its gall are attacked by a diverse community of natural enemies, including parasitoids, hyperparasitoids, and inquilines. Determining what structures these species-rich natural enemy communities across cynipid gall wasp species is a major question in gall wasp biology. Additionally, gall wasps are ecosystem engineers, as the abandoned gall is used by other invertebrates. The gall-associated insect communities residing on live oaks (Quercus geminata Small and Q. virginiana Mill.) are emerging as a model system for answering ecological and evolutionary questions ranging from community ecology to the evolution of new species. Documenting the invertebrates associated with cynipids in this system will expand our understanding of the mechanisms influencing eco-evolutionary processes, record underexplored axes of biodiversity, and facilitate future work. Here, we present the community of natural enemies and other associates of the asexual generation of the crypt gall wasp, Bassettia pallida Ashmead. We compare the composition of this community to communities recently documented from two other cynipid gall wasps specializing on live oaks along the U.S. Gulf coast, Disholcaspis quercusvirens Ashmead and Belonocnema treatae Mayr. B. pallida and their crypts support a diverse arthropod community, including over 25 parasitoids, inquilines, and other associated invertebrates spanning 5 orders and 16 families.

ecology↗

bioRxiv2019

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition, but most studies to date have evaluated its effectiveness in single habitats and for conspicuous taxonomic groups in temperate ecosystems. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean.

ecology↗

bioRxiv2019

A keeper of many crypts: the parasitoid Euderus set manipulates the behavior of a taxonomically diverse array of oak gall wasp species

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 hosts behavior, the complexity of that manipulation may further limit the parasites host species range. The recently described crypt-keeper wasp, Euderus set, changes the behavior of the gall wasp Bassettia pallida such that B. pallida chews an incomplete exit hole in the side of its larval chamber and \"plugs\" that hole with its head. E. set benefits from this head plug, as it facilitates the escape of the parasitoid from the crypt after it completes development. Here, we ask whether this behavioral manipulator is limited to Bassettia hosts. We find that E. set attacks and manipulates the behavior of at least six additional gall wasp species, and that these hosts are taxonomically diverse. Interestingly, each of E. sets hosts has converged upon similarities in the extended phenotypes they induce in their plant hosts: the galls they induce on oaks share characters that may make them vulnerable to attack by E. set. Behavioral manipulation in this parasitoid system may be less important to its host range than other dimensions of the host-parasitoid interaction, like the hosts physical defenses.

ecology↗