61 Works

Forecasting suppression of invasive Sea Lamprey in Lake Superior: data and code for Bayesian forecast model

Sean Lewandoski
Resource managers frequently are tasked with mitigating or reversing adverse effects of invasive species through management policies and actions. In Lake Superior, of the Laurentian Great Lakes, invasive sea lamprey populations are suppressed to protect valuable fish stocks. However, the relationship between choice of long-term control strategy and the future chance of achieving the suppression target is unclear. Using a 60+ year time-series of suppression effort and monitoring data from 50 assessment sites located on...

Physics-Informed Neural Networks (PINNs) For DVCS Cross Sections

Manal Almaeen, Jake Grigsby, Joshua Hoskins, Brandon Kriesten, Yaohang Li, Huey-Wen Lin, Simonetta Liuti & Sorawich Maichum
We present a physics informed deep learning technique for Deeply Virtual Compton Scattering (DVCS) cross sections from an unpolarized proton target using both an unpolarized and polarized electron beam. Training a deep learning model typically requires a large size of data that might not always be available or possible to obtain. Alternatively, a deep learning model can be trained using additional knowledge gained by enforcing some physics constraints such as angular symmetries for better accuracy...

Microbiomes of guppy populations translocated in Trinidadian streams

Sarah Evans
An organisms’ gut microbiome can alter its fitness, yet we do not know how gut microbiomes change as their hosts evolve in the wild. We took advantage of a five-decade ‘chronosequence’ of translocated fish populations to examine associated changes in the gut microbiome. Populations of Trinidadian guppies have displayed parallel phenotypic convergence six times when moved from high predation (HP) to low predation (LP) environments. Across four drainages, we found microbiomes of fish translocated 5-6...

Data from: Chromosome scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus and Juncus inflexus

Jose Planta, Yu Ya Liang, Haoyang Xin, Matthew Chansler, Alan Prather, Jiming Jiang, Ning Jiang & Kevin Childs
The majority of sequenced genomes in the Monocots are from species belonging to the Poaceae, which includes many commercially important crops. Here, we expand the number of sequenced genomes from the Monocots to include the genomes of four related Cyperids: Carex cristatella and Carex scoparia from Cyperaceae and Juncus effusus and Juncus inflexus from Juncaceae. The high-quality, chromosome-scale genome sequences from these four Cyperids were assembled by combining whole-genome shotgun sequencing of Nanopore long reads,...

The ecological stage maintains preference differentiation and promotes speciation

Janette Boughman & Maria Servedio
Influential models of speciation by sexual selection posit either a single shared preference for a universal display, expressed only when males are locally adapted and hence in high condition, or that shared loci evolve population-specific alleles for displays and preferences. However, many closely related species instead show substantial differences across categorically different traits. We present a model of secondary contact whereby females maintain preferences for distinct displays that indicate both male condition and their match...

Short-range C-signaling restricts cheating behavior during Myxococcus xanthus development

Y Hoang, Joshua Franklin, Yann Dufour & Lee Kroos
Starving Myxococcus xanthus bacteria use short-range C-signaling to coordinate building of multicellular mounds with differentiation from rods into spores during fruiting body development. A csgA mutant deficient in C-signaling can cheat on wild type (WT) in mixtures and form spores disproportionately, but our understanding of cheating behavior is incomplete. We report that cheating requires excess WT cells in the initial mixture and occurs during the mound-building phase of development. We subjected mixtures of WT and...

Larval yellow perch locations during locomotion assays after exposure to MeHg and PCB126

Janice Albers, Rebekah Klingler, Michael Carvan & Cheryl Murphy
Fish swimming behavior is a commonly measured response in aquatic ecotoxicology because behavior is considered a whole organism-level effect that integrates many sensory systems. Recent advancements in animal behavior models, such as hidden Markov chain models (HMM), suggest an improved analytical approach for toxicology. Using both new and traditional approaches, we examined the sublethal effects of PCB126 and methylmercury on yellow perch (YP) larvae (Perca flavescens) using three doses. Both approaches indicate larvae increase activity...

Suction feeding by predators limits direct release of alarm cues in fishes

Brian Wisenden, Alexis Taylor, Jessica Undem & Michael Wagner
Chemical alarm cues alert aquatic prey to the presence of an actively foraging predator. There is a large literature based upon responses to alarm cues derived from skin extract, because it is anticipated that prey skin is damaged when prey are attacked by a predator. However, many predators feed by suction feeding whereby prey are quickly drawn into the buccal cavity and swallowed whole with little, if any, direct contact between the teeth of the...

