66 Works

Data from: A method to generate multi-locus barcodes of pinned insect specimens using MiSeq

Trace Akankunda, Hien To, Carlos R Lopez, Remko Leijs & Katja Hogendoorn
For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost effective approach for targeting small sets of informative genes from multiple samples. In this context, high-throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of less than 500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences...

Data from: Gender diversity of editorial boards and gender differences in the peer review process at six journals of ecology and evolution.

Charles Fox, Meghan Duffy, Daphne Fairbairn & Jennifer Meyer
Despite substantial progress for women in science, women remain underrepresented in many aspects of the scholarly publication process. We examined how the gender diversity of editors and reviewers changed over time for six journals in ecology and evolution (2003-2015 for four journals, 2007-2015 or 2009-2015 for the other two), and how several aspects of the peer review process differed between female and male editors and reviewers. We found that, for five of the six journals,...

The evolution of broadly polylectic behaviour in Lasioglossum (Chilalictus) (Halictidae, Apoidea)

Trace Akankunda, Carlos Rodriguez Lopez, Remko Leijs & Ken Walker
Based on the number of pollen hosts utilised, bees have been categorised as generalists (polylectic) or specialists (oligolectic). Faced with a changing habitat, polylectic bees can diversify their pollen ‘portfolio’, while oligolectic bees cannot and therefore may go locally extinct. Research into the evolution and maintenance of broad polylecty is scant. Instead, research has mainly focussed on the factors that constrain oligolectic species to a narrow diet. Here, we developed a molecular phylogeny of a...

Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals

Kelsie E Hunnicutt, George P Tiley, Rachel C Williams, Peter A Larsen, Marina B Blanco, Rodin M Rasoloarison, Christopher Ryan Campbell, Kevin Zhu, David W Weisrock, Hiroaki Matsunami & Anne D Yoder
Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within...

Data from: Nonconsumptive predator effects modify crayfish-induced bioturbation as mediated by limb loss: field and mesocosm experiments

Luc Dunoyer, Dakota Coomes & Philip Crowley
1. We addressed the implications of limb loss and regeneration for multi-species interactions and their impacts on ecosystem engineering in freshwater stream environments. 2. We included regenerative and non-regenerative crayfish as well as fish predators in a 2x2 factorial design to assess the effects on water turbidity of interactions between crayfish ecosystem engineers differing in regenerative status and their fish predators. 3. We demonstrated that crayfish limb loss and predation risks lead to more turbidity...

Data from: Hollows in living trees develop slowly but considerably influence the estimate of forest biomass

Zheng Zheng, Shubin Zhang, Carol Baskin, Jerry Baskin, Doug Schaefer, Xiaodong Yang & Lianyan Yang
The decomposition of wood inside living tree hollows influences forest structure and processes. Although the decomposition rate controls the formation of hollows, it has not previously been measured. In an old-growth subtropical montane evergreen broad-leaved forest in south-west China, we measured respiration rates of decaying wood inside living tree hollows, logs (downed tree trunks) and snags (standing dead trees) using infrared CO2 analysis. We compared stem radial growth rates to the horizontal expansion rates of...

Data from: Editor and reviewer gender influence the peer review process but not peer review outcomes at an ecology journal

Charles W. Fox, C. Sean Burns & Jennifer A. Meyer
Lack of diversity on editorial boards might generate disparities in editorial and peer review that contribute to gender and geographic disparities in scholarly publishing. We use a comprehensive data set of the peer review process for all papers submitted to the journal Functional Ecology from January 2004 to June 2014 to examine how gender, seniority and geographic location of editors and reviewers influence reviewer recruitment and scores given to papers by reviewers. The gender ratio...

Data from: Multiple aspects of plasticity in clutch size vary among populations of a globally distributed songbird

David F. Westneat, Veronika Bókony, Terry Burke, Olivier Chastel, Henrik Jensen, Thomas Kvalnes, Ádám Z. Lendvai, András Liker, Douglas Mock, Julia Schroeder, P. L. Schwagmeyer, Gabriele Sorci & Ian R. K. Stewart
1. Plasticity in life-history characteristics can influence many ecological and evolutionary phenomena, including how invading organisms cope with novel conditions in new locations or how environmental change affects organisms in native locations. Variation in reaction norm attributes is a critical element to understanding plasticity in life history, yet we know relatively little about the ways in which reaction norms vary within and among populations. 2. We amassed data on clutch size from marked females in...

Data from: The role of inbreeding depression and mating system in the evolution of heterostyly

Jennifer J. Weber, Stephen G. Weller, Ann K. Sakai, Olga V. Tsyusko, Travis C. Glenn, Cesar A. Dominguez, Francisco E. Molina-Freaner, Juan Fornoni, Mike Tran, Nhu Nguyen, Karen Nguyen, Lien-Khuong Tran, Greg Joice & Ellen Harding
We investigated the role of morph-based differences in the expression of inbreeding depression in loss of the mid-styled morph from populations of tristylous Oxalis alpina as proposed by theoretical analyses. The extent of self-compatibility of reproductive morphs, the degree of self-fertilization, and the magnitude of inbreeding depression were investigated in three populations of O. alpina differing in their tristylous incompatibility relationships. All three populations exhibited significant inbreeding depression. In two populations with highly modified tristylous...

