632 Works

Data from: Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages

Timothy Trevor Caughlin, Jake M. Ferguson, Jeremy W. Lichstein, Pieter A. Zuidema, Sarayudh Bunyavejchewin & Douglas J. Levey
Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on tree population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed tree abundance in overhunted forests contradict demographic models which predict minimal sensitivity of tree population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could...

Data from: Differential responses of marine communities to natural and anthropogenic changes

Michal Kowalewski, Jacelyn M. Wittmer, Troy A. Dexter, Alessandro Amorosi & Daniele Scarponi
Responses of ecosystems to environmental changes vary greatly across habitats, organisms, and observational scales. The Quaternary fossil record of the Po Basin demonstrates that marine communities of Northern Adriatic reemerged unchanged following the most recent glaciation, which lasted ~100,000 years. The Late Pleistocene and Holocene interglacial ecosystems were both dominated by the same species, species turnover rates approximated predictions of resampling models of a homogenous system, and comparable bathymetric gradients in species composition, sample-level diversity,...

Data from: Ancestral polyploidy in seed plants and angiosperms

Yuannian Jiao, Norman J. Wickett, Ayyampalayam Saravanaraj, André S. Chanderbali, Lena Landherr, Paula E. Ralph, Lynn P. Tomsho, Yi Hu, Haiying Liang, Pamela S. Sotis, Douglas E. Soltis, Sandra W. Clifton, Scott E. Schlarbaum, Stephan C. Schuster, Hong Ma, Jim Leebens-Mack & Claude W. DePamphilis
Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive...

Data from: De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome

Péter Szövényi, Pierre-François Perroud, Aikaterini Symeonidi, Sean Stevenson, Ralph S. Quatrano, Stefan A. Rensing, Andrew C. Cuming & Stuart F. McDaniel
The bryophytes are a morphologically and ecologically diverse group of plants that have recently emerged as major model systems for a variety of biological processes. In particular, the genome sequence of the moss, Physcomitrella patens, has significantly enhanced our understanding of the evolution of developmental processes in land plants. However, to fully explore the diversity within bryophytes, we need additional genomic resources. Here we describe analyses of the transcriptomes of a male and a female...

Data from: A selective fungal transport organ (mycangium) maintains coarse phylogenetic congruence between fungus-farming ambrosia beetles and their symbionts

James Skelton, Andrew J. Johnson, Michelle A. Jusino, Craig C. Bateman, You Li & Jiri Hulcr
Thousands of species of ambrosia beetles excavate tunnels in wood to farm fungi. They maintain associations with particular lineages of fungi, but the phylogenetic extent and mechanisms of fidelity are unknown. We test the hypothesis that selectivity of their mycangium enforces fidelity at coarse phylogenetic scales, while permitting promiscuity among closely related fungal mutualists. We confirm a single evolutionary origin of the Xylosandrus complex – a group of several xyleborine genera that farm fungi in...

Data from: High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales

Rosanne A. Healy, Matthew E. Smith, Gregory M. Bonito, Donald H. Pfister, Gonzalo G. Guevara, Caroline Hobart, Leticia Kumar, Thai Lee, Katherine Stafford, Zai-Wei Ge, Rytas Vilgalys, Gwendolyn Williams, James Trappe, David J. McLaughlin &
Fungal mitospores may function as dispersal units and/ or spermatia and thus play a role in distribution and/or mating of species that produce them. Mitospore production in ectomycorrhizal (EcM) Pezizales is rarely reported, but here we document mitospore production by a high diversity of EcM Pezizales on three continents, in both hemispheres. We sequenced the internal transcribed spacer (ITS) and partial large subunit (LSU) nuclear rDNA from 292 spore mats (visible mitospore clumps) collected in...

