191 Works

Data from: Differentiating the evolution of female song and male-female duets in the New World blackbirds: can tropical natural history traits explain duet evolution?

Karan J. Odom, Kevin E. Omland & J. Jordan Price
Female bird song and combined vocal duets of mated pairs are both frequently associated with tropical, monogamous, sedentary natural histories. Little is known, however, about what selects for duetting behavior versus female song. Female song likely preceded duet evolution and could drive apparent relationships between duets and these natural histories. We compared the evolution of female song and male-female duets in the New World blackbirds (Icteridae) by investigating patterns of gains and losses of both...

Data from: The incidence and pattern of co-pollinator diversification in dioecious and monoecious figs

Li Yuan Yang, Carlos A. Machado, Xiao-Dong Dang, Yan-Qiong Peng, Da-Rong Yang, Wan-Jin Liao, Da-Yong Zhang & Li-Yuan Yang
Differences in breeding system are associated with correlated ecological and morphological changes in plants. In Ficus, dioecy and monoecy are strongly associated with different suites of traits (tree height, population density, fruiting frequency, pollinator dispersal ecology). Although ~30% of fig species are pollinated by multiple species of fig-pollinating wasps it has been suggested that co-pollinators are rare in dioecious figs. Here we test whether there is a connection between fig breeding system and co-pollinator incidence...

Data from: Neighborhood defense gene similarity effects on tree performance: a community transcriptomic approach

Jenny Zambrano, Yoshiko Iida, Robert Howe, Luxiang Lin, Maria Natalia Umana, Amy Wolf, Samantha J. Worthy & Nathan G. Swenson
The structure and dynamics of ecological communities are ultimately the outcome of the differential demographic rates of individuals. Individual growth and mortality rates largely result from the interaction between an organism's phenotype and the abiotic and biotic environment. Functional traits have been used extensively over the past decade to elucidate links among phenotypes, demography and community dynamics. A fundamental weakness of most functional trait approaches is the use of ‘soft’ traits associated with resource acquisition...

Data from: Year-round spatiotemporal distribution of harbour porpoises within and around the Maryland wind energy area

Jessica E. Wingfield, Michael O'Brien, Vyacheslav Lyubchich, Jason J. Roberts, Patrick N. Halpin, Aaron N. Rice, Helen Bailey & Michael O’Brien
Offshore windfarms provide renewable energy, but activities during the construction phase can affect marine mammals. To understand how the construction of an offshore windfarm in the Maryland Wind Energy Area (WEA) off Maryland, USA, might impact harbour porpoises (Phocoena phocoena), it is essential to determine their poorly understood year-round distribution. Although habitat-based models can help predict the occurrence of species in areas with limited or no sampling, they require validation to determine the accuracy of...

Data from: Combined effects of seed and soil quality drive seedling performance of a late-successional canopy tree in a tropical forest

Jenny Zambrano, Henry F. Howe & Miquel Gonzalez-Meler
Habitat loss and fragmentation affect the structure and functioning of forested ecosystems worldwide, yet we lack an understanding of how species respond to environmental changes. Here, we examined reproductive success and seedling performance of Poulsenia armata (Moraceae) in continuous and fragmented forests of Los Tuxtlas, southern Mexico. We further investigated how maternal habitat and soil conditions manifested in the seedling stage. We determined seed quality and seedling performance by combining isotopic analyses in seed quality...

Data from: Limited pollen dispersal, small genetic neighborhoods, and biparental inbreeding in Vallisneria americana Michx. (Hydrocharitaceae)

Michael Warren Lloyd, Hayley R. Tumas & Maile C. Neel
Premise of the study: Pollen dispersal is a key process that influences ecological and evolutionary dynamics of plant populations by facilitating sexual reproduction and gene flow. Habitat loss and fragmentation have the potential to reduce pollen dispersal within and among habitat patches. We assessed aquatic pollen dispersal and mating system characteristics in Vallisneria americana -- a water-pollinated plant with a distribution that has been reduced from historic levels. Methods: We examined pollen neighborhood size, biparental...

