@article{madeleine_duffy_johnson_2025, title={Does Predation Environment Affect Repeated Responses to Predation Cues in the Fish Brachyrhaphis rhabdophora?}, url={http://dx.doi.org/10.1016/j.beproc.2025.105165}, DOI={10.1016/j.beproc.2025.105165}, journal={Behavioural Processes}, author={Madeleine and Duffy, Alexandra G. and Johnson, Jerald B.}, year={2025}, month={Feb} }
 @article{duffy_pew_johnson_2025, title={Mate choice copying behaviour in the livebearing fish Brachyrhaphis rhabdophora}, url={https://doi.org/10.1016/j.anbehav.2025.123148}, DOI={10.1016/j.anbehav.2025.123148}, journal={Animal Behaviour}, author={Duffy, Alexandra G. and Pew, Megan Gunn and Johnson, Jerald B.}, year={2025}, month={Apr} }
 @article{gould_fraser_parker_nakagawa_griffith_vesk_fidler_hamilton_abbey-lee_abbott_et al._2025, title={Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology}, volume={23}, ISSN={1741-7007}, url={http://dx.doi.org/10.1186/s12915-024-02101-x}, DOI={10.1186/s12915-024-02101-x}, abstractNote={Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small "many analyst" study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.}, number={1}, journal={BMC Biology}, publisher={Springer Science and Business Media LLC}, author={Gould, Elliot and Fraser, Hannah S. and Parker, Timothy H. and Nakagawa, Shinichi and Griffith, Simon C. and Vesk, Peter A. and Fidler, Fiona and Hamilton, Daniel G. and Abbey-Lee, Robin N. and Abbott, Jessica K. and et al.}, year={2025}, month={Feb} }
 @article{duffy_johnson_2024, title={Behavioral response to chemical cues from injured conspecifics in the livebearing fish, Brachyrhaphis rhabdophora}, url={https://doi.org/10.1111/eth.13490}, DOI={10.1111/eth.13490}, abstractNote={Abstract Predator–prey dynamics have led to a strong selection of prey's ability to detect and respond to information about the risk environment. Further, intrinsic factors, such as sex, may cause prey to perceive and respond to information differently. Chemical alarm cues from injured conspecifics are a classic example of how prey have evolved to use publicly available information to shape their behavior and enhance fitness, yet sex‐specific alarm reactions are rarely considered. The purpose of our study was to compare how males and females respond to conspecific chemical alarm cues in the livebearing fish species, Brachyrhaphis rhabdophora . Furthermore, we tested males and females from populations with a high‐ or low‐predation environment. Brachyrhaphis rhabdophora showed strong alarm reactions, but contrary to our predictions, showed limited variation due to sex or predation environment. We found that males and females from both populations displayed lower activity levels and increased their swimming depth when exposed to an alarm cue, despite variable and consistent baseline behaviors among individuals. These data further contribute to our understanding of what factors shape the evolution of behavioral responses to chemical alarm cues in fishes.}, journal={Ethology}, author={Duffy, Alexandra G. and Johnson, Jerald B.}, year={2024}, month={Sep} }
 @article{powell_saxton_duffy_bybee_cameron_cline_mcelrath_gimmel_johnson_leschen_et al._2024, title={Repeated feeding guild evolution: the impact of competition on diversification}, volume={3}, ISSN={2752-938X}, url={http://dx.doi.org/10.1093/evolinnean/kzae011}, DOI={10.1093/evolinnean/kzae011}, abstractNote={Abstract Adaptive zones are defined as ecological opportunities for lineages to diversify. Cucujoid beetles provide a unique system to investigate adaptive zones, specifically the interplay between factors that may predict diversity and mechanisms such as competition that may limit diversification. Using a taxon-rich, time-calibrated phylogeny of cucujoid beetles, we report clade ages in conjunction with estimated ages for major shifts in feeding ecology within this group. With these ages, we calculate the delay in time-to-colonization of food resources compared with the extant diversity of each group. We uncovered a pattern of increased lineage diversity specifically with shifts to novel food resources probably devoid of competition from other cucujoid beetles. Neither diversity of the food resource, age of the food resource, nor age of the beetle lineage were able to predict species diversity of these groups. Our results provide evidence that shifting to a resource first is a strong predictor of extant diversity.}, number={1}, journal={Evolutionary Journal of the Linnean Society}, publisher={Oxford University Press (OUP)}, author={Powell, Gareth S and Saxton, Natalie A and Duffy, Alexandra G and Bybee, Seth M and Cameron, Stephen L and Cline, Andrew R and McElrath, Thomas C and Gimmel, Matthew L and Johnson, Jerald B and Leschen, Richard A B and et al.}, year={2024}, month={Jan} }