Data from: Phylogeny of the island archipelago frog genus Sanguirana: another endemic Philippine radiation that diversified 'Out-of-Palawan'

Rafe M. Brown, Yong-Chao Su, Brenna Barger, Cameron D. Siler, Marites B. Sanguila, Arvin C. Diesmos & David C. Blackburn
Recent higher-level frog phylogenetic analyses have included a few members of the endemic Philippine frog genus Sanguirana. Although the monophyly of the group has never been disputed, the recent phylogenetically-supported inclusion of the Palawan Wood Frog (Sanguirana sanguinea) in this clade was highly unexpected. In addition, species boundaries and relationships remain unclear and new species continue to be discovered. We estimate the phylogeny for this endemic Philippine genus using two mitochondrial gene regions and six...

Data from: A hyperspectral image can predict tropical tree growth rates in single-species stands

T. Trevor Caughlin, Sarah J. Graves, Gregory P. Asner, Michiel Van Breugel, Jefferson S. Hall, Roberta E. Martin, Mark S. Ashton & Stephanie A. Bohlman
Remote sensing is increasingly needed to meet the critical demand for estimates of forest structure and composition at landscape to continental scales. Hyperspectral images can detect tree canopy properties, including species identity, leaf chemistry and disease. Tree growth rates are related to these measurable canopy properties but whether growth can be directly predicted from hyperspectral data remains unknown. We used a single hyperspectral image and LiDAR-derived elevation to predict growth rates for twenty tropical tree...

Data from: Microbe biogeography tracks water masses in a dynamic oceanic frontal system

Anni Djurhuus, Philipp H. Boersch-Supan, Svein-Ole Mikalsen, Alex D. Rogers & Helge-Ansgar Giebel
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN ANOTHER PUBLICATION. PLEASE SEE http://dx.doi.org/10.1098/rsos.160829. Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance–decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a...

Data from: Short-term effects of elevated precipitation and nitrogen on soil fertility and plant growth in a Neotropical savanna

Stella M. Copeland, Emilio M. Bruna, Laura V. Barbosa Silva, Michelle C. Mack & Heraldo L. Vasconcelos
Increasing nitrogen (N) deposition and changing precipitation patterns in Neotropical savannas could alter plant growth, reproduction, and nutrients by altering soil nutrient and water availability. We examined the potential for simulated N deposition and increased dry season precipitation to have interactive effects on reproduction and growth of two abundant native Cerrado (Brazilian savanna) grasses – Loudetiopsis chrysothrix and Tristachya leiostachya – via feedbacks with soil nutrient status. Plant growth and reproduction responses consistently varied by...

Data from: Changing light conditions in pine rockland habitats affect the intensity and outcome of ant–plant interactions

Ian M. Jones, Suzanne Koptur, Hilma R. Gallegos, Joseph P. Tardanico, Patricia A. Trainer & Jorge Peña
Extrafloral nectar (EFN) mediates food-for-protection mutualisms between plants and ants. Such mutualisms exist within a complex web of biotic interactions, and in a framework provided by the abiotic environment. Both biotic and abiotic factors, therefore, affect the outcome of ant–plant interactions. We conducted an experiment to determine the effects of ant activity, and light intensity, on herbivory rates, growth, and reproductive fitness in Senna mexicana var. chapmanii, a perennial legume native to pine rockland habitats...

Data from: Orchid phylogenomics and multiple drivers of their extraordinary diversification

Thomas J. Givnish, Daniel Spalink, Mercedes Ames, Stephanie P. Lyon, Steven J. Hunter, Alejandro Zuluaga, William J. D. Iles, Mark A. Clements, Mary T. K. Arroyo, James Leebens-Mack, Lorena Endara, Ricardo Kriebel, Kurt M. Neubig, W. Mark Whitten, Norris H. Williams & Kenneth M. Cameron
Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144...

Data from: Rapid diversification associated with ecological specialization in Neotropical Adelpha butterflies

Emily R. Ebel, Jeffrey M. DaCosta, Michael D. Sorenson, Ryan I. Hill, Adriana D. Briscoe, Keith R. Willmott & Sean P. Mullen
Rapid diversification is often associated with morphological or ecological adaptations that allow organisms to radiate into novel niches. Neotropical Adelpha butterflies, which comprise over 200 species and subspecies, are characterized by extraordinary breadth in host plant use and wing colour patterns compared to their closest relatives. To examine the relationship between phenotypic and species diversification, we reconstructed the phylogenetic history of Adelpha and its temperate sister genus Limenitis using genomewide restriction-site-associated DNA (RAD) sequencing. Despite...

