65 Works

Data from: Effects of reduced-impact selective logging on palm regeneration in Belize

Boris Arevalo, Jair Valladarez, Shahira Muschamp, Elma Kay, Alex Finkral, Anand Roopsind & Francis E. Putz
To assess the impacts of a low-intensity selective timber harvest on a palm community in Belize, we mapped logging infrastructure (i.e., roads, log landings, skid trails, and stumps) and measured palm regeneration 1 year after a timber harvest carried out using reduced-impact logging (RIL) practices. We sampled palms across a gradient of increasing harvest impact severity from areas not directly affected by logging, in felling gaps, on secondary and primary skid trails, and on log...

Data from: Machine learning for characterization of insect vector feeding

Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski & Stephen L. Lapointe
Insects that feed by ingesting plant and animal fluids cause devastating damage to humans, livestock, and agriculture worldwide, primarily by transmitting pathogens of plants and animals. The feeding processes required for successful pathogen transmission by sucking insects can be recorded by monitoring voltage changes across an insect-food source feeding circuit. The output from such monitoring has traditionally been examined manually, a slow and onerous process. We taught a computer program to automatically classify previously described...

Data from: Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila

Diego N. De Panis, Julián Padró, Pedro Furió-Tarí, Sonia Tarazona, Pablo S. Milla Carmona, Ignacio M. Soto, Hernán Dopazo, Ana Conesa & Esteban Hasson
High-throughput transcriptome studies are breaking new ground to investigate the responses that organisms deploy in alternative environments. Nevertheless, much remains to be understood about the genetic basis of host plant adaptation. Here, we investigate genome-wide expression in the fly Drosophila buzzatii raised in different conditions. This species uses decaying tissues of cactus of the genus Opuntia as primary rearing substrate and secondarily, the necrotic tissues of the columnar cactus Trichocereus terscheckii. The latter constitutes a...

Data from: A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution

Akito Y. Kawahara, David Plotkin, Issei Ohshima, Carlos Lopez-Vaamonde, Peter R. Houlihan, Jesse W. Breinholt, Atsushi Kawakita, Lei Xiao, Jerome C. Regier, Donald R. Davis, Tosio Kumata, Jay-Cheon Sohn, Jurate De Prins, Charles Mitter & JAE-CHEON SOHN
Gracillariidae are one of the most diverse families of internally feeding insects, and many species are economically important. Study of this family has been hampered by lack of a robust and comprehensive phylogeny. In the present paper, we sequenced up to 22 genes in 96 gracillariid species, representing all previously recognized subfamilies and genus groups, plus 20 outgroups representing other families and superfamilies. Following objective identification and removal of two rogue taxa, two datasets were...

Data from: Horses in the Cloud: big data exploration and mining of fossil and extant Equus (Mammalia: Equidae)

Bruce J. MacFadden & Robert P. Guralnick
Extant species of the genus Equus (e.g., horses, asses, and zebras) have a widespread distribution today on all continents except Antarctica. Extinct species of Equus represented by fossils were likewise widely distributed in the Pliocene and even more so during the Pleistocene. In order to understand the efficacy of “big data” for (paleo)biogeographic analyses, location records (latitude, longitude) and fossil occurrences for the genus Equus were mined and further explored from six databases, including iDigBio,...

Data from: Trait-demography relationships underlying small mammal population fluctuations

Koen J. Van Benthem, Hannah Froy, Tim Coulson, Lowell L. Getz, Madan K. Oli & Arpat Ozgul
Large-scale fluctuations in abundance are a common feature of small mammal populations and have been the subject of extensive research. These demographic fluctuations are often associated with concurrent changes in the average body mass of individuals, sometimes referred to as the ‘Chitty effect’. Despite the long-standing recognition of this phenomenon, an empirical investigation of the underlying coupled dynamics of body mass and population growth has been lacking. Using long-term life-history data combined with a trait-based...

