68 Works

Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Matthew G. Johnson, Lisa Pokorny, Steven Dodsworth, Laura R. Botigue, Robyn S. Cowan, Alison Devault, Wolf L. Eiserhardt, Niroshini Epitawalage, Félix Forest, Jan T. Kim, James Leebens-Mack, Ilia J. Leitch, Olivier Maurin, Doug Soltis, Pamela S. Soltis, Gane Ka-Shu Wong, William J. Baker & Norman Wickett
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used...

Data from: Phylotocol: promoting transparency and overcoming bias in phylogenetics

Melissa B. DeBiasse & Joseph F. Ryan
The integrity of science requires that the process be based on sound experimental design and objective methodology. Strategies that increase reproducibility and transparency in science protect this integrity by reducing conscious and unconscious biases. Given the large number of analysis options and the constant development of new methodologies in phylogenetics, this field is one that would particularly benefit from more transparent research design. Here, we introduce phylotocol (fī·lō·´tə·kôl), an a priori protocol-driven approach in which...

Data from: Community assembly of the ferns of Florida

Emily B. Sessa, Sally M. Chambers, Daijiang Li, Lauren Trotta, Lorena Endara, J. Gordon Burleigh & Benjamin Baiser
Premise of the study: Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales. Methods: We built a phylogeny for 125 of the 141 species of ferns in Florida using five chloroplast markers. We calculated mean pairwise dissimilarity (MPD) and mean nearest taxon distance (MNTD) from phylogenetic...

Data from: The future of cold-adapted plants in changing climates: Micranthes (Saxifragaceae) as a case study

Rebecca L. Stubbs, Douglas E. Soltis & Nico Cellinese
As a result of changing climates, research has shown species undergoing range contractions and/or northward and higher elevational movements. Here, we evaluate how the distribution of a group of cold-adapted plant species with similar evolutionary histories changes in response to warming climates. We selected 29 species of Micranthes (Saxifragaceae) representing the mountain and Arctic biomes of the northern hemisphere. For this analysis, 24,755 data points were input into ecological niche models to assess both present...

Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta

Zhe Cao, Yufang Guo, Qian Yang, Yanhong He, Mohammed Fetouh, Ryan M. Warner, Zhanao Deng & Mohammed I. Fetouh
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve...

Data from: Museum specimens provide phylogenomic data to resolve relationships of sack-bearer moths (Lepidoptera, Mimallonoidea, Mimallonidae)

Ryan A. St Laurent, Chris A. Hamilton & Akito Y. Kawahara
Mimallonidae, the sack‐bearer moths, are a family of predominantly Neotropical moths containing nearly 300 described species. Mimallonidae feed on over 40 host plant families and are found in a variety of environments, but phylogenetic relationships of species within the family have never been investigated. We sequenced 515 loci using anchored hybrid enrichment target capture on ethanol‐preserved and dried museum specimens, with dates of collection ranging from 1985 to 2017. We sampled 47 species, representing 32...

Data from: Insights into the genetic basis of blueberry fruit-related traits using diploid and polyploid models in a GWAS context

Luis Felipe V. Ferrão, Juliana Benevenuto, Ivone De Bem Oliveira, Catherine Cellon, James Olmstead, Matias Kirst, , Patricio Munoz & Marcio F. R. Resende
Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations and plant breeding strategies. Polyploidization occurs in many important crops; however, its effects on inheritance of many agronomic traits are still poorly understood compared with diploid species. Higher levels of allelic dosage or more complex interactions between alleles could affect the phenotype expression. Hence, the present study aimed to dissect the genetic basis of fruit-related traits in autotetraploid blueberries...

Data from: Bioturbation by mammals and fire interact to alter ecosystem-level nutrient dynamics in longleaf pine forests

Kenneth L. Clark, Lyn C. Branch & Jennifer Farrington
Activities of ecosystem engineers can interact with other disturbances to modulate rates of key processes such as productivity and nutrient cycling. Bioturbation, movement of soil by organisms, is a widespread form of ecosystem engineering in terrestrial ecosystems. We propose that bioturbation by southeastern pocket gophers (Geomys pinetis), an abundant but declining ecosystem engineer in longleaf pine (Pinus palustris Mill.) forests, accelerates nutrient dynamics of the forest floor by burying litter and then reduces litter consumption...

