550 Works

Changes in tree community structures in defaunated forests are not driven only by dispersal limitation

Kirstie Hazelwood, C. E. Timothy Paine, Fernando H. Cornejo-Valverde, Elizabeth G. Pringle, Harald Beck & John Terborgh
1. Bushmeat hunting has reduced population sizes of large frugivorous vertebrates throughout the tropics, thereby reducing the dispersal of seeds. This is believed to affect tree population dynamics, and therefore community composition, because the seed dispersal of large-seeded trees depends upon large-bodied vertebrates. 2. We report on a long-running study of the effect of defaunation on a tropical tree community. In three censuses over 11 years, we compared sapling recruitment between a hunted and a...

MHC variation is similar in little brown bats before and after white-nose syndrome outbreak

Xueling Yi, Emily Latch, Deahn Donner, Paula Marquardt, Jonathan Palmer, Michelle Jusino, Jacqueline Frair & Daniel Lindner
White-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans (Pd), has driven alarming declines in North American hibernating bats, such as little brown bat (Myotis lucifugus). During hibernation, infected little brown bats are able to initiate anti-Pd immune responses, indicating pathogen-mediated selection on the major histocompatibility complex (MHC) genes. However, such immune responses may not be protective as they interrupt torpor, elevate energy costs, and potentially lead to higher mortality rates. To assess whether...

Functional trait table for mixed-species flocking birds in the Western Andes of Colombia

Harrison Jones & Scott Robinson
These data represent functional traits relevant to the foraging ecology and habitat preferences of mixed-species flock joining bird species from the Western Andes of Colombia. We collected these data based on published data for the species from the Handbook of the Birds Alive online database (del Hoyo et al. 2020), supplemented with additional natural history references were available, with the objective of calculating the functional richness contained in mixed-species flock compositions sampled across a patch...

Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology

Sean Wu, Penny Hancock, Arnaud Le Menach, Tanya Russell, Thomas Burkot, , Derek Cummings, Kelly Compton, Daniel Citron, John Marshall, Biyonka Liang, Catherine Moyes, Qian Zhang, David Smith, Samson Kiware, Anne Wilson, Thomas Scott, John Henry, Steven Lindsay, Amit Verma & Hector Sanchez C.
Mosquitoes are important vectors for pathogens that infect humans and other vertebrate animals. Some aspects of adult mosquito behavior and mosquito ecology play an important role in determining the capacity of vector populations to transmit pathogens. Here, we re-examine factors affecting the transmission of pathogens by mosquitoes using a new approach. Unlike most previous models, this framework considers the behavioral states and state transitions of adult mosquitoes through a sequence of activity bouts. We developed...

Amborella pangenome and supplementary tables v3

Ricky Hu , , , , , , , , &

Woody encroachment happens via intensification, not extensification, of species ranges in an African savanna

Yong Zhou, Morgan Tingley, Madelon Case, Corli Coetsee, Gregory Kiker, Rheinhardt Scholtz, Freek Venter & Carla Staver
Widespread woody encroachment is a prominent concern for savanna systems as it is often accompanied by losses in productivity and biodiversity. Extensive ecosystem-level work has advanced our understanding of its causes and consequences. However, there is still debate over whether local management can override regional and global drivers of woody encroachment, and it remains largely unknown how encroachment influences woody community assemblages. Here, we examined species-level changes in woody plant distributions and size structure from...

Hemipteran defensive odors trigger predictable color biases in jumping spider predators

Michael Vickers & Lisa Taylor
Multimodal warning displays often pair one signal modality (odor) with a second modality (color) to avoid predation. Experiments with bird predators suggest these signal components interact synergistically, with aversive odors triggering otherwise hidden aversions to particular prey colors. In a recent study, this phenomenon was found in a jumping spider (Habronattus trimaculatus), with the defensive odor from a coreid bug (Acanthocephala femorata) triggering an aversion to red. Here, we explore how generalizable this phenomenon is...