 @article{garretson_cuddy_duffy_forkner_2023, title={Citizen science data reveal regional heterogeneity in phenological response to climate in the large milkweed bug, <i>Oncopeltus fasciatus}, volume={13}, ISSN={2045-7758 2045-7758}, url={http://dx.doi.org/10.1002/ece3.10213}, DOI={10.1002/ece3.10213}, abstractNote={Regional populations of geographically widespread species may respond to different environmental factors across the species' range, generating divergent effects of climate change on life-history phenology. Using thousands of citizen science observations extracted from iNaturalist and associated with corresponding temperature, precipitation, elevation, and daylength information, we examined the drivers of adult mating and of nymphal phenology, development, and group size for populations of the large milkweed bug, Oncopeltus fasciatus, in different ecoregions. Research-grade iNaturalist images were correctly identified 98.3% of the time and yielded more than 3000 observations of nymphal groups and 1000 observations of mating adults spanning 18 years. Mating phenology showed distinct regional patterns, ranging from year-round mating in California to temporally restricted mating in the Great Lakes Northeastern Coast ecoregion. Relative temperature increases of 1°C for a given daylength expanded the mating season by more than a week in western ecoregions. While increases in relative temperature delayed mating phenology in all ecoregions, greater winter precipitation advanced mating in the California ecoregion. In the eastern ecoregions, nymphal phenology was delayed by increases in summer rainfall but was advanced by relative temperature increases, whereas in western regions, relative temperature increases delayed nymphal phenology. Furthermore, accumulated growing degree days (AGDD) was a poor predictor of developmental progression, as we found a positive but weak correlation between AGDD and age structure only for the Appalachian Southeast North America and the Great Lakes Northern Coast ecoregions. These complex phenological responses of O. fasciatus are just one example of how populations may be differentially susceptible to a diversity of climatic effects; using data across a species' whole distribution is critical for exposing regional variations, especially for species with large, continental-scale ranges. This study demonstrates the potential of photodocumented biodiversity data to aid in the monitoring of life history, host plant-insect interactions, and climate responsiveness.}, number={7}, journal={Ecology and Evolution}, publisher={Wiley}, author={Garretson, Alexis and Cuddy, Tedra and Duffy, Alexandra G. and Forkner, Rebecca E.}, year={2023}, month={Jul} }
 @inproceedings{henderson_mendez_mccaffrey_ruckman_duffy_hughes_2023, title={Exploring the relationship between melanic coloration and aggression in Drosophila melanogaster}, booktitle={Florida State University. Undergraduate Research Symposium}, author={Henderson, Taylor and Mendez, Paulina Montes and McCaffrey, Katelyn and Ruckman, Sarah and Duffy, Alexandra and Hughes, Kimberly}, year={2023}, month={Mar} }
 @inproceedings{tan_crews_romero_ruckman_duffy_hughes_2023, title={The correlation between coloration and aggression in Drosophila melanogaster}, booktitle={Florida State University. Undergraduate Research Symposium}, author={Tan, Nicholas and Crews, Addison and Romero, Anthony and Ruckman, Sarah and Duffy, Alexandra and Hughes, Kimberly}, year={2023}, month={Mar} }
 @inproceedings{duffy_ingley_williams_johnson_2022, title={Reinforcement or hybridization? Puzzling mate choice behavior in sympatric populations of Brachyrhaphis sister species}, booktitle={Conference of Poeciliid Biologists}, author={Duffy, A.G. and Ingley, S. and Williams, T. and Johnson, J.B.}, year={2022} }