Data from: Automated identification of insect vectors of Chagas disease in Brazil and Mexico: the Virtual Vector Lab

Rodrigo Gurgel-Gonçalves, Ed Komp, Lindsay P. Campbell, Ali Khalighifar, Jarrett Mellenbruch, Vagner José Mendonça, Hannah L. Owens, Keynes De La Cruz Felix, A. Townsend Peterson & Janine M. Ramsey
Identification of arthropods important in disease transmission is a crucial, yet difficult, task that can demand considerable training and experience. An important case in point is that of the 150+ species of Triatominae, vectors of Trypanosoma cruzi, causative agent of Chagas disease across the Americas. We present a fully automated system that is able to identify triatomine bugs from Mexico and Brazil with an accuracy consistently above 80%, and with considerable potential for further improvement....

Data from: A social-ecological database to advance research on infrastructure development impacts in the Brazilian Amazon

Joanna M. Tucker Lima, Denis Valle, Evandro M. Moretto, Sergio M. P. Pulice, Nadia L. Zuca, Daniel R. Roquetti, Liviam E. C. Beduschi, Amanda S. Praia, Claudia P. F. Okamoto, Vinicius L. S. Carvalhaes, Evandro A. Branco, Bruna Barbezani, Emily Labandera, Kelsie Timpe & David Kaplan
Recognized as one of the world's most vital natural and cultural resources, the Amazon faces a wide variety of threats from natural resource and infrastructure development. Within this context, rigorous scientific study of the region's complex social-ecological system is critical to inform and direct decision-making toward more sustainable environmental and social outcomes. Given the Amazon's tightly linked social and ecological components and the scope of potential development impacts, effective study of this system requires an...

Data from: How habitat-modifying organisms structure the food web of two coastal ecosystems

Els M. Van Der Zee, Christine Angelini, Laura L. Govers, Marjolijn J. A. Christianen, Andrew H. Altieri, Karin J. Van Der Reijden, Brian R. Silliman, Johan Van De Koppel, Matthijs Van Der Geest, Jan A. Van Gils, Henk W. Van Der Veer, Theunis Piersma, Peter C. De Ruiter, Han Olff & Tjisse Van Der Heide
The diversity and structure of ecosystems has been found to depend both on trophic interactions in food webs and on other species interactions such as habitat modification and mutualism that form non-trophic interaction networks. However, quantification of the dependencies between these two main interaction networks has remained elusive. In this study, we assessed how habitat-modifying organisms affect basic food web properties by conducting in-depth empirical investigations of two ecosystems: North American temperate fringing marshes and...

Data from: Carbon recovery dynamics following disturbance by selective logging in Amazonian forests

Camille Piponiot, Plinio Sist, Lucas Mazzei, Marielos Peña-Claros, Francis E. Putz, Ervan Rutishauser, Alexander Shenkin, Nataly Ascarrunz, Celso P. De Azevedo, Christopher Baraloto, Mabiane França, Marcelino Guedes, Eurídice N. Honorio Coronado, Marcus V. N. D'Oliveira, Ademir R. Ruschel, Katia E. Da Silva, Eleneide Doff Sotta, Cintia R. De Souza, Edson Vidal, Thales A. P. West, Bruno Hérault & Thales AP West
When 2 Mha of Amazonian forests are disturbed by selective logging each year, more than 90 Tg of carbon (C) is emitted to the atmosphere. Emissions are then counterbalanced by forest regrowth. With an original modelling approach, calibrated on a network of 133 permanent forest plots (175 ha total) across Amazonia, we link regional differences in climate, soil and initial biomass with survivors' and recruits' C fluxes to provide Amazon-wide predictions of post-logging C recovery....

Data from: Immunoglobulin detection in wild birds: effectiveness of three secondary anti-avian IgY antibodies in direct ELISAs in 41 avian species

Carol A. Fassbinder-Orth, Travis E. Wilcoxen, Tiffany Tran, Raoul K. Boughton, Jeanne M. Fair, Erik K. Hofmeister, Jennifer L. Grindstaff & Jen C. Owen
1.Immunological reagents for wild, non-model species are limited or often non-existent for many species. 2. In this study, we compare the reactivity of a new anti-passerine IgY secondary antibody with existing secondary antibodies developed for use with birds. Samples from 41 species from the following six avian orders were analysed: Anseriformes (1 family, 1 species), Columbiformes (1 family, 2 species), Galliformes (1 family, 1 species), Passeriformes (16 families, 34 species), Piciformes (1 family, 2 species)...