Rare missense functional variants at COL4A1 and COL4A2 in sporadic intracerebral hemorrhage

Jaeyoon Chung, Graham Hamilton, Minsup Kim, Sandro Marini, Bailey Montgomery, Jonathan Henry, Art Cho, Devin Brown, Bradford Worrall, James Meschia, Scott Silliman, Magdy Selim, David Tirschwell, Chelsea Kidwell, Brett Kissela, Steven Greenberg, Anand Viswanathan, Joshua Goldstein, Carl Langefeld, Kristiina Rannikmae, Catherine Sudlow, Neshika Samarasekera, Mark Rodrigues, Rustam Salman, James Prendergast … & Christopher Anderson
Objective To test the genetic contribution of rare missense variants in COL4A1 and COL4A2 in which common variants are genetically associated with sporadic intracerebral hemorrhage (ICH), we performed rare variant analysis in multiple sequencing data for the risk for sporadic ICH. Methods We performed sequencing across 559Kbp at 13q34 including COL4A1 and COL4A2 among 2,133 individuals (1,055 ICH cases; 1,078 controls) in US-based and 1,492 individuals (192 ICH cases; 1,300 controls) from Scotland-based cohorts, followed...

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: 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: 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...

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: 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: Simulated hatching failure predicts female plasticity in extra-pair behavior over successive broods

Teru Yuta, Daisuke Nomi, Malika Ihle & Itsuro Koizumi
While many studies have investigated the occurrence of extra-pair paternity (EPP) and its adaptive significance in wild population of birds, we still know surprising little about the plasticity in mating behavior of females at the individual level and how it affects the patterns of paternity. To address this question, we focused on the direct fertility benefit hypothesis for the function of EPP and studied if female birds react in extra-pair mating behavior after reproductive failures...

Data from: Fire, fragmentation, and windstorms: a recipe for tropical forest degradation

Divino V. Silvério, Paulo M. Brando, Mercedes M.C. Bustamante, Francis E. Putz, Daniel Magnabosco Marra, Shaun R. Levick & Susan E. Trumbore
1. Widespread degradation of tropical forests is caused by a variety of disturbances that interact in ways that are not well understood. 2. To explore potential synergies between edge effects, fire and windstorm damage as causes of Amazonian forest degradation, we quantified vegetation responses to a 30-minute high-intensity windstorm that in 2012, swept through a large-scale fire experiment that borders an agricultural field. Our pre- and post-windstorm measurements include tree mortality rates and modes of...

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: Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use

Ryan A. Long, Alois Wambua, Jacob R. Goheen, Todd M. Palmer & Robert M. Pringle
Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance. We sought to understand (i) how LMH indirectly shape small-mammal habitat use by altering the density and distribution of understorey...

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: 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: 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 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: Molecular phylogenetics and the evolution of fruit and leaf morphology of Dichaea (Orchidaceae: Zygopetalinae)

Kurt M. Neubig, Norris H. Williams, W. Mark Whitten & Franco Pupulin
BACKGROUND AND AIMS: The orchid genus Dichaea, with over 100 species found throughout the neotropics, is easily recognized by distichous leaves on long stems without pseudobulbs and flowers with infrastigmatic ligules. The genus has previously been divided into four sections based primarily on presence of ovary bristles and a foliar abscission layer. The aim of this work is to use DNA sequence data to estimate phylogenetic relationships within Dichaea and map the distribution of major...

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: Greenhouse biogeography: the relationship of geographic range to invasion and extinction in the Cretaceous Western Interior Seaway

Corinne E. Myers, , Bruce S. Lieberman & Richard A. MacKenzie
Significant warming of Earth's climate in the near term seems increasingly likely. If significant enough, this climatic regime could, in the long term, come to resemble previous greenhouse intervals in earth history. Consequently, analysis of the fossil record during periods of extreme warmth may provide important lessons for species biology, including biogeography, in a much warmer world. To explore this issue, we analyzed the biogeographic response of 63 molluscan species to the long-term global warmth...

Data from: A maximum likelihood approach to generate hypotheses on the evolution and historical biogeography in the Lower Volga Valley regions (southwest Russia)

Evgeny V. Mavrodiev, Alexy P. Laktionov & Nico Cellinese
The evolution of the diverse flora in the Lower Volga Valley (LVV) (southwest Russia) is complex due to the composite geomorphology and tectonic history of the Caspian Sea and adjacent areas. In the absence of phylogenetic studies and temporal information, we implemented a maximum likelihood (ML) approach and stochastic character mapping reconstruction aiming at recovering historical signals from species occurrence data. A taxon-area matrix of 13 floristic areas and 1018 extant species was constructed and...

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