Data from: Estimating field capacity from volumetric soil water content time series using automated processing algorithms

Eban Z. Bean, Ray G. Huffaker & Kati W. Migliaccio
Vadose zone measurements of volumetric soil water content (θ) using soil moisture sensors (SMSs) have become more common due to advances in technology and reduction of costs. Soil moisture sensor data exhibit a characteristic cyclical pattern reflecting water flux dynamics into and out of the observed soil volume. Expert review of SMS datasets to distinguish valid from corrupt or incomplete soil water cycles is arguably the most precise method for determining field capacity (θFC) but...

Data from: Do an ecosystem engineer and environmental gradient act independently or in concert to shape juvenile plant communities? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna

Alan N. Costa, Emilio M. Bruna & Heraldo L. Vasconcelos
Background. Ecosystem Engineers are species that transform habitats in ways that influence other species. While the impacts of many engineers have been well described, our understanding of how their impact varies along environmental gradients remains limited. Although disentangling the effects of gradients and engineers on biodiversity is complicated – the gradients themselves can be altered by engineers – doing so is necessary to advance conceptual and mathematical models of ecosystem engineering. We used leaf-cutter ants...

Data from: Grass invasion and drought interact to alter the diversity and structure of native plant communities

Catherine Fahey, Christine Angelini & S. Luke Flory
Understanding the interactive effects of species invasions and climate change is essential for predicting future shifts in biodiversity. Because multiple stressors can interact in synergistic or antagonistic ways, it is notoriously difficult to anticipate their combined effects on species assemblages. However, some hypotheses predict that plant invasions will become increasingly problematic as climate change improves conditions for invaders or lowers the biotic resistance of native communities. In a four-year field experiment, we quantified the individual...

Data from: Machine learning to classify animal species in camera trap images: applications in ecology

Micheal A. Tabak, Mohammad Sadegh Norouzzadeh, Michael A. Tabak, David W. Wolfson, Steven J. Sweeney, Paul A. Di Salvo, Ryan S. Miller, Jesse S. Lewis, Jeff Clune, Ryan K. Brook, Elizabeth G. Mandeville, Paul M. Lukacs, Anna K. Moeller, Raoul K. Boughton, Bethany Wight, James C. Beasley & Peter E. Schlichting
Motion‐activated cameras (“camera traps”) are increasingly used in ecological and management studies for remotely observing wildlife and are amongst the most powerful tools for wildlife research. However, studies involving camera traps result in millions of images that need to be analysed, typically by visually observing each image, in order to extract data that can be used in ecological analyses. We trained machine learning models using convolutional neural networks with the ResNet‐18 architecture and 3,367,383 images...

Data from: Rituximab vs placebo induction prior to glatiramer acetate monotherapy in multiple sclerosis

Justin M. Honce, Kavita V. Nair, Stefan Sillau, Brooke Valdez, Augusto Miravalle, Enrique Alvarez, Teri L. Schreiner, John R. Corboy & Timothy L. Vollmer
Objective: To examine whether rituximab induction followed by glatiramer acetate (GA) monotherapy is more effective than GA alone for the treatment of relapsing MS with active disease. Methods: This was a single center, double-blind, placebo-controlled study(NCT01569451). Fifty-five participants were randomly assigned (1:1ratio) to either rituximab (R-GA) or placebo induction (P-GA), followed by all participants initiating GA therapy. Participants were followed up to 3-years. The primary endpoint was the number of participants with no evidence of...

Data from: Odor alters color preference in a foraging jumping spider

Michael E. Vickers & Lisa A. Taylor
In many prey taxa with aposematic coloration, prey defenses also involve signals in other modalities (odors, sounds, etc.), yet the selective forces that have driven multimodality in warning displays are not well understood. One potential hypothesis that has recently received support in the avian literature (but has yet to be examined in invertebrates) is that different signal components may interact synergistically, such that one component of a signal (odor) may trigger a predator’s aversion to...