 @article{duffy_richmond_2020, title={Hunting Billbug Sphenophorus venatus (Coleoptera: Dryophthoridae) adult feeding and attraction to warm- and cool-season turfgrasses}, volume={53}, ISSN={0090-0222}, url={http://dx.doi.org/10.22543/0090-0222.2359}, DOI={10.22543/0090-0222.2359}, abstractNote={The hunting billbug Sphenophorus venatus Say (Coleoptera: Curculionidae: Dryophothorinae) is a generalist stem-boring pest on warm- and cool-season grasses. The objectives of this work were to (1) investigate adult feeding preference for four common turfgrass host species and (2) explore whether adults are attracted to the volatile odors emitted by these grasses. In laboratory feeding assays, S. venatus adults preferred zoysiagrass Zoysia japonica Steud ‘Meyer’ over all other species tested: Bermudagrass Cynodon dactylon ‘Patriot’, Kentucky bluegrass Poa pratensis ‘Barron’, and creeping bentgrass Agrostis stolonifera ‘Penncross’. In y-tube olfactometry assays, only males were attracted to bermudagrass. Our findings suggest that although S. venatus odor recognition potentially influence dispersal and host-seeking behavior, it may not ultimately determine feeding preference, where more close-range cues may be important. Further investigations on the mechanisms that cause variation in these behaviors could aid in the pursuit of more sustainable management techniques, such as strategic plant species selection and development of synthetic semiochemical lures for monitoring and trapping.}, number={1}, journal={The Great Lakes Entomologist}, publisher={Valparaiso University}, author={Duffy, Alexandra Grace and Richmond, Douglas S}, year={2020}, month={Sep} }
 @article{mbaluto_ayelo_duffy_erdei_tallon_xia_caballero-vidal_spitaler_szelényi_duarte_et al._2020, title={Insect chemical ecology: chemically mediated interactions and novel applications in agriculture}, volume={14}, ISSN={1872-8855 1872-8847}, url={http://dx.doi.org/10.1007/s11829-020-09791-4}, DOI={10.1007/s11829-020-09791-4}, abstractNote={Insect chemical ecology (ICE) evolved as a discipline concerned with plant-insect interactions, and also with a strong focus on intraspecific pheromone-mediated communication. Progress in this field has rendered a more complete picture of how insects exploit chemical information in their surroundings in order to survive and navigate their world successfully. Simultaneously, this progress has prompted new research questions about the evolution of insect chemosensation and related ecological adaptations, molecular mechanisms that mediate commonly observed behaviors, and the consequences of chemically mediated interactions in different ecosystems. Themed meetings, workshops, and summer schools are ideal platforms for discussing scientific advancements as well as identifying gaps and challenges within the discipline. From the 11th to the 22nd of June 2018, the 11th annual PhD course in ICE was held at the Swedish University of Agricultural Sciences (SLU) Alnarp, Sweden. The course was made up of 35 student participants from 22 nationalities (Fig. 1a) as well as 32 lecturers. Lectures and laboratory demonstrations were supported by literature seminars, and four broad research areas were covered: (1) multitrophic interactions and plant defenses, (2) chemical communication focusing on odor sensing, processing, and behavior, (3) disease vectors, and (4) applied aspects of basic ICE research in agriculture. This particular article contains a summary and brief synthesis of these main emergent themes and discussions from the ICE 2018 course. In addition, we also provide suggestions on teaching the next generation of ICE scientists, especially during unprecedented global situations.}, number={6}, journal={Arthropod-Plant Interactions}, publisher={Springer Science and Business Media LLC}, author={Mbaluto, Crispus M. and Ayelo, Pascal M. and Duffy, Alexandra G. and Erdei, Anna L. and Tallon, Anaїs K. and Xia, Siyang and Caballero-Vidal, Gabriela and Spitaler, Urban and Szelényi, Magdolna O. and Duarte, Gonçalo A. and et al.}, year={2020}, month={Nov}, pages={671–684} }
 @article{powell_cline_duffy_zaspel_2020, title={Phylogeny and reclassification of Carpophilinae (Coleoptera: Nitidulidae), with insights into the origins of anthophily}, volume={189}, ISSN={0024-4082 1096-3642}, url={http://dx.doi.org/10.1093/zoolinnean/zlaa001}, DOI={10.1093/zoolinnean/zlaa001}, abstractNote={Abstract The family Nitidulidae is known for its diverse life histories, with some species considered economically detrimental pests, while others perform critical ecosystem functions. Despite this, their evolutionary relationships still lack support and understanding. A robust phylogenetic hypothesis and revised taxonomic classification for this group, particularly the subfamily Carpophilinae, could help delineate key lineages for assessing the