Data from: Patterns of authorship in ecology and evolution: first, last and corresponding authorship vary with gender and geography

Charles W. Fox, Josiah P. Ritchey, C.E. Timothy Paine & C. E. Timothy Paine
The position of an author on the byline of a paper affects the inferences readers make about their contributions to the research. We examine gender differences in authorship in the ecology literature using two datasets: submissions to six journals between 2010 and 2015 (regardless of whether they were accepted), and manuscripts published by 151 journals between 2009 and 2015. Women were less likely to be last (i.e., ‘senior’) authors (averaging ~23% across journals, years and...

Data from: Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean

Zhi-Yong Yuan, Bao-Lin Zhang, Christopher J. Raxworthy, David W. Weisrock, Paul M. Hime, Jie-Qiong Jin, Emily M. Lemmon, Alan R. Lemmon, Sean D. Holland, Michelle L. Kortyna, Wei-Wei Zhou, Min-Sheng Peng, Jing Che, Elizabeth Prendini, Paul M Hime, Emily M Lemmon, Sean D Holland, Michelle L Kortyna, David W Weisrock & Alan R Lemmon
Natatanura raw assembled sequencesNatatanura_seqs.zip

Data from: The effectiveness of journals as arbiters of scientific quality

C.E. Timothy Paine, Charles W. Fox & C. E. Timothy Paine
Academic publishers purport to be arbiters of knowledge, aiming to publish studied that advance the frontiers of their research domain. Yet the effectiveness of journal editors at identifying novel and important research is generally unknown, in part because of the confidential nature of the editorial and peer-review process. Using questionnaires, we evaluated the degree to which journals are effective arbiters of scientific impact in the domain of Ecology, quantified by three key criteria. First, journals...

Data from: Lake regionalization and diatom metacommunity structuring in tropical South America

Xavier Benito, Sherilyn C. Fritz, Miriam Steinitz-Kannan, Maria I. Vélez & Michael M. McGlue
Lakes and their topological distribution across Earth’s surface impose ecological and evolutionary constraints on aquatic metacommunities. In this study, we group similar lake ecosystems as metacommunity units influencing diatom community structure. We assembled a database of 195 lakes from the tropical Andes and adjacent lowlands (8ºN–30ºS and 58–79ºW) with associated environmental predictors to examine diatom metacommunity patterns at two different levels: taxon and functional (deconstructed species matrix by ecological guilds). We also derived spatial variables...

Data from: Geographic clines in wing morphology relate to colonization history in New World but not Old World populations of yellow dung flies

Martin A. Schaefer, David Berger, Patrick T. Rohner, Anders Kjaersgaard, Stephanie S. Bauerfeind, Frédéric Guillaume, Charles W. Fox, Wolf Blanckenhorn & Wolf U. Blanckenhorn
Geographic clines offer insights about putative targets and agents of natural selection as well as tempo and mode of adaptation. However, demographic processes can lead to clines that are indistinguishable from adaptive divergence. Using the widespread yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae), we examine quantitative genetic differentiation (QST) of wing shape across North America, Europe and Japan, and compare this differentiation with that of ten microsatellites (FST). Morphometric analyses of 28 populations reared at...

Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

Dorothee Hodapp, Elizabeth T. Borer, W. Stanley Harpole, Eric M. Lind, Eric W. Seabloom, Peter B. Adler, Juan Alberti, Carlos A. Arnillas, Jonathan D. Bakker, Lori Biederman, Marc Cadotte, Elsa E. Cleland, Scott Collins, Philip A. Fay, Jennifer Firn, Nicole Hagenah, Yann Hautier, Oscar Iribarne, Johannes M.H. Knops, Rebecca L. McCulley, Andrew MacDougall, Joslin L. Moore, John W. Morgan, Brent Mortensen, Kimberly J. La Pierre … & Johannes M. H. Knops
Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta-diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major...

Data from: A genomic assessment of population structure and gene flow in an aquatic salamander identifies the roles of spatial scale, barriers, and river architecture

Mason O. Murphy, Kara S. Jones, Steven J. Price & David W. Weisrock
Population structure and gene flow of species in lotic environments can be constrained by river network architecture, species life history and heterogeneous local barriers. Identifying the factors that influence population structure and gene flow, especially in species limited to movement within a river network, is vital for understanding the evolutionary and demographic history of a species. We explored population structure and gene flow for a fully aquatic salamander, the common mudpuppy (Necturus maculosus), in Kentucky...

Data from: Evolution of larval competitiveness and associated life history traits in response to host shifts in a seed beetle

Charles W. Fox, Frank J. Messina, F. J. Messina & C. W. Fox
Resource competition is frequently strong among parasites that feed within small discrete resource patches, such as seeds or fruits. The properties of a host can influence the behavioral, morphological, and life history traits of associated parasites, including traits that mediate competition within the host. For seed parasites, host size may be an especially important determinant of competitive ability. Using the seed beetle, Callosobruchus maculatus, we performed replicated, reciprocal host shifts to examine the role of...