Data from: Sound settlement: noise surpasses land cover in explaining breeding habitat selection of secondary cavity-nesting birds

Nathan J. Kleist, Robert P. Guralnick, Alexander Cruz & Clinton D. Francis
Birds breeding in heterogeneous landscapes select nest sites by cueing in on a variety of factors from landscape features and social information to the presence of natural enemies. We focus on determining the relative impact of anthropogenic noise on nest site occupancy, compared to amount of forest cover, which is known to strongly influence the selection process. We examine chronic, industrial noise from natural gas wells directly measured at the nest box as well as...

Data from: Consistent scaling of population structure across landscapes despite intraspecific variation in movement and connectivity

Brian E. Reichert, , Christopher E. Cattau, Wiley M. Kitchens & Robert J. Fletcher
Understanding the spatial scale of population structure is fundamental to long-standing tenets of population biology, landscape ecology and conservation. Nonetheless, identifying such scales has been challenging because a key factor that influences scaling – movement among patches or local populations – is a multicausal process with substantial phenotypic and temporal variation. We resolve this problem via a novel application of network modularity. When applied to movements, modularity provides a formal description of the functional aggregation...

Data from: Phylogenomics of Lophotrochozoa with consideration of systematic error

Kevin M. Kocot, Torsten H. Struck, Julia Merkel, Damien S. Waits, Christiane Todt, Pamela M. Brannock, David A. Weese, Johanna T. Cannon, Leonid L. Moroz, Bernhard Lieb & Kenneth M. Halanych
Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or...

Data from: The Achilles' heel hypothesis: misinformed keystone individuals impair collective learning and reduce group success

Jonathan Pruitt, Colin Wright, Carl Keiser, Alexander DeMarco, Matt Grobis, Noa Pinter-Wollman, Matthew M. Grobis, Alex E. DeMarco, Carl N. Keiser, Jonathan N. Pruitt & Colin M. Wright
Many animal societies rely on highly influential keystone individuals for proper functioning. When information quality is important for group success, such keystone individuals have the potential to diminish group performance if they possess inaccurate information. Here we test whether information quality (accurate or inaccurate) influences collective outcomes when keystone individuals are the first to acquire it. We trained keystone or generic individuals to attack or avoid novel stimuli and implanted these seed individuals within groups...

Data from: Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum

Christian Kehlmaier, Axel Barlow, Alexander K. Hastings, Melita Vamberger, Johanna L. A. Paijmans, David W. Steadman, Nancy A. Albury, Richard Franz, Michael Hofreiter & Uwe Fritz
Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise...

Data from: Re-evaluating the distribution of cooperative breeding in birds: is it tightly linked with altriciality?

Ning Wang, Rebecca Kimball & Rebecca T. Kimball
The evolution of cooperative breeding (CB) in birds has aroused intensive interest for decades, largely due to the paradox that some adults forgo independent breeding to help others. While much effort has been directed at understanding the adaptive significance of CB behavior, much less effort has been spent on understanding its origin. Ligon and Burt argued that the evolution of altriciality played a key role in the origin of CB since CB occurs more frequently...

Data from: On the widespread capacity for and functional significance of extreme inbreeding in ferns

Emily B. Sessa, Weston L. Testo, & James E. Watkins
Homosporous vascular plants utilize three different mating systems, one of which, gametophytic selfing, is an extreme form of inbreeding only possible in homosporous groups. This mating system results in complete homozygosity in all progeny and has important evolutionary and ecological implications. Ferns are the largest group of homosporous land plants, and the significance of extreme inbreeding for fern evolution has been the subject of debate for decades. We cultured gametophytes in the laboratory and quantified...

Data from: Agonistic character displacement in social cognition of advertisement signals

Bret Pasch, Rachel Sanford & Steven M. Phelps
Interspecific aggression between sibling species may enhance discrimination of competitors when recognition errors are costly, but proximate mechanisms mediating increased discriminative ability are unclear. We studied behavioral and neural mechanisms underlying responses to conspecific and heterospecific vocalizations in Alston’s singing mouse (Scotinomys teguina), a species in which males sing to repel rivals. We performed playback experiments using males in allopatry and sympatry with a dominant heterospecific (Scotinomys xerampelinus) and examined song-evoked induction of egr-1 in...

