76 Works

Data from: Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

Henrik Krehenwinkel, Madeline Wolf, Jun Ying Lim, Andrew J. Rominger, Warren B. Simison & Rosemary G. Gillespie
Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved...

Data from: Invasive legumes can associate with many mutualists of native legumes, but usually do not

Kimberly J. La Pierre, Ellen L. Simms, Mohsin Tariq, Marriam Zafar & Stephanie S. Porter
Mutualistic interactions can strongly influence species invasions, as the inability to form successful mutualisms in an exotic range could hamper a host’s invasion success. This barrier to invasion may be overcome if an invader either forms novel mutualistic associations or finds and associates with familiar mutualists in the exotic range. Here we ask (1) does the community of rhizobial mutualists associated with invasive legumes in their exotic range overlap with that of local native legumes...

Data from: Variation in thermal niche of a declining river-breeding frog: from counter-gradient responses to population distribution patterns

Alessandro Catenazzi & Sarah J. Kupferberg
When dams or climate change alter the thermal regimes of rivers, conditions can shift outside optimal ranges for aquatic poikilothermic vertebrates. Plasticity in thermal performance and preference, however, may allow temperature-vulnerable fauna to persist under challenging conditions. To determine the effects of thermal regime on Rana boylii (Ranidae), a threatened frog species endemic to rivers of California and Oregon, we quantified tadpole thermal preferences and performance in relation to thermal conditions. We monitored temperature and...

Data from: Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

Rayna C. Bell, Juan L. Parra, Gabriel Badjedjea, Michael F. Barej, David C. Blackburn, Marius Burger, Alan Channing, J. Maximilian Dehling, Eli Greenbaum, Václav Gvoždík, Jos Kielgast, Chifundera Kusamba, Stefan Lötters, Patrick J. McLaughlin, Zoltán T. Nagy, Mark-Oliver Rödel, Daniel M. Portik, Bryan L. Stuart, Jeremy VanDerWal, Ange-Ghislain Zassi Boulou & Kelly R. Zamudio
Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a...

Data from: The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than twofold overestimation

Christopher H. Martin, Sