48 Works

Data from: Variation in predation regime drives sex-specific differences in mosquitofish foraging behaviour

Varpu Pärssinen, Kaj Hulthén, Christer Brönmark, Gustaf Ekelund Ugge, Raphael Gollnisch, Simon David Herzog, Nan Hu, Marcus Lee, Yongcui Sha, Martin Škerlep, Jerker Vinterstare, R. Brian Langerhans, P. Anders Nilsson, Caroline Björnerås, Lars-Anders Hansson, Emma Johansson, Karin Rengefors & Huan Zhang
Predation is a well-studied driver of ecological selection on prey traits, which frequently drives divergence in anti-predator performance across environments that vary in predation risk. However, predation also alters prey mortality regimes, where low predation risk often results in higher prey densities and consequently higher intensities of intraspecific resource competition. In addition, predation risk alters the foraging context, as acquiring food can be risky in the presence of predators. Thus, different predation regimes can drive...

Data from: Long-term trends in the occupancy of ants revealed through use of multi-sourced datasets

Julie Sheard, Carsten Rahbek, Robert Dunn, Nathan Sanders & Nick Isaac
We combined participatory science data and museum records to understand long-term changes in occupancy for 29 ant species in Denmark over 119 years. Bayesian occupancy modelling indicated change in occupancy for 15 species: five increased, four declined and six showed fluctuating trends. We consider how trends may have been influenced by life-history and habitat changes. Our results build on an emerging picture that biodiversity change in insects is more complex than implied by the simple...

PacBio IsoSeq reference transcriptomes for Pinus taeda L.

Edwin Lauer & Fikret Isik
Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. In this report, we detail the genomic localization and sequence-level discovery of candidate race-nonspecific broad-spectrum fusiform rust resistance genes in Pinus taeda L. Two full-sib families, each with ~1000 progeny, were challenged with a complex inoculum consisting of over 150 pathogen isolates. High-density linkage mapping revealed three...

Supplemental information for: An early burst in brachiopod evolution corresponding with significant climatic shifts during the great Ordovician biodiversification event

Curtis Congreve, Mark Patzkowsky & Peter Wagner
We employ modified tip-dating methods to date divergence times within the Strophomenoidea, one of the most abundant and species-rich brachiopod clades to radiate during the Great Ordovician Biodiversification Event (GOBE), to determine if significant environmental changes at this time correlate with the diversification of the clade. Models using origination, extinction and sampling rates to estimate prior probabilities of divergence times strongly support both high rates of anatomical change per million-years and rapid divergences shortly before...

Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur

Ryan Campbell, George Tiley, Jelmer Poelstra, Kelsie Hunnicutt, Peter Larsen, Hui-Jie Lee, Jeffrey Thorne, Mario Dos Reis & Anne Yoder
Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprise nearly half of the primate clade. Using high-coverage...

Knockdown resistance (kdr) genotypes and collection information for Aedes aegytpi from Iquitos, Peru (2000 - 2017)

Jennifer Baltzegar
This study describes the evolution of knockdown resistance (kdr) haplotypes in Aedes aegypti in response to pyrethroid insecticide use over the course of 18 years in Iquitos, Peru. Based on the duration and intensiveness of sampling (~10,000 samples), this is the most thorough study of kdr population genetics in Ae. aegypti to date within a city. We provide evidence for the direct connection between programmatic citywide pyrethroid spraying and the increase in frequency of specific...

Natural and anthropogenic sources of habitat variation influence exploration behaviour, stress response, and brain morphology in a coastal fish

R. Brian Langerhans, Matthew Jenkins, John Cummings, Alex Cabe, Kaj Hulthén & M. Nils Peterson
1. Evolutionary ecology aims to better understand how ecologically important traits respond to environmental heterogeneity. Environments vary both naturally and as a result of human activities, and investigations that simultaneously consider how natural and human-induced environmental variation affect diverse trait types grow increasingly important as human activities drive species endangerment. 2. Here, we examine how habitat fragmentation and structural habitat complexity, affect disparate trait types in Bahamas mosquitofish (Gambusia hubbsi) inhabiting tidal creeks. We tested...

Uncertainty in health impact assessments of smoke from a wildfire event

Megan Johnson & Fernando Garcia-Menendez
Manuscript abstract: Wildfires cause elevated air pollution that can be detrimental to human health. However, health impact assessments associated with emissions from wildfire events are subject to uncertainty arising from different sources. Here, we quantify and compare major uncertainties in mortality and morbidity outcomes of exposure to fine particulate matter (PM2.5) pollution estimated for a series of wildfires in the Southeastern U.S. We present an approach to compare uncertainty in estimated health impacts specifically due...