Data from: Irreproducible text-book 'knowledge': the effects of color bands on zebra finch fitness

Daiping Wang, Wolfgang Forstmeier, Malika Ihle, Mehdi Khadraoui, Sofia Jerónimo, Katrin Martin & Bart Kempenaers
Many fields of science currently experience a heated debate about the extent of publication bias against null-findings. Here, we show a case where putatively well-established text-book knowledge cannot be confirmed. Across four decades, zebra finch (Taeniopygia guttata) studies have reported effects of bands of certain colors on male or female attractiveness and further on behavior, physiology, life-history and fitness. Only 8 out of 39 publications presented exclusively null-findings. Here, we analyze the results of eight...

Data from: Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus

Heather Rose Kates, Matthew G. Johnson, Elliot M. Gardner, Nyree J.C. Zerega, Norman J. Wickett & Nyree J. C. Zerega
Premise of the study: Untapped information about allelic diversity within populations and individuals (i.e. heterozygosity) could improve phylogenetic resolution and accuracy. Many phylogenetic reconstructions ignore heterozygosity because it is difficult to assemble allele sequences and combine allelic data across unlinked loci and it is unclear how reconstruction methods accommodate variable sequences. We review the common methods of including heterozygosity in phylogenetic studies and present a novel method for assembling allele sequences from target enriched Illumina...

Data from: Globally consistent impact of tropical cyclones on the structure of tropical and subtropical forests

Thomas Ibanez, Gunnar Keppel, Christophe Menkes, Thomas W. Gillespie, Matthieu Lengaigne, Morgan Mangeas, Gonzalo Rivas-Torres & Philippe Birnbaum
1. Tropical cyclones (TCs) are large-scale disturbances that regularly impact tropical forests. Although long-term impacts of TCs on forest structure have been proposed, a global test of the relationship between forest structure and TC frequency and intensity is lacking. We test on a pantropical scale whether TCs shape the structure of tropical and subtropical forests in the long-term. 2. We compiled forest structural features (stem density, basal area, mean canopy height and maximum tree size)...

Data from: The evolution of anti-bat sensory illusions in moths

Juliette J. Rubin, Chris A. Hamilton, Chris J. W. McClure, Brad A. Chadwell, Akito Y. Kawahara & Jesse R. Barber
Prey transmit sensory illusions to redirect predatory strikes, creating a discrepancy between what a predator perceives and reality. We use the acoustic arms race between bats and moths to investigate the evolution and function of a sensory illusion. The spinning hindwing tails of silk moths (Saturniidae) divert bat attack by reflecting sonar to create a misleading echoic target. We characterized geometric morphometrics of moth hindwings across silk moths, mapped these traits onto a new, robust...

Data from: Rapid evolution and the genomic consequences of selection against interspecific mating

Martha O. Burford Reiskind, Paul Labadie, Irka Bargielowski, L. Philip Lounibos & Michael H. Reiskind
While few species introduced into a new environment become invasive, those that do provide critical information on ecological mechanisms that determine invasions success and the evolutionary responses that follow invasion. Aedes albopictus (the Asian tiger mosquito) was introduced into the naturalized range of Aedes aegypti (the yellow fever mosquito) in the USA in the mid-1980s, resulting in the displacement of A. aegypti in much of the southeastern USA. The rapid displacement was likely due to...

Data from: Temperature drives Zika virus transmission: evidence from empirical and mathematical models

Blanka Tesla, Leah Demakovsky, Erin Mordecai, Sadie Ryan, Matthew Bonds, Calistus Ngonghala, Melinda Brindley & Courtney Murdock
Temperature is a strong driver of vector-borne disease transmission. Yet, for emerging arboviruses we lack fundamental knowledge on the relationship between transmission and temperature. Current models rely on the untested assumption that Zika virus responds similarly to dengue virus, potentially limiting our ability to accurately predict the spread of Zika. We conducted experiments to estimate the thermal performance of Zika virus (ZIKV) in field-derived Aedes aegypti across eight constant temperatures. We observed strong, unimodal effects...

