397 Works

2014 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

Effective Strategies for Recording Interviewer Observations: Evidence from the PASS Study in Germany

Brady T. West & Mark Trappmann

Multilevel Group Selection

Garry Sotnik
The Multilevel Group Selection I (MGS I) model simulates a population of agents in the process of adopting a common-pool-resource-related collective action, while being influenced by individual- and group-level selection pressures. It may be useful to both scientists and students in hypothesis testing, theory development, or more generally in understanding multilevel selection.

Data from: Ecological selection as the cause and sexual differentiation as the consequence of species divergence?

Elen Oneal & L. Lacey Knowles
Key conceptual issues about speciation go unanswered without consideration of non-mutually exclusive factors. With tests based on speciation theory, we exploit the island distribution and habitat differences exhibited by the Caribbean cricket Amphiacusta sanctaecrucis, and with an analysis of divergent ecological selection, sexually selected differentiation, and geographic isolation, address how these different factors interact. After testing for divergent selection by comparing neutral genetic and morphological divergence in one ecological (mandible shape) and one sexual (male...

Data from: Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika.

Jason L. Brown & L. Lacey Knowles
A central goal of phylogeography is to identify and characterize the processes underlying divergence. One of the biggest impediments currently faced is how to capture the spatiotemporal dynamic under which a species evolved. Here we described an approach that couples species distribution models (SDMs), demographic and genetic models in a spatiotemporally explicit manner. Analyses of American Pika (Ochotona priniceps) from the sky islands of the central Rocky Mountains of North America are used to provide...

Data from: Food plant-derived disease tolerance and resistance in a natural butterfly-plant-parasite interaction

Eleanore D. Sternberg, Thierry LeFèvre, James Li, Carlos Lopez Fernandez De Castillejo, Hui Li, Mark D. Hunter & Jacobus C. De Roode
Organisms can protect themselves against parasite-induced fitness costs through resistance or tolerance. Resistance includes mechanisms that prevent infection or limit parasite growth while tolerance alleviates the fitness costs from parasitism without limiting infection. Although tolerance and resistance affect host-parasite coevolution in fundamentally different ways, tolerance has often been ignored in animal-parasite systems. Where it has been studied, tolerance has been assumed to be a genetic mechanism, unaffected by the host environment. Here we studied the...

Data from: Temporal population genetic instability in range edge Western Toads, Anaxyrus boreas

Iris A. Holmes
In this article, we address the temporal stability of population genetic structure in a range-edge population that is undergoing continual, short-distance colonization events. We sampled western toad, Anaxyrus boreas, breeding populations over 2 seasons near their northern range limit in southeast Alaska. We sampled 20 ponds each during the summers of 2008 and 2009, with 14 ponds sampled in both summers. We found considerable turnover in the population genetic relationships among ponds in those 2...

Data from: Integrative testing of how environments from the past to the present shape genetic structure across landscapes

Qixin He, Danielle L. Edwards & L. Lacey Knowles
Tests of the genetic structure of empirical populations typically focus on the correlative relationships between population connectivity and geographic and/or environmental factors in landscape genetics. However, such tests may overlook or misidentify the impact of such factors on genetic structure, especially when connectivity patterns differ between past and present populations because of shifting environmental conditions over time. Here we account for the underlying demographic component of population connectivity associated with a temporarily dynamic landscape in...

Data from: Trends in shell fragmentation as evidence of mid- Paleozoic changes in marine predation

Przemysław Gorzelak, Mariusz A. Salamon, Robert Niedźwiedzki, Dawid Trzęsiok & Tomasz K. Baumiller
Recent observations indicate that shell fragmentation can be a useful tool in assessing crushing predation in marine communities. However, criteria for recognizing shell breakage caused by durophagous predators versus physical factors are still not well established. Here, we provide data from tumbling and aquarium experiments to argue that physical and biotic processes lead to different patterns of shell damage, specifically that angular shell fragments are good indicators of durophagous predation. Using such angular shell fragments...

Data from: Analysis and visualization of complex macroevolutionary dynamics: an example from Australian scincid lizards

Daniel L. Rabosky, Stephen C. Donnellan, Michael Grundler & Irby J. Lovette
The correlation between species diversification and morphological evolution has long been of interest in evolutionary biology. We investigated the relationship between these processes during the radiation of 250+ scincid lizards that constitute Australia's most species-rich clade of terrestrial vertebrates. We generated a time-calibrated phylogenetic tree for the group that was more than 85% complete at the species level and collected multivariate morphometric data for 183 species. We reconstructed the dynamics of species diversification and trait...