Data from: Phylogenomic analyses support traditional relationships within Cnidaria

Felipe Zapata, Freya E. Goetz, Stephen A. Smith, Mark Howison, Stefan Siebert, Samuel H. Church, Steven M. Sanders, Cheryl Lewis Ames, Catherine S. McFadden, Scott C. France, Marymegan Daly, Allen G. Collins, Steven H. D. Haddock, Casey W. Dunn & Paulyn Cartwright
Cnidaria, the sister group to Bilateria, is the most diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses...

Data from: Cherry-picking by trialists and meta-analysts can drive conclusions about intervention efficacy

Evan Mayo-Wilson, Tianjing Li, Nicole Fusco, Lorenzo Bertizzolo, Joseph K. Canner, Terrie Cowley, Peter Doshi, Jeffrey Ehmsen, Gillian Gresham, Nan Guo, Jennifer A. Haythornthwaite, James Heyward, Hwanhee Hong, Diana Pham, Jennifer L. Payne, Lori Rosman, Elizabeth A. Stuart, Catalina Suarez-Cuervo, Elizabeth Tolbert, Claire Twose, Swaroop Vedula & Kay Dickersin
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN SUBSEQUENT PUBLICATIONS. PLEASE SEE http://dx.doi.org/10.1016/j.jclinepi.2017.05.007 FOR MORE INFORMATION. Objectives The objective of this study was to determine whether disagreements among multiple data sources affect systematic reviews of randomized clinical trials (RCTs). Study Design and Setting Eligible RCTs examined gabapentin for neuropathic pain and quetiapine for bipolar depression, reported in public (e.g., journal articles) and nonpublic sources (clinical study reports [CSRs] and individual participant data [IPD]). Results...

Data from: An auditory illusion reveals the role of streaming in the temporal misallocation of perceptual objects

Anahita H. Mehta, Nori Jacoby, Ifat Yasin, Andrew J. Oxenham & Shihab A. Shamma
This study investigates the neural correlates and processes underlying the ambiguous percept produced by a stimulus similar to Deutsch's ‘octave illusion’, in which each ear is presented with a sequence of alternating pure tones of low and high frequencies. The same sequence is presented to each ear, but in opposite phase, such that the left and right ears receive a high–low–high … and a low–high–low … pattern, respectively. Listeners generally report hearing the illusion of...

Data from: Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)

Jessica A. Goodheart, Adam L. Bazinet, Ángel Valdés, Allen G. Collins & Michael P. Cummings
Background: The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric divergence may play a fundamental role in the generation of biodiversity. In this context, shifts between major prey types could constitute important factors explaining the biodiversity of marine taxa, particularly in groups with highly specialized diets. However, the scarcity of...

Data from: A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0

Adam L. Bazinet, Derrick J. Zwickl & Michael P. Cummings
We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic...

Data from: Quantifying hummingbird preference for floral trait combinations: the role of selection on trait interactions in the evolution of pollination syndromes

Charles B. Fenster, Richard J. Reynolds, Christopher W. Williams, Robert Makowsky & Michele R. Dudash
Darwin recognized the flower's importance for the study of adaptation and emphasized that the flower's functionality reflects the coordinated action of multiple traits. Here we use a multi-trait manipulative approach to quantify the potential role of selection acting on floral trait combinations underlying the divergence and maintenance of three related North American species of Silene (Caryophyllaceae). We artificially generated 48 plant phenotypes corresponding to all combinations of key attractive traits differing among the three Silene...

Data from: How topography induces reproductive asynchrony and alters gypsy moth invasion dynamics

Jonathan A. Walter, Marcia S. Meixler, Thomas Mueller, William F. Fagan, Patrick C. Tobin & Kyle J. Haynes
1. Reproductive asynchrony, a temporal mismatch in reproductive maturation between an individual and potential mates, may contribute to mate-finding failure and Allee effects that influence the establishment and spread of invasive species. Variation in elevation is likely to promote variability in maturation times for species with temperature-dependent development, but it is not known how strongly this influences reproductive asynchrony or the population growth of invasive species. 2. We examined whether spatial variation in reproductive asynchrony,...