Cryptic species in a colorful genus: integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species

Yang Liu, Chentao Wei, George Sangster, Urban Olsson, Pamela Rasmussen, Lars Svensson, Cheng-Te Yao, Geoff Carey, Paul Leader, Ruiying Zhang, Guoling Chen, Gang Song, Fumin Lei, David Wilcove & Per Alström
Several cryptic avian species have been validated by recent integrative taxonomic efforts in the Sino-Himalayan mountains, indicating that avian diversity in this global biodiversity hotspot may be underestimated. In the present study,we investigated species limits in the genus Tarsiger, the bush robins, a group of montane forest specialists with high species richness in the Sino-Himalayan region. Based on comprehensive sampling of all 11 subspecies of the six currently recognized species, we applied an integrative taxonomic...

X-ray imaging of 30 year old wine grape wood reveals cumulative impacts of rootstocks on scion secondary growth and harvest index

Michelle Y. Quigley, Joey Mullins & Daniel H. Chitwood
Annual rings from vines in a 30 year old, California rootstock trial were measured to determine the effects of 15 different rootstocks on Chardonnay and Cabernet Sauvignon scions. Viticultural traits measuring vegetative growth, yield, berry quality, and nutrient uptake were measured at the beginning and end of the lifetime of the vineyard. X-ray Computed Tomography (CT) was used to measure ring widths in 103 vines. Ring width was modeled as a function of ring number...

Data for: The visual ecology of selective predation: Are unhealthy hosts less stealthy hosts?

Nina Wale
Predators can strongly influence disease transmission and evolution, particularly when they prey selectively on infected hosts. Although selective predation has been observed in numerous systems, why predators select infected prey remains poorly understood. Here, we use a mathematical model of predator vision to test a longstanding hypothesis about the mechanistic basis of selective predation in a Daphnia-microparasite system, which serves as a model for the ecology and evolution of infectious diseases. Bluegill sunfish feed selectively...

Radical Humility Forum

Gretel Van Weiren, Todd Shaw, Beronda Montgomery, Nimot Ogunfemi, Morgan Shipley, Paulina Camacho Valencia, Rebekah Modrak, Jamie Vander Broek, Ruth Nicole Brown & Christian B. Miller

Weightlifting injuries in master athletes

Marianne Huebner
Data collection: A total of 976 Masters weightlifters from Australia, Canada, Europe, and the USA, ages 35 to 88 (51.1% female), completed an online survey in June 2021 that included questions on weightlifting injuries, chronic diseases, sport history, and training practices. Definition of injuries: Injuries were defined in relation to participation to weightlifting, namely whether training restriction occurred due to acute injuries sustained during weightlifting. The correspoding srurvey question was “Have you ever had training...

Incorporating Complex Sampling Weights in Multilevel Analyses of Educational Data

Ting Shen & Spyros Konstantopoulos
Large-scale assessment survey (LSAS) data are collected via complex sampling designs with special features (e.g., clustering and unequal probability of selection). Multilevel models have been utilized to account for clustering effects whereas the probability weighting approach (PWA) has been used to deal with design informativeness derived from the unequal probability selection. However, the difficulty of applying PWA in multilevel models (MLM) has been generally underestimated and practical guidance is scarce. This study utilizes an empirical...

Extreme natural size variation in both sexes of a sexually cannibalistic mantidfly

Laurel Lietzenmayer, Lauren Goldstein, Josephine Pasche & Lisa Taylor
In sexually cannibalistic animals, the relative sizes of potential mates often predict the outcome of aggressive encounters. Mantidflies are spider egg predators as larvae and generalist predators as adults. Unlike most cannibalistic species, individual mantidflies can be substantially larger than other individuals, regardless of sex. Using preserved collections of Dicromantispa sayi, we focused on three body size metrics that we found to be positively correlated and accurately measured across researchers. We found extreme size variation...

Does the presence of the biological control agent, Hypena opulenta (Lepidoptera: Erebidae) on Swallow-Worts deter Monarch oviposition?

Marianna Szucs, Brianna Alred, Ruth Hufbauer, Nathan Haan & Douglas A Landis
Abstract Invasive black and pale swallow-worts (Vincetoxicum nigrum (L.) Moench, and Vincetoxicum rossicum Kelopow), which are related to milkweeds, can act as ecological traps for monarch butterflies (Danaus plexippus L. (Lepidoptera: Nymphalidae)) as they lay eggs on them that fail to develop. A recently approved biological control agent against swallow-worts, Hypena opulenta Christoph, occupies the same feeding guild on swallow-worts as monarch larvae and could be perceived as a competitor to monarchs. We tested how...

dLOC as Practice: Decolonial Approaches to Listening and Remembering

Ricia Anne Chansky & Christina Boyles

Sandy seeds: Armor or invisibility cloak? Mucilage-bound sand physically protects seeds from rodents and invertebrates

Eric LoPresti, Vincent Pan, Cecilia Girvin, Gabhriel Barber, Sierra Jaeger & John Orrock
Seeds represent a stage of a plant’s life cycle that is extremely vulnerable to predation, which, unlike most vegetative herbivory, is fatal to the individual. As such, understanding the distribution and abundance of plants may rely upon understanding seed defenses: characteristics of seeds that make them more difficult for granivores to locate, make them less beneficial for granivores to consume, or both. Seeds that produce mucilage are widespread and found across many families and species....

