630 Works

Data from: Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data

Xuankun Li, Ryan St Laurent, Chandra Earl, Camiel Doorenweerd, Erik Van Nieukerken, Don Davis, Atsushi Kawakita, Shigeki Kobayashi, Andreas Zwick, Carlos Lopez-Vaamonde, Issei Ohshima & Akito Kawahara
Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially at the subfamily level, remain largely uncertain. Genomic data (83 taxa and 589 loci) were integrated with Sanger data (130 taxa and...

Phylogeny of African long-fingered frogs (Arthroleptidae: Cardioglossa) reveals recent allopatric divergences in coloration

David Blackburn
The African anuran genus Cardioglossa contains 19 described species, most of which are distinguished from one another by striking patterns and colors. We present a well- resolved phylogeny based on analyses of mitochondrial and nuclear loci for 18 species of Cardioglossa. This provides the basis for species-delimitation analyses and interpreting historical biogeography in the genus. Whereas much of the diversification within the genus occurred among Central African lineages during the Miocene following the origin of...

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: Tropical bird species have less variable body sizes

Quentin D. Read, Benjamin Baiser, John M. Grady, Phoebe L. Zarnetske, Sydne Record & Jonathan Belmaker
Ecologists have often predicted that species’ niche breadths should decline toward the equator. Dan Janzen arrived at this prediction based on climatic constraints, while Robert MacArthur argued that a latitudinal gradient in resource specialization drives the pattern. This idea has some support when it comes to thermal niches, but has rarely been explored for other niche dimensions. Body size is linked to niche dimensions related to diet, competition, and environmental tolerance in vertebrates. We identified...

Data from: A survey of digitized data from U.S. fish collections in the iDigBio data aggregator

Randal A. Singer, Kevin J. Love & Lawrence M. Page
Recent changes in institutional cyberinfrastructure and collections data storage methods have dramatically improved accessibility of specimen-based data through the use of digital databases and data aggregators. This analysis of digitized fish collections in the U.S. demonstrates how information from data aggregators, in this case iDigBio, can be extracted and analyzed. Data from U.S. institutional fish collections in iDigBio were explored through a strictly programmatic approach using the ridigbio package and fishfindR web application. iDigBio facilitates...

Data from: Character evolution and the origin of Caimaninae (Crocodylia) in the New World Tropics: new evidence from the Miocene of Panama and Venezuela

Alexander K. Hastings, Moritz Reisser & Torsten M. Scheyer
Alligators and caimans share a close relationship, supported by both molecular and morphological characters. The divergence between alligators and caimans has been difficult to discern in the fossil record. Two basal taxa have recently been described from the Miocene of Panama and Venezuela but have not yet been presented in a joint phylogeny. Continued preparation of the type material of the Venezuelan Globidentosuchus brachyrostris Scheyer et al., 2013 has revealed new characters for scoring in...

Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence

Yibo Dong, Shichao Chen, Shifeng Cheng, Wenbin Zhou, Qing Ma, Zhiduan Chen, Cheng-Xin Fu, Xin Liu, Yun-Peng Zhao, Pamela S. Soltis, Gane Ka-Shu Wong, Douglas E. Soltis & Jenny Xiang
Background: Geographic speciation is a major force in generating biodiversity. However, how genomes diverge over time after geographic isolation has halted gene flow has remained unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) from transcriptomes in 20 allopatric species/variety pairs from diverse angiosperm clades. Sixteen of these pairs reflect the well-known eastern Asia – eastern North America floristic disjunction; these species have been isolated for different lengths of time, from the Miocene...

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: Three keys to the radiation of angiosperms into freezing environments

Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O'Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafaël Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman … & Alejandro Ordonez
Early flowering plants are thought to have been woody species restricted to warm habitats1, 2, 3. This lineage has since radiated into almost every climate, with manifold growth forms4. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf...

Data from: Size, sex, and individual-level behavior drive intra-population variation in cross-ecosystem foraging of a top-predator

James C. Nifong, Craig A. Layman & Brian R. Silliman
1. Large-bodied, top-predators are often highly mobile, with the potential to provide important linkages between spatially distinct food webs. What biological factors contribute to variation in cross-ecosystem movements, however, have rarely been examined. 2. Here, we investigated how ontogeny (body size), sex, and individual-level behavior impacts intra-population variation in cross-ecosystem foraging (i.e., between freshwater and marine systems), by the top-predator Alligator mississippiensis. 3. Field surveys revealed A. mississippiensis uses marine ecosystems regularly and are abundant...

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: 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: Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

Kamal Choudhary, Faical Yannick P. Congo, Tao Liang, Chandler Becker, Richard G. Hennig & Francesca Tavazza
Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT)...

Data from: Oxidative stress-mediated NFκB phosphorylation upregulates p62/SQSTM1 and promotes retinal pigmented epithelial cell survival through increased autophagy

Chunjuan Song, Sayak K. Mitter, Xiaoping Qi, Eleni Beli, Haripriya V. Rao, Jindong Ding, Colin S. Ip, Hongmei Gu, Debra Akin, William A. Dunn, Catherine Bowes Rickman, Alfred S. Lewin, Maria B. Grant & Michael E. Boulton
p62 is a scaffolding adaptor implicated in the clearance of protein aggregates by autophagy. Reactive oxygen species (ROS) can either stimulate or inhibit NFκB-mediated gene expression influencing cellular fate. We studied the effect of hydrogen peroxide (H2O2)-mediated oxidative stress and NFκB signaling on p62 expression in the retinal pigment epithelium (RPE) and investigated its role in regulation of autophagy and RPE survival against oxidative damage. Cultured human RPE cell line ARPE-19 and primary human adult...