Data from: Modeling the effects of anthropogenic exploitation and climate change on an endemic stag beetle, Lucanus miwai, of Taiwan

Jen-Pan Huang
Loss of biodiversity is a worldwide phenomenon and conservation of endemic species is becoming a pressing issue. However, species differ in life history characteristics, causing the best strategy for conservation to vary among species. Lucanus miwai is an endemic stag beetle of Taiwan, but the natural history and the conservation status of L. miwai have not been fully studied. Lucanus miwai adults live in forest-edge grassland habitats and are experiencing threats from anthropogenic exploitation. Additionally,...

Data from: Are thyroid hormones mediators of incubation temperature-induced phenotypes in birds?

Sarah E. DuRant, Amanda W. Carter, Robert J. Denver, Gary R. Hepp & William A. Hopkins
Incubation temperature influences a suite of traits in avian offspring. However, the mechanisms underlying expression of these phenotypes are unknown. Given the importance of thyroid hormones in orchestrating developmental processes, we hypothesized that they may act as an upstream mechanism mediating the effects of temperature on hatchling phenotypic traits such as reduced growth and thermoregulation. We found that plasma T3, but not T4 concentrations, differed among newly-hatched wood ducks (Aix sponsa) from different embryonic incubation...

Data from: Diversification of mammals from the Miocene of Spain

M. Soledad Domingo, Catherine Badgley, Beatriz Azanza, Daniel DeMiguel & M. Teresa Alberdi
The mammalian fossil record of Spain is long and taxonomically well resolved, offering the most complete record of faunal change for the Neogene of Europe. We evaluated changes in diversification, composition, trophic structure, and size structure of large mammals over the middle and late Miocene with methods applied to this record for the first time, including ordination of fossil localities to improve temporal resolution and estimation of confidence intervals on taxa temporal ranges. By contrast,...

Data from: Consequences of divergence and introgression for speciation in Andean cloud forest birds

Benjamin M. Winger
Divergence with gene flow is well documented and reveals the influence of ecological adaptation on speciation. Yet it remains intuitive that gene exchange inhibits speciation in many scenarios, particularly among ecologically similar populations. The influence of gene flow on the divergence of populations facing similar selection pressures has received less empirical attention than scenarios where differentiation is coupled with local environmental adaptation. I used a paired study design to test the influence of genomic divergence...

Data from: Safari science: assessing the reliability of citizen science data for wildlife surveys

Cara Steger, Bilal Butt & Mevin B. Hooten
1. Protected areas are the cornerstone of global conservation, yet financial support for basic monitoring infrastructure is lacking in 60% of them. Citizen science holds potential to address these shortcomings in wildlife monitoring, particularly for resource-limited conservation initiatives in developing countries - if we can account for the reliability of data produced by volunteer citizen scientists (VCS) . 2. This study tests the reliability of VCS data vs. data produced by trained ecologists, presenting a...

Data from: Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles

Sonal Singhal, Maggie Grundler, Guarino Colli & Daniel L. Rabosky
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches – anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) – and both approaches have proven useful for addressing questions in...

Data from: Stress in biological invasions: introduced invasive grey squirrels increase physiological stress in native Eurasian red squirrels

Francesca Santicchia, Ben Dantzer, Freya Van Kesteren, Rupert Palme, Adriano Martinoli, Nicola Ferrari & Lucas Armand Wauters
1. Invasive alien species can cause extinction of native species through processes including predation, interspecific competition for resources, or disease-mediated competition. Increases in stress hormones in vertebrates may be associated with these processes and contribute to the decline in survival or reproduction of the native species. 2. Eurasian red squirrels (Sciurus vulgaris) have gone extinct across much of the British Isles and parts of Northern Italy following the introduction of North American invasive grey squirrels...

Data from: Within-host priority effects systematically alter pathogen coexistence

Patrick A. Clay, Kailash Dhir, Volker H.W. Rudolf, Meghan A. Duffy & Volker H. W. Rudolf
Coinfection of host populations alters pathogen prevalence, host mortality, and pathogen evolution. Because pathogens compete for limiting resources, whether multiple pathogens can coexist in a host population can depend on their within-host interactions which, in turn, can depend on the order in which pathogens infect hosts (within-host priority effects). However, the consequences of within-host priority effects for pathogen coexistence have not been tested. Using laboratory studies with a coinfected zooplankton system, we found that pathogens...