Data from: Cryptotermes colombianus a new drywood termite and distribution record of Cryptotermes in Colombia

Robin Casalla, Rudolf H. Scheffrahn, Judith Korb & Rudolf Scheffrahn
A new species of drywood termite (Kalotermitidae), Cryptotermes colombianus, is described and new records for Cryptotermes cylindroceps and Cryptotermes mangoldi are presented from the Caribbean coast of Colombia. C. colombianus is described from two soldiers and genetic sequences. This unusual species differs noticeably from other regional Cryptotermes species for its weak and inconspicuous definition of the frontal and genal horns and its acute angle of the frons with respect to the vertex. C. colombianus clustered...

Data from: A newly identified left–right asymmetry in larval sea urchins

Jason Hodin, Keegan Lutek & Andreas Heyland
Directional asymmetry (DA) in body form is a widespread phenomenon in animals and plants alike, and a functional understanding of such asymmetries can offer insights into the ways in which ecology and development interface to drive evolution. Echinoids (sea urchins, sand dollars and their kin) with planktotrophic development have a bilaterally symmetrical feeding pluteus larva that undergoes a dramatic metamorphosis into a pentameral juvenile that enters the benthos at settlement. The earliest stage of this...

Data from: Biotic-drivers of seedling establishment in Neotropical savannas: selective granivory and seedling herbivory by leaf-cutter ants as an ecological filter

Alan N. Costa, Heraldo L. Vasconcelos & Emilio M. Bruna
Herbivory has been shown to have prominent top-down effects on vegetation in Paleotropical savannas, where consumers of early stages of life history act as demographic bottlenecks. Such impact has been largely ignored in Neotropical savannas, however, despite insect consumption being linked to reduced recruitment of woody species. We hypothesize that Atta leaf-cutter ants – the prevalent herbivores in the Neotropics – alter the establishment of woody plant seedlings in the Brazilian Cerrado by reducing seed...

Data from: Tectonic collision and uplift of Wallacea triggered the global songbird radiation

Robert G. Moyle, Carl H. Oliveros, Michael J. Andersen, Peter A. Hosner, Brett W. Benz, Joseph D. Manthey, Scott L. Travers, Rafe M. Brown & Brant C. Faircloth
Songbirds (oscine passerines) are the most species rich and cosmopolitan bird group, comprising almost half of global avian species diversity. Because of their diversity and ubiquity, songbirds are used extensively in studies of evolutionary ecology, diversification, and ethology. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Prior research suggested songbird diversification scenarios that are largely uncoupled from Earth history, including extensive...

Data from: Disparities in influenza mortality and transmission related to sociodemographic factors within Chicago in the pandemic of 1918

Kyra H. Grantz, Madhura S. Rane, Henrik Salje, Gregory E. Glass, Stephen E. Schachterle & Derek A. T. Cummings
Social factors have been shown to create differential burden of influenza across different geographic areas. We explored the relationship between potential aggregate-level social determinants and mortality during the 1918 influenza pandemic in Chicago using a historical dataset of 7,971 influenza and pneumonia deaths. Census tract-level social factors, including rates of illiteracy, homeownership, population, and unemployment, were assessed as predictors of pandemic mortality in Chicago. Poisson models fit with generalized estimating equations (GEEs) were used to...

Data from: Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

Scott P. Egan, Gregory J. Ragland, Lauren Assour, Thomas H. Q. Powell, Glen R. Hood, Scott Emrich, Patrik Nosil, Jeffrey L. Feder & Thomas H.Q. Powell
Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple...

Registration Year

  • 2016
    65

Resource Types

  • Dataset
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Affiliations

  • University of Florida
    65
  • University of California, Berkeley
    5
  • University of California System
    3
  • Duke University
    3
  • United States Department of Agriculture
    3
  • California Polytechnic State University
    2
  • University of Kansas
    2
  • University of Washington
    2
  • Princeton University
    2
  • University of Notre Dame
    2