Data from: Ecological genomics meets community-level modeling of biodiversity: mapping the genomic landscape of current and future environmental adaptation

Matthew C. Fitzpatrick & Stephen R. Keller
Local adaptation is a central feature of most species occupying spatially heterogeneous environments, and may factor critically in responses to environmental change. However, most efforts to model the response of species to climate change ignore intraspecific variation due to local adaptation. Here, we present a new perspective on spatial modelling of organism–environment relationships that combines genomic data and community-level modelling to develop scenarios regarding the geographic distribution of genomic variation in response to environmental change....

Late Cretaceous domatia reveals the antiquity of plant–mite mutualisms in flowering plants

S. Augusta Maccracken, Ian Miller & Conrad Labandeira
Mite houses, or acarodomatia, are found on the leaves of over 2,000 living species of flowering plants today. These structures facilitate tri-trophic interactions between the host plant, its fungi or herbivore adversaries, and fungivorous or predaceous mites by providing shelter for the consumers. Previously, the oldest acarodomatia were described on a Cenozoic Era fossil leaf dating to 49 million years in age. Here, we report the first occurrence of Mesozoic Era acarodomatia in the fossil...

Data from: Polyandry and polygyny in a social rodent: an integrative perspective based on social organization, copulations, and genetics

John L. Hoogland, Regina Trott & Stephen R. Keller
Animal mating systems have fascinated biologists for thousands of years. Ways to describe amating systeminclude determining social organization, observing copulations, or using genetics to assign parentage. Social organization can be difficult to quantify, however, documentation of copulations is often challenging, many copulations do not produce offspring, and genetic variation is sometimes minimal. Here we use data from a 7-year study of wild white-tailed prairie dogs (WTPDs, Cynomys leucurus) living in Colorado USA to estimate the...

Data from: Challenges in the conservation of wide-ranging nomadic species

Dejid Nandintsetseg, Chloe Bracis, Kirk A. Olson, Katrin Böhning-Gaese, Justin M. Calabrese, Buyanaa Chimeddorj, William F. Fagan, Christen H. Fleming, Michael Heiner, Petra Kaczensky, Peter Leimgruber, Dalannast Munkhnast, Theresa Stratmann & Thomas Mueller
1. Conservation of nomadic ungulates presents significant conservation challenges because of unpredictability in their movements and space use. Long-term studies on nomadic ungulates offering insights into the variability in space use within and between years are largely missing but are necessary to develop effective conservation strategies. 2. We examined the temporal variability in space-use of 22 Mongolian gazelle, tracked for one to three years with GPS and used the resulting movement patterns to evaluate conservation...

Data from: A comprehensive analysis of autocorrelation and bias in home range estimation

Michael J. Noonan, Marlee A. Tucker, Christen H. Fleming, Tom S. Akre, Susan C. Alberts, Abdullahi H. Ali, Jeanne Altmann, Pamela C. Antunes, Jerrold L. Belant, Dean Beyer, Niels Blaum, Katrin Böhning-Gaese, , Rogerio De Paula Cunha, Jasja Dekker, Jonathan Drescher-Lehman, Nina Farwig, Claudia Fichtel, Christina Fischer, Adam T. Ford, Jacob R. Goheen, René Janssen, Florian Jeltsch, Matthew Kauffman, Peter M. Kappeler … & Justin M. Calabrese
Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of...

Multiscale analysis of canopy arthropod diversity in a volcanically fragmented landscape

Elske K. Tielens, Maile N. Neel, Devin R. Leopold, Christian P. Giardina & Daniel S. Gruner
Dataset and code associated with the article "Multiscale analysis of canopy arthropod diversity in a volcanically fragmented landscape" (Tielens et al 2019, Ecosphere). Article abstract: Habitat fragmentation resulting in habitat loss and increased isolation is a dominant driver of global species declines. Habitat isolation and connectivity vary across scales, and understanding how con- nectivity affects biodiversity can be challenging because the relevant scale depends on the taxa involved. A multiscale analysis can provide insight in...