evolution of both beneficial and pestiferous traits. The most complete molecular phylogeny of Carpophilinae to date, based on 37 ingroup taxa, covering four of the six recognized genera, is presented. Six genetic loci were used (16S, 18S, 28S, COI, H3 and ITS2), providing a total of 3500 bp of data. These data were generated using a novel method discussed here: wide-seq. Wide-seq utilizes next-generation sequencing platforms to generate data for specific loci that overlap with traditional Sanger sequences for the group. Carpophilinae recover as a well-supported clade with respect to the outgroup taxa. The genera Nitops, Urophorus and Caplothorax stat. nov. recover as monophyletic with high support. Caplothorax is formally given generic rank with a redescription and diagnosis. Anthophilous behaviour is coded for all taxa and an ancestral state reconstruction is performed, predicting multiple origins of this behaviour within Carpophilinae.}, number={4}, journal={Zoological Journal of the Linnean Society}, publisher={Oxford University Press (OUP)}, author={Powell, Gareth S and Cline, Andrew R and Duffy, Alexandra G and Zaspel, Jennifer M}, year={2020}, month={Mar}, pages={1359–1369} }
 @article{duffy_powell_zaspel_richmond_2018, title={Billbug (Coleoptera: Dryophthoridae: Sphenophorus spp.) Seasonal Biology and DNA-Based Life Stage Association in Indiana Turfgrass}, volume={111}, ISSN={0022-0493 1938-291X}, url={http://dx.doi.org/10.1093/jee/tox340}, DOI={10.1093/jee/tox340}, abstractNote={Eleven species of billbugs (Coleoptera: Dryophthoridae: Sphenophorus spp. Schönherr) infest managed turfgrass in North America. However, the regional variation in species composition remains unresolved and the seasonal phenology of several species has not been well documented. The latter gap is largely due to the inability to identify the larval stage to species-a confounding problem with several sympatric insect species. We used field trapping (adults) and soil sampling (larvae and pupae) surveys along with a DNA-based life-stage association to characterize the biology of billbugs associated with turfgrass in the Midwestern United States. Pitfall trapping at four locations in Indiana revealed four billbug species: S. venatus Say, S. parvulus Gyllenhaal, S. minimus Hart, and S. inaequalis Say. Sphenophorus venatus was the most abundant species on warm-season turfgrass while S. parvulus was most abundant on cool-season turfgrass. Investigation of S. venatus seasonal biology revealed two overwintered life stages-larva and adult-which resulted in two overlapping cohorts and two larval generations. Degree-day models describing S. venatus activity were more accurate for first-generation adults and larvae than for overwintering life stages. Maximum-likelihood analyses provided the first molecular species identification of billbug larvae and direct evidence that S. venatus larvae are capable of overwintering above 40°N latitude. Findings clarify the utility of molecular markers (CO1, 18S, and ITS2) for describing billbug larval population dynamics and seasonal phenology in regions where several sympatric billbug species occur. These results support the development of sustainable management strategies based on billbug seasonal phenology in different regions of North America.}, number={1}, journal={Journal of Economic Entomology}, publisher={Oxford University Press (OUP)}, author={Duffy, Alexandra G and Powell, Gareth S and Zaspel, Jennifer M and Richmond, Douglas S}, year={2018}, month={Jan}, pages={304–313} }
 @article{duffy_hughes_ginzel_richmond_2018, title={Volatile and Contact Chemical Cues Associated with Host and Mate Recognition Behavior of Sphenophorus venatus and Sphenophorus parvulus (Coleoptera: Dryophthoridae)}, volume={44}, ISSN={0098-0331 1573-1561}, url={http://dx.doi.org/10.1007/s10886-018-0967-8}, DOI={10.1007/s10886-018-0967-8}, number={6}, journal={Journal of Chemical Ecology}, publisher={Springer Science and Business Media LLC}, author={Duffy, Alexandra G. and Hughes, Gabriel P. and Ginzel, Matthew D. and Richmond, Douglas S.}, year={2018}, month={May}, pages={556–564} }
 @misc{duffy_2016, title={Chemically-mediated dispersal and mating behavior of billbugs (Coleoptera: Curculionidae) associated with turfgrass}, url={http://dx.doi.org/10.1603/ice.2016.111180}, DOI={10.1603/ice.2016.111180}, journal={2016 International Congress of Entomology}, publisher={Entomological Society of America}, author={Duffy, Alexandra Grace}, year={2016} }