Data from: Impacts of inference method and dataset filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini)

Bryan S. McLean, Kayce C. Bell, Julia M. Allen, Kristofer M. Helgen, Joseph A. Cook & Julie M Allen
Phylogenomic datasets are illuminating many areas of the Tree of Life. However, the large size of these datasets alone may be insufficient to resolve problematic nodes in the most rapid evolutionary radiations, because inferences in zones of extraordinarily low phylogenetic signal can be sensitive to the model and method of inference, as well as the information content of loci employed. We used a dataset of >3,950 ultraconserved element (UCE) loci from a classic mammalian radiation,...

Data from: Collective aggressiveness of an ecosystem engineer is associated with coral recovery

Jonathan N. Pruitt, Carl N. Keiser, Brett T. Banka, John S. Liedle, Andrew J. Brooks, Russ J. Schmitt & Sally J. Holbrook
The ecological impacts of animal groups may be different and predictable depending on their collective behavior. Farmerfish (Stegastes nigricans) live in social groups and collectively defend gardens of palatable algae. These gardens also serve as settlement and nursery habitats for corals because farmerfish mob corallivores that attempt to forage on corals within their gardens. We detected large among-colony differences in farmerfish collective aggression towards intruder fish that persist across years. We further found that the...

Data from: Competition and coexistence in plant communities: intraspecific competition is stronger than interspecific competition

Peter B. Adler, Danielle Smull, Karen H. Beard, Ryan T. Choi, Tucker Furniss, Andrew Kulmatiski, Joan M. Meiners, Andrew T. Tredennick & Kari E. Veblen
Theory predicts that intraspecific competition should be stronger than interspecific competition for any pair of stably coexisting species, yet previous literature reviews found little support for this pattern. We screened over 5400 publications and identified 39 studies that quantified phenomenological intraspecific and interspecific interactions in terrestrial plant communities. Of the 67% of species pairs in which both intra- and interspecific effects were negative (competition), intraspecific competition was, on average, four to five-fold stronger than interspecific...

Data from: Defaunation and fragmentation erode small mammal diversity dimensions in tropical forests

Ricardo S. Bovendorp, Fernanda T. Brum, Robert A. McCleery, Benjamin Baiser, Rafael Loyola, Marcus V. Cianciaruso & Mauro Galetti
Forest fragmentation and defaunation are considered the main drivers of biodiversity loss, yet the synergistic effects of landscape changes and biotic interactions on assemblage structure have been poorly investigated. Here, we use an extensive dataset of 283 assemblages and 105 species of small mammals to understand how defaunation of medium and large mammals and forest fragmentation change the community composition and diversity of rodents and marsupials in tropical forests of South America. We used structured...

Data from: Terrestrial species adapted to sea dispersal: differences in propagule dispersal of two Caribbean mangroves

Richard G.J. Hodel, L. Lacey Knowles, Stuart F. McDaniel, Adam C. Payton, Jordan F. Dunaway, Pam S. Soltis, Douglas E. Soltis, Richard G. J. Hodel & Pamela S. Soltis
A central goal of comparative phylogeography is to understand how species-specific traits interact with geomorphological history to govern the geographic distribution of genetic variation within species. One key biotic trait with an immense impact on the spatial patterns of intraspecific genetic differentiation is dispersal. Here we quantify how species-specific traits directly related to dispersal affect genetic variation in terrestrial organisms with adaptations for dispersal by sea, not land—the mangroves of the Caribbean. We investigate the...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Florida
  • University of Georgia
  • Michigan State University
  • University of Michigan-Ann Arbor
  • Florida Museum of Natural History
  • Max Planck Institute for Ornithology
  • University of Montana
  • University of Adelaide
  • Rice University
  • Stanford University