Data from: The Red Death meets the abdominal bristle: polygenic mutation for susceptibility to a bacterial pathogen in Caenorhabditis elegans

Veronique Etienne, Erik C. Andersen, José Miguel Ponciano, Dustin Blanton, Analucia Cadavid, Joanna Joyner-Matos, Chikako Matsuba, Brandon Tabman & Charles F. Baer
Understanding the genetic basis of susceptibility to pathogens is an important goal of medicine and of evolutionary biology. A key first step toward understanding the genetics and evolution of any phenotypic trait is characterizing the role of mutation. However, the rate at which mutation introduces genetic variance for pathogen susceptibility in any organism is essentially unknown. Here we quantify the per-generation input of genetic variance by mutation (VM) for susceptibility of Caenorhabditis elegans to the...

Data from: From refugia to rookeries: phylogeography of Atlantic green turtles

Eugenia Naro-Maciel, Brendan N. Reid, S. Elizabeth Alter, George Amato, Karen A. Bjorndal, Alan B. Bolten, Meredith Martin, Campbell J. Nairn, Brian Shamblin & Oscar Pineda-Catalan
Investigating species’ distribution and abundance over time is central to evolutionary biology, and provides important context for conservation and management. With respect to population genetic structure in green sea turtles (Chelonia mydas), certain processes such as female philopatry to natal rookeries are well understood, while others, such as male philopatry and historical changes in distribution and abundance, remain relatively understudied. Further, although inferences from mitochondrial DNA and nuclear microsatellites have both been critical in identifying...

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: Chronic anthropogenic noise disrupts glucocorticoid signaling and has multiple effects on fitness in an avian community

Nathan J. Kleist, Robert P. Guralnick, Alexander Cruz, Christopher A. Lowry & Clinton D. Francis
Anthropogenic noise is a pervasive pollutant that decreases environmental quality by disrupting a suite of behaviors vital to perception and communication. However, even within populations of noise-sensitive species, individuals still select breeding sites located within areas exposed to high noise levels, with largely unknown physiological and fitness consequences. We use a study system in the natural gas fields of northern New Mexico to test the prediction that exposure to noise causes glucocorticoid-signaling dysfunction and decreases...

Data from: Changing measurements or changing movements? Sampling scale and movement model identifiability across generations of biologging technology

Leah R. Johnson, Philipp H. Boersch-Supan, Richard A. Phillips & Sadie J. Ryan
1. Animal movement patterns contribute to our understanding of variation in breeding success and survival of individuals, and the implications for population dynamics. 2. Over time, sensor technology for measuring movement patterns has improved. Although older technologies may be rendered obsolete, the existing data are still valuable, especially if new and old data can be compared to test whether a behavior has changed over time. 3. We used simulated data to assess the ability to...

Data from: Multi-decadal time series of remotely sensed vegetation improves prediction of soil carbon in a subtropical grassland

Chris H. Wilson, T. Trevor Caughlin, Sami W. Rifai, Elizabeth H. Boughton, Michelle C. Mack & S. Luke Flory
Soil carbon sequestration in agroecosystems could play a key role in climate change mitigation but will require accurate predictions of soil organic carbon (SOC) stocks over spatial scales relevant to land management. Spatial variation in underlying drivers of SOC, such as plant productivity and soil mineralogy, complicates these predictions. Recent advances in the availability of remotely sensed data make it practical to generate multidecadal time series of vegetation indices with high spatial resolution and coverage....