Code of Best Practices in Fair Use for Open Educational Resources

Meredith Jacob, Peter Jaszi, Prudence S. Adler & William Cross

Resonance Raman confirms partial hemoglobin preservation in dinosaur remains

Brandon Long
Still-soft, hollow, and flexible structures that are morphologically consistent with blood vessels were recovered from demineralized dinosaur bone and studied with resonance Raman techniques to test the hypothesis that these vessel-like structures are original to the dinosaur, and that they maintain endogenous molecular characteristics. We probed these ancient samples using resonance Raman at two different wavelengths, and the existence of a stronger resonance Raman signal level in the green compared to blue excitation is consistent...

National survey of college students' beliefs, attitudes, and behaviors related to hunting, fishing, and wildlife conservation

Lincoln Larson
This dataset contains responses from an online survey of diverse undergraduate students (ages 18-34 years) attending 22 different universities across 22 U.S. states (total n = 17,203). Survey questions focused on students' beliefs, attitudes, and behaviors related to hunting, fishing, and wildlife conservation. The survey was conducted from 2018-2020.

Deconstructing incubation behaviour in response to ambient temperature over different timescales

David Diez-Méndez, Caren Cooper, Juan José Sanz, Jose Verdejo & Emilio Barba
Avian embryos need a stable thermal environment to develop optimally, while incubating females need to allocate time to self-maintenance off the nest. In species with female-only incubation, eggs are exposed to ambient temperatures that usually cool them down during female absences. The lower the ambient temperature the sooner females should return to re-warm the eggs. When incubation constraints ease at increasing ambient temperatures, females respond by increasing either incubation effort or self-maintenance time. These responses...

A greenhouse experiment partially supports inferences of ecogeographic isolation from niche models of Clarkia sister species

Kathleen Kay, Kaleb Goff & Cormac Martinez Del Rio
Premise: Ecogeographic isolation, or geographic isolation caused by ecological divergence, is thought to be of primary importance in speciation, yet is difficult to demonstrate and quantify. To determine whether distributions are limited by divergent adaptation or historical contingency, the gold standard is to reciprocally transplant taxa between their geographic ranges. Alternatively, ecogeographic isolation is inferred from species distribution models and niche divergence tests based on widely available environmental and occurrence data. Methods: We test for...

R/QTL datasets for fusiform rust resistance QTL mapping

Fikret Isik & Edwin Lauer
Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. In this report, we detail the genomic localization and sequence-level discovery of candidate race-nonspecific broad-spectrum fusiform rust resistance genes in Pinus taeda L. Two full-sib families, each with ~1000 progeny, were challenged with a complex inoculum consisting of over 150 pathogen isolates. High-density linkage mapping revealed three...

Data for: Many-body thermodynamics on quantum computers via partition function zeros

Akhil Francis, Daiwei Zhu, Cinthia Huerta Alderete, Sonika Johri, Xiao Xiao, James K. Freericks, Christopher Monroe, Norbert M. Linke & Alexander F. Kemper
Partition functions are ubiquitous in physics: they are important in determining the thermodynamic properties of many-body systems, and in understanding their phase transitions. As shown by Lee and Yang, analytically continuing the partition function to the complex plane allows us to obtain its zeros and thus the entire function. Moreover, the scaling and nature of these zeros can elucidate phase transitions. Here we show how to find partition function zeros on noisy intermediate-scale trapped ion...

Data from: Mammal-bearing gastric pellets potentially attributable to Troodon formosus at the Cretaceous Egg Mountain locality, Two Medicine Formation, Montana, U.S.A.

William Freimuth, David Varricchio, Alexandria Brannick, Lucas Weaver & Gregory Wilson Mantilla
Fossil gastric pellets (regurgitalites) have distinct taphonomic characteristics that facilitate inferences of behavioural ecology in deep time, despite their rarity in the fossil record. Using the taphonomic patterns of both extant and fossil small mammals from more recent geologic deposits as a guide, we assess the taphonomy of three unusual multi-individual aggregates of mammal skeletons from paleosols at Egg Mountain, a dinosaur nesting locality from the Upper Cretaceous Two Medicine Formation, Montana, USA. One aggregate...

Searching for deep-seated thrust faults on the moon

Matthew Collins
The lunar maria are large expanses of basalt that infill antecedent impact basins and show evidence for post-emplacement deformation. Landforms within many of these basins suggest a period of compressive tectonics, although the mechanism for their formation remains an open question. Previous work for Mare Crisium demonstrated that basin-circumferential wrinkle ridges, which typically demarcate the inner edge of an annulus of elevated terrain, are the result of deep-seated thrust faults that preferentially form along the...

Microevolutionary change in mimicry? Erosion of rattling behaviour among nonvenomous snakes on islands lacking rattlesnakes

Bradley Allf, Amanda Sparkman & David Pfennig
Batesian mimics––harmless species that converge on the warning signals of a dangerous species––are spectacular examples of adaptation, but few documented cases involve acoustic signals. Even fewer studies have documented microevolutionary change in mimicry of any kind. Here, we describe potential evolutionary change in acoustic mimicry. Many nonvenomous snakes vibrate their tail tip when threatened, making a sound resembling a venomous rattlesnake. When we compared this behaviour between gopher snakes from mainland California where rattlesnakes are...