Data from: Delayed dispersal and prolonged brood care in a family-living beetle

Jacqueline R. Dillard, Thomas A. Maigret, J. R. Dillard & T. A. Maigret
Delayed juvenile dispersal is an important prerequisite for the evolution of family-based social systems, such as cooperative breeding and eusociality. In general, young adults forego dispersal if there are substantial benefits to remaining in the natal nest and/or the likelihood of dispersing and breeding successfully is low. We investigate some general factors thought to drive delayed juvenile dispersal in the horned passalus beetle, a family-living beetle in which young adults remain with their families in...

Data from: Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs

Hu Li, Leavengood Jr., John M., Eric G. Chapman, Daniel Burkhardt, Fan Song, Pei Jiang, Jinpeng Liu, Xuguo Zhou, Wanzhi Cai & John M. Leavengood
Hemiptera, the largest non-holometabolous order of insects, represents ~7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through ~300 million years of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized...

Data from: History, geography, and host use shape genome-wide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei)

Robin K. Bagley, Vitor C. Sousa, Matthew L. Niemiller & Catherine R. Linnen
Divergent host use has long been suspected to drive population differentiation and speciation in plant-feeding insects. Evaluating the contribution of divergent host use to genetic differentiation can be difficult, however, as dispersal limitation and population structure may also influence patterns of genetic variation. In this study, we use double-digest restriction-associated DNA (ddRAD) sequencing to test the hypothesis that divergent host use contributes to genetic differentiation among populations of the redheaded pine sawfly (Neodiprion lecontei), a...

Data from: Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species

Schyler O. Nunziata, Stacey L. Lance, David E. Scott, Emily M. Lemmon, David W. Weisrock & Emily Moriarty Lemmon
Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Surveying genetic variation is a potential alternative to census-based estimates of population size, and can yield insight into the demography of a population. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography. Here, we leveraged...

Data from: Author-suggested reviewers: gender differences and influences on the peer review process at an ecology journal

Charles W. Fox, C. Sean Burns, Anna D. Muncy & Jennifer A. Meyer
Peer review is the primary method by which journals evaluate the quality and importance of scientific papers. To help editors find suitable reviewers, many journals allow or require authors to suggest names of preferred and nonpreferred reviewers. Though authors should know best who is qualified to review their papers, they also have a strong incentive to suggest reviewers that they expect to review their paper positively. In this study, we examine the reviewers that are...

Data from: Phylogenetic patterns of trait and trait plasticity evolution: Insights from amphibian embryos

Rick Relyea, Patrick R. Stephens, Lisa N. Barrow, Andrew Blaustein, Paul Bradley, Julia Buck, Ann Chang, Brian I Crother, James Collins, Julia Earl, Stephanie Gervasi, Jason T. Hoverman, Olliver Hyman, Emily Claire Moriarty Lemmon, Thomas Luhring, Moses Michelsohn, Christopher M. Murray, Steven Price, Raymond Semlitsch, Andy Sih, Aaron Stoler, Nick VandenBroek, Alexa Warwick, Greta Wengert, John Hammond … & Stephanie S. Gervasi
Environmental variation favors the evolution of phenotypic plasticity. For many species, we understand the costs and benefits of different phenotypes, but we lack a broad understanding of how plastic traits evolve across large clades. Using identical experiments conducted across North America, we examined prey responses to predator cues. We quantified five life history traits and the magnitude of their plasticity for 23 amphibian species/populations (spanning three families and five genera) when exposed to no cues,...

Data from: Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs

Scott Hotaling, Mary Foley, Nicolette Lawrence, Jose Bocanegra, Marina B. Blanco, Rodin Rasoloarison, Peter M. Kappeler, Meredith A. Barrett, Anne D. Yoder, David W. Weisrock, Mary E. Foley & Nicolette M. Lawrence
Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the analysis of multilocus data, and complement more traditional methods based on phenotypic and ecological characteristics. Recognized as two species 20 years ago, mouse lemurs (genus Microcebus) now comprise more than 20 species, largely diagnosed from mtDNA sequence data. With each...

Data from: Effects of mountaintop removal mining and valley filling on the occupancy and abundance of stream salamanders

Steven J. Price, Brenee' L. Muncy, Simon J. Bonner, Andrea N. Drayer & Christopher D. Barton
Human-induced land-use changes are among the primary causes of ecosystem degradation and biodiversity loss. Across central Appalachia (USA), mountaintop removal mining and valley filling (MTR/VF) is the prevailing form of land-use change and represents a stressor to stream ecosystems. Salamanders are the dominant vertebrate in Appalachian headwater streams. Thus, we addressed the question: Is salamander occupancy and conditional abundance reduced in streams impacted by MTR/VF? We conducted repeated counts of adult and larval salamanders within...

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