Data from - Ecological insights from three decades of animal movement tracking across a changing Arctic

Gil Bohrer, Sarah Davidson, Eliezer Gurarie, Scott LaPoint, Peter Mahoney, Emma Grier, Ophélie Couriot, Allicia Kelly, Bryan Bedrosian, Jerrold Belant, Travis Booms, Bridget Borg, Stan Boutin, Erica Craig, Tracy Davison, Robert Domenech, James Hodson, Kyle Joly, Nicholas Larter, A. David M. Latham, Stephen Lewis, Carol McIntyre, Tricia Miller, Kelsey Russell, Dale Seip … & Judy Williams
We provide here the data used in analysis of 3 test cases, presented in the manuscript "Ecological insights from three decades of animal movement tracking across a changing Arctic". We utilized the new Arctic Animal Movement Archive (AAMA), a growing collection of 201 standardized terrestrial and marine animal tracking studies from 1991–present. The AAMA supports public data discovery, preserves fundamental baseline data for the future, and facilitates efficient, collaborative data analysis. With three AAMA-based case...

Diurnal timing of nonmigratory movement by birds: the importance of foraging spatial scales

Julie Mallon, Marlee Tucker, Annalea Beard, , Keith Bildstein, Katrin Böhning-Gaese, John Brzorad, Evan Buechley, Javier Bustamante, Carlos Carrapato, José Castillo-Guerrero, Elizabeth Clingham, Mark Desholm, Christopher DeSorbo, Robert Domenech, Hayley Douglas, Olivier Duriez, Peter Enggist, Nina Farwig, Wolfgang Fiedler, Anna Gagliardo, Clara García-Ripollés, Juan Antonio Gil, Morgan Gilmour, Roi Harel … & Bill Fagan
Timing of activity can reveal an organism’s efforts to optimize foraging either by minimizing energy loss through passive movement or by maximizing energetic gain through foraging. Here, we assess whether signals of either of these strategies are detectable in the timing of activity of daily, local movements by birds. We compare the similarities of timing of movement activity among species using six temporal variables: start of activity relative to sunrise, end of activity relative to...

Are native and non-native pollinator friendly plants equally valuable for native wild bee communities?

Nicola Seitz, Dennis VanEngelsdorp & Sara D. Leonhardt
Bees rely on floral pollen and nectar for food. Therefore, pollinator friendly plantings are often used to enrich habitats in bee conservation efforts. As part of these plantings, non-native plants may provide valuable floral resources, but their effects on native bee communities have not been assessed in direct comparison with native pollinator friendly plantings. In this study, we performed a common garden experiment by seeding mixes of 20 native and 20 non-native pollinator friendly plant...

Data from: Estimating encounter location distributions from animal tracking data

Michael Noonan, Ricardo Martinez-Garcia, Grace H. Davis, Margaret C. Crofoot, Roland Kays, Ben T. Hirsch, Damien Caillaud, Eric Payne, Andrew Sih, David L. Sinn, Orr Spiegel, William F. Fagan, Christen H. Fleming & Justin M. Calabrese
1. Ecologists have long been interested in linking individual behavior with higher-level processes. For motile species, this 'upscaling' is governed by how well any given movement strategy maximizes encounters with positive factors, and minimizes encounters with negative factors. Despite the importance of encounter events for a broad range of ecological processes, encounter theory has not kept pace with developments in animal tracking or movement modeling. Furthermore, existing work has focused primarily on the relationship between...

Data from: How climate extremes—not means—define a species' geographic range boundary via a demographic tipping point

Heather J. Lynch, Marc Rhainds, Justin M. Calabrese, Stephen Cantrell, Chris Cosner & William F. Fagan
Species’ geographic range limits interest biologists and resource managers alike; however, scientists lack strong mechanistic understanding of the factors that set geographic range limits in the field, especially for animals. There exists a clear need for detailed case studies that link mechanisms to spatial dynamics and boundaries because such mechanisms allow us to predict whether climate change is likely to change a species’ geographic range and, if so, how abundance in marginal populations compares to...

Data from: From cellular characteristics to disease diagnosis: uncovering phenotypes with supercells

Julián Candia, Ryan Maunu, Meghan Driscoll, Angélique Biancotto, Pradeep Dagur, , H. Nida Sen, Lai Wei, Amos Maritan, Kan Cao, Robert B. Nussenblatt, Jayanth R. Banavar, Wolfgang Losert & J. Philip McCoy
Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology. We introduce an approach that identifies a disease phenotype from multiparameter single-cell measurements, which is based on the concept of “supercell statistics”, a single-cell-based averaging procedure followed by a machine learning classification scheme. We are able to assess the optimal tradeoff between the number of single cells averaged and the number...

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