Schizophrenia and Bartonella spp. infection: A pilot case–control study

Erin Lashnits, Ricardo Maggi, Fredrik Jarskog, Julie Bradley, Edward Breitschwerdt & Flavio Frohlich
Recently, infections with emerging zoonotic bacteria of the genus Bartonella have been reported in association with a range of CNS symptoms. Currently, it remains unknown if Bartonella spp. infection is associated with symptoms of schizophrenia/schizoaffective disorder (SCZ/SAD). The objective of this study was to determine if there is an association between Bartonella species infection and SCZ/SAD. A secondary objective was to determine if SCZ/SAD symptoms were more severe among participants with documented Bartonella spp. infection....

Data for: Predation risk and the evolution of a vertebrate stress response: parallel evolution of stress reactivity and sexual dimorphism

Jerker Vinterstare, Gustaf MO Ekelund Ugge, Kaj Hulthén, Alexander Hegg, Christer Brönmark, P Anders Nilsson, U Ronja Zellmer, Marcus Lee, Varpu Pärssinen, Yongcui Sha, Caroline Björnerås, Huan Zhang, Raphael Gollnisch, Simon David Herzog, Lars-Anders Hansson, Martin Škerlep, Nan Hu, Emma Johansson & R Brian Langerhans
Predation risk is often invoked to explain variation in stress responses. Yet, the answers to several key questions remain elusive, including: 1) how predation risk influences the evolution of stress phenotypes, 2) the relative importance of environmental versus genetic factors in stress reactivity, and 3) sexual dimorphism in stress physiology. To address these questions, we explored variation in stress reactivity (ventilation frequency) in a post-Pleistocene radiation of live-bearing fish, where Bahamas mosquitofish (Gambusia hubbsi) inhabit...

Detecting flying insects using car nets and DNA metabarcoding

Cecilie Svenningsen, Tobias Guldberg Frøslev, Jesper Bladt, Lene Bruhn Pedersen, Jonas Colling Larsen, Rasmus Ejrnæs, Camilla Fløjgaard, Anders Hansen, Jacob Heilmann-Clausen, Robert Dunn & Anders Tøttrup
Monitoring insects across space and time is challenging, due to their vast taxonomic and functional diversity. This study demonstrates how nets mounted on rooftops of cars (car nets) and DNA metabarcoding can be applied to sample flying insect richness and diversity across large spatial scales within a limited time period. During June 2018, 365 car net samples were collected by 151 volunteers during two daily time intervals on 218 routes in Denmark. Insect bulk samples...

G-Quadruplex Structure Improves the Immunostimulatory Effects of CpG Oligonucleotides

Kazuaki Hoshi, TOMOHIKO YAMAZAKI, Yuuki Sugiyama, Kaori Tsukakoshi, Wakako Tsugawa, Koji Sode & Kazunori Ikebukuro
Single-strand oligodeoxynucleotides (ODNs) containing unmethylated cytosine-phosphate-guanine (CpG) are recognized by the toll-like receptor 9, a component of the innate immunity. Therefore, they could act as immunotherapeutic agents. Chemically modified CpG ODNs containing a phosphorothioate backbone instead of phosphodiester (PD) were developed as immunotherapeutic agents resistant to nuclease degradation. However, they cause adverse side effects, and so there is a necessity to generate novel CpG ODNs. In the present study, we designed a nuclease-resistant nonmodified CpG...

Combining epidemiological and ecological methods to quantify social effects on E. coli transmission

Trevor Farthing, Daniel Dawson, Michael Sanderson, Hannah Seger & Cristina Lanzas
Enteric microparasites like Escherichia coli utilize multiple transmission pathways to propagate within and between host populations. Characterizing the relative transmission risk attributable to host social relationships, and direct physical contact between individuals is paramount for understanding how microparasites like E. coli spread within affected communities and estimating colonization rates. To measure these effects, we carried out commensal E. coli transmission experiments in two cattle (Bos taurus) herds, wherein all individuals were equipped with real-time location...

A new pipeline for removing paralogs in target enrichment data

Wenbin Zhou, John Soghigian &
Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper...

Data From: Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)

Xuankun Li, Luisa C. Teasdale, Keith M. Bayless, Allan G. Ellis, Brian M. Wiegmann, Carlos José E. Lamas, Christine L. Lambkin, Neal L. Evenhuis, James A. Nicholls, Diana Hartley, Seunggwan Shin, Michelle Trautwein, Andreas Zwick, Bryan D. Lessard & David K. Yeates
Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Text
  • Audiovisual


  • North Carolina State University
  • Lund University
  • Duke University
  • University of North Carolina at Chapel Hill
  • Pennsylvania State University
  • University of Michigan-Ann Arbor
  • Universidade Federal Rural do Rio de Janeiro
  • University of North Carolina
  • University of Minnesota
  • University of Copenhagen