Data from: Logging and indigenous hunting impacts on persistence of large Neotropical animals

Anand Roopsind, T. Trevor Caughlin, Hemchandranauth Sambhu, Jose M.V. Fragoso, Francis E. Putz., Francis E. Putz & Jose M. V. Fragoso
Areas allocated for industrial logging and community-owned forests account for over 50% of all remaining tropical forests. Landscape-scale conservation strategies that include these forests are expected to have substantial benefits for biodiversity, especially for large mammals and birds that require extensive habitat but that are susceptible to extirpation due to synergies between logging and hunting. In addition, their responses to logging alone are poorly understood due to their cryptic behavior and low densities. In this...

Numbers of individuals and endemicity for birds in three study sites of the Himalayas-Hengduan mountains of China

Yiming Hu, Brett Scheffers, Xinyuan Pan, Huijian Hu, Zhixin Zhou, Dan Liang, Cheng Wenda, Zhixin Wen & Luke Gibson
1. Describing the patterns and revealing the underlying mechanisms responsible for variations in community structure remains a central focus in ecology. However, important gaps remain, including our understanding of species abundance. Most studies on abundance-based relationships are from either temperate ecosystems or tropical ecosystems, and few have explicitly tested abundance-based relationships across a temperate to tropical ecotone. 2. Here, we use a comprehensive dataset of breeding birds across elevation spanning a temperate to subtropical gradient...

Data from: Ancestral polyploidy in seed plants and angiosperms

Yuannian Jiao, Norman J. Wickett, Ayyampalayam Saravanaraj, André S. Chanderbali, Lena Landherr, Paula E. Ralph, Lynn P. Tomsho, Yi Hu, Haiying Liang, Pamela S. Sotis, Douglas E. Soltis, Sandra W. Clifton, Scott E. Schlarbaum, Stephan C. Schuster, Hong Ma, Jim Leebens-Mack & Claude W. DePamphilis
Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive...

Data from: Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity

Jonathan L. Payne, Alison G. Boyer, James H. Brown, Seth Finnegan, Michal Kowaleski, , S. Kathleen Lyons, Craig R. McClain, Daniel W. McShea, Phillip M. Novack-Gottshall, Felisa A. Smith, Jennifer A. Stempien, Steve C. Wang, D. W. McShea, M. Kowalewski, J. L. Payne, R. A. Krause, S. C. Wang, P. M. Novack-Gottshall, A. G. Boyer, J. H. Brown & F. A. Smith
NOTE: See also http://bodysize.nescent.org. ABSTRACT: The maximum size of organisms has increased enormously since the initial appearance of life >3.5 billion years ago (Gya), but the pattern and timing of this size increase is poorly known. Consequently, controls underlying the size spectrum of the global biota have been difficult to evaluate. Our period-level compilation of the largest known fossil organisms demonstrates that maximum size increased by 16 orders of magnitude since life first appeared in...

Data from: The geographical and institutional distribution of ecological research in the tropics

Gabriela Stocks, Lisa Seales, Franklin Paniagua, Erin Maehr & Emilio M. Bruna
We reviewed 1333 papers published in Biotropica and the Journal of Tropical Ecology from 1995 to 2004. Only 62 percent of tropical countries were represented in our survey, with 62 percent of the publications based on research conducted in only ten countries. Sixty-two percent of papers had lead authors that were based at institutions outside the country where the research was conducted. Cross-national collaboration was limited, accounting for only 28 percent of papers with multiple...

Data from: Splitting an ancient icon: mummy DNA resurrects a cryptic Nile crocodile

Evon Hekkala, Matthew H. Shirley, George Amato, James D. Austin, Suellen Charter, John Thorbjarnarson, Kent A. Vliet, Marlys L. Houck, Robert DeSalle & Michael J. Blum
The Nile crocodile (Crocodylus niloticus) is an ancient icon of both cultural and scientific interest. The species is emblematic of the great civilizations of the Nile River valley and serves as a model for international wildlife conservation. Despite its familiarity, a centuries-long dispute over the taxonomic status of the Nile crocodile remains unresolved. This dispute not only confounds our understanding of the origins and biogeography of the “true crocodiles” of the crown genus Crocodylus, but...

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