Climate and land-use effects on dung beetle assemblages

Jana Englmeier, Christian Von Hoermann, Daniel Rieker, Eric M. Benbow, Caryl Benjamin, Ute Fricke, Cristina Ganuza, Maria Haensel, Tomáš Lackner, Oliver Mitesser, Sarah Redlich, Rebekka Riebl, Sandra Rojas-Botero, Thomas Rummler, Jörg-Alfred Salamon, David Sommer, Ingolf Steffan-Dewenter, Cynthia Tobisch, Johannes Uhler, Lars Uphus, Jie Zhang & Jörg Müller
This dataset contains data from a field study conducted in 2019 and described in the paper "Dung beetle diversity is mainly affected by land use, while community specialization is driven by climate" by Englmeier et al. To test the effects of land use and climate on α-diversity, local community specialization (H2'), and γ-diversity of dung beetles, we used pitfall traps baited with four different dung types at 114 study sites, distributed over a spatial extent...

Feasibility of hybrid in-stream generator–photovoltaic systems for Amazonian off-grid communities

Erik Brown, Igor Cavallini Johansen, Ana Paula Bortoleto, Yadu Pokhrel, Suyog Chaudhari, Anthony Cak, Samer Sulaeman, Laura Castro-Diaz, Maria Claudia Lopez, Adam Mayer, Judith Walgren, Norbert Müller & Emilio Moran
While there have been efforts to supply off-grid energy in the Amazon, these attempts have focused on low upfront costs and deployment rates. These “get-energy-quick” methods have almost solely adopted diesel generators, ignoring the environmental and social risks associated with the known noise and pollution of combustion engines. Alternatively, it is recommended, herein, to supply off-grid needs with renewable, distributed microgrids comprised of photovoltaics (PV) and in-stream generators (ISG). Utilization of a hybrid combination of...

Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

Genevieve Hoopes, Xiaoxi Meng, John P. Hamilton, Sai Reddy Achakkagari, Fernanda De Alves Freitas Guesdes, Marie E. Bolger, Joseph J. Coombs, Danny Esselink, Natalie R. Kaiser, Linda Kodde, Maria Kyriakidou, Brian Lavrijssen, Natascha Van Lieshout, Rachel Shereda, Heather K. Tuttle, Brieanne Vaillancourt, Joshua C. Wood, Jan M. De Boer, Nolan Bornowski, Peter Bourke, David Douches, Herman J. Van Eck, Dave Ellis, Max J. Feldman, Kyle M. Gardner … & Richard Finkers
Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas Guesdes F., Bolger M.E., Coombs J.J., Esselink D., Kaiser N.R., Kodde L., Kyriakidou M., Lavrijssen B., van Lieshout N., Shereda R., Tuttle H.K., Vaillancourt B., Wood J.C., de Boer J.M., Bornowski N., Bourke P., Douches D., van Eck H.J., Ellis D., Feldman M.J., Gardner K.M., Hopman J.C.P., Jiang J., De Jong W.S., Kuhl J.C., Novy R.G., Oome S., Sathuvalli V., Tan E.H., Ursum R.A.,...

Enslaved.org Recommended Practices for Historical Slavery Data

Catherine Foley & Alicia M. Sheill

Data from: Traits across trophic levels interact to influence parasitoid establishment in biological control releases

Benjamin Jarrett & Marianna Szűcs
A central goal in ecology is to predict what governs a species’ ability to establish in a new environment. One mechanism driving establishment success is individual species’ traits, but the role of trait combinations among interacting species across different trophic levels are less clear. Deliberate or accidental species additions to existing communities provide opportunities to study larger scale patterns of establishment success. Biological control introductions are especially valuable because they contain data on both the...

Data from: Local diversity in phenological responses of migratory lake sturgeon to warm winters

Tyler Buchinger, Darryl Hondorp & Charles Krueger
Rich intraspecific diversity in traits that shape responses to environmental conditions implies that effects of climate change will differ within species or even populations. Nevertheless, few studies investigate how different groups within species respond to climatic fluctuations, and most risk assessments rely upon species-wide generalizations. We studied effects of among-year variation in air temperature on the spring migratory phenology of a metapopulation of lake sturgeon (Acipenser fulvescens) within waters connecting Lake Huron and Lake Erie...

Anchorage by seed mucilage prevents seed dislodgement in high surface flow: a mechanistic investigation

Vincent Pan, Cecilia Girvin & Eric LoPresti
Background and Aims: Seed mucilage is a common and highly diverse trait shared among thousands of angiosperm species. While long recognized that mucilage allows seeds to anchor to substrates (antitelechory), resisting abiotic and biotic dislodgement, we still lack a mechanistic understanding of this process. Methods: We propose a mechanistic model of how mucilage affects substrate anchorage and fluid resistance, ultimately contributing to dislodgement resistance. To test this model, we subjected mucilaginous seeds of 52 species,...

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