Data from: An inverse latitudinal gradient in speciation rate for marine fishes

Daniel L. Rabosky, Jonathan Chang, Pascal O. Title, Peter F. Cowman, Lauren Sallan, Matt Friedman, Kristin Kaschner, Cristina Garilao, Thomas J. Near, Marta Coll & Michael E. Alfaro
Far more species of organisms are found in the tropics than in temperate and polar regions, but the evolutionary and ecological causes of this pattern remain controversial1,2. Tropical marine fish communities are much more diverse than cold-water fish communities found at higher latitudes3,4, and several explanations for this latitudinal diversity gradient propose that warm reef environments serve as evolutionary ‘hotspots’ for species formation5,6,7,8. Here we test the relationship between latitude, species richness and speciation rate...

Data from: Analyzing contentious relationships and outlier genes in phylogenomics

Joseph F. Walker, Joseph W. Brown & Stephen A. Smith
Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive species tree inference in supermatrix analyses. Here, we examined two datasets where supermatrix and coalescent-based species trees conflict. We identified two highly influential “outlier” genes in each dataset. When removed from each dataset, the inferred supermatrix trees matched the topologies obtained from coalescent analyses. We also demonstrate that, while the...

Prehistoric baseline reveals substantial decline of oyster reef condition in a Gulf of Mexico conservation priority area

Stephen Hesterberg, Gregory Herbert, Thomas Pluckhahn, Ryan Harke, Nasser Al-Qattan, C. Trevor Duke, Evan Moore, Megan Smith, Alexander Delgado & Christina Sampson
This dataset contains oyster shell height measurements for prehistoric and modern oysters collected near Crystal River, Florida, USA. Oxygen and carbon stable isotope values for large prehistoric and modern oysters are also reported.

Data from: Detecting aquatic invasive species in bait and pond stores with targeted environmental (e) DNA high-throughput sequencing metabarcode assays: angler, retailer, and manager implications

Matt Snyder, Carol Stepien, Nathaniel Marshall, Hannah Scheppler, Christopher Black & Kevin Czajkowski
Bait and pond stores comprise potential, yet poorly understood, vectors for aquatic invasive species (AIS). We tested for AIS and illegal native species in 51 bait and 21 pond stores from the central Great Lakes (Lake Erie, Ohio and Lake St. Clair, Michigan) and the adjacent Wabash River (Indiana) using environmental DNA (eDNA) metabarcode assays of water samples and morphological identifications. Retailers were questioned about supply chains, and anglers surveyed about baitfish use and disposal....

Data from: The evolutionary origins of natural pedagogy: Rhesus monkeys show sustained attention following nonsocial cues versus social communicative signals

Rosemary Bettle & Alexandra Rosati
The natural pedagogy hypothesis proposes that human infants preferentially attend to communicative signals from others, facilitating rapid cultural learning. In this view, sensitivity to such signals are a uniquely human adaptation and as such nonhuman animals should not produce or utilize these communicative signals. We test these evolutionary predictions by examining sensitivity to communicative cues in 206 rhesus monkeys (Macaca mulatta) using an expectancy looking time task modeled on prior work with infants. Monkeys observed...

Spatial variation in diet-microbe associations across populations of a generalist North American carnivore

A. Shawn Colborn, Corbin C. Kuntze, Gabriel I. Gadsden & Nyeema C. Harris
1. Generalist species, by definition, exhibit variation in niche attributes that promote survival in changing environments. Increasingly, phenotypes previously associated with a species, particularly those with wide or expanding ranges, are dissolving and compelling greater emphasis on population-level characteristics. 2. In the present study, we assessed spatial variation in diet characteristics, gut microbiome, and the association between these two ecological traits across populations of coyotes (Canis latrans). We highlight the influence of the carnivore community...

Data from: Large-bodied sabre-toothed anchovies reveal unanticipated ecological diversity in early Palaeogene teleosts

Alessio Capobianco, Hermione Beckett, Etienne Steurbaut, Philip Gingerich, Giorgio Carnevale & Matthew Friedman
Many modern groups of marine fishes first appear in the fossil record during the early Palaeogene (66–40 million years ago), including iconic predatory lineages of spiny-rayed fishes that appear to have originated in response to ecological roles left empty after the Cretaceous/Palaeogene extinction. The hypothesis of extinction-mediated ecological release likewise predicts that other fish groups have adopted novel predatory ecologies. Here we report remarkable trophic innovation in early Palaeogene clupeiforms (herrings and allies), a group...

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