Data from: Community phylogeny of the globally critically imperiled pine rockland ecosystem

Lauren B. Trotta, Benjamin Baiser, Jennifer Possley, Daijiang Li, James Lange, Sarah Martin & Emily B. Sessa
Premise of the study: Community phylogenetic methods incorporate information on evolutionary relationships into studies of organismal assemblages. We used a community phylogenetic framework to investigate relationships and biogeographic affinities and calculate phylogenetic signal of endemism and invasiveness for the flora of the pine rocklands, a globally critically imperiled ecosystem with a significant portion of its distribution in South Florida, United States. Methods: We reconstructed phylogenetic relationships of 538 vascular plant taxa, which represents 92.28% of...

Data from: Unmanned aerial systems measure structural habitat features for wildlife across multiple scales

Peter J. Olsoy, Lisa A. Shipley, Janet L. Rachlow, Jennifer S. Forbey, Nancy F. Glenn, Matthew A. Burgess & Daniel H. Thornton
1.Assessing habitat quality is a primary goal of ecologists. However, evaluating habitat features that relate strongly to habitat quality at fine-scale resolutions across broad-scale extents is challenging. Unmanned aerial systems (UAS) provide an avenue for bridging the gap between relatively high spatial resolution, low spatial extent field-based habitat quality measurements and lower spatial resolution, higher spatial extent satellite-based remote sensing. Our goal in this study was to evaluate the potential for UAS structure from motion...

Data from: Population genomics and morphometric assignment of western honey bees (Apis mellifera L.) in the Republic of South Africa

Amin Eimanifar, Samantha A. Brooks, Tomas Bustamante & James D. Ellis
Backgrounds: Apis mellifera scutellata and A.m. capensis (the Cape honey bee) are western honey bee subspecies indigenous to the Republic of South Africa (RSA). Both bees are important for biological and economic reasons. First, A.m. scutellata is the invasive "African honey bee" of the Americas and exhibits a number of traits that beekeepers consider undesirable. They swarm excessively, are prone to absconding (vacating the nest entirely), usurp other honey bee colonies, and exhibit heightened defensiveness....

Data from: A comprehensive and dated phylogenomic analysis of butterflies

Marianne Espeland, Jesse W. Breinholt, Keith R. Willmott, Andrew D. Warren, Roger Vila, Emmanuel F. A. Toussaint, Sarah C. Maunsell, Kwaku Aduse-Poku, Gerard Talavera, Rodney Eastwood, Marta A. Jarzyna, Robert Guralnick, David J. Lohman, Naomi E. Pierce, Akito Y. Kawahara, Jesse Breinholt & Emmanuel F.A. Toussaint
Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species...

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: Snail herbivory affects seedling establishment in a temperate forest in the Ozark region

Anna J. Liang, Claudia Stein, Eleanor Pearson, Jonathan A. Myers, Raelene M. Crandall & Scott A. Mangan
1. Species-specific herbivores are hypothesized to maintain plant diversity by preventing the dominance of any one plant species. However, a large proportion of herbivores have wide host ranges, and these generalists could have similar effects on plant community composition if they exhibit differences in their host preference. Here, we coupled lab and field experiments to test whether a common forest-understory snail (Neohelix alleni), a generalist herbivore, has the potential to influence forest composition through differential...

Data from: A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India

Seenapuram Palaniswamy Vijayakumar, Robert Alexander Pyron, K. P. Dinesh, Varun R. Torsekar, Achyuthan N. Srikanthan, Priyanka Swamy, Edward L. Stanley, David C. Blackburn & Kartik Shanker
The Western Ghats (WG) is an escarpment on the west coast of Peninsular India, housing one of the richest assemblages of frogs in the world, with three endemic families. Here, we report the discovery of a new ancient lineage from a high-elevation massif in the Wayanad Plateau of the southern WG. Phylogenetic analysis reveals that the lineage belongs to Natatanura and clusters with Nyctibatrachidae, a family endemic to the WG/Sri Lanka biodiversity hotspot. Based on...

Data from: Distance-decay differs among vertical strata in a tropical rainforest

Edmund W. Basham, Christa M. Seidl, Lydou R. Andriamahohatra, Brunno F. Oliveira & Brett R. Scheffers
1. Assemblage similarity decays with geographic distance—a pattern known as the distance-decay relationship. While this pattern has been investigated for a wide range of organisms, ecosystems, and geographical gradients, whether these changes vary more cryptically across different forest strata (from ground to canopy) remains elusive. 2. Here, we investigated the influence of ground vs arboreal assemblages to the general distance-decay relationship observed in forests. We seek to explain differences in distance-decay relationships between strata in...

Data from: Patterns of reproductive isolation in Nolana (Chilean Bellflower)

Cathleen Jewell, Amy Douglas Papineau, Rosanna Freyre & Leonie Clare Moyle
We examined reproductive isolating barriers at four postmating stages among 11 species from the morphologically diverse genus Nolana (Solanaceae). At least one stage was positively correlated with both genetic and geographic distance between species. Postzygotic isolation was generally stronger and faster evolving than postmating prezygotic isolation. In addition, there was no evidence for mechanical isolation or for reproductive character displacement in floral traits that can influence pollinator isolation. In general, among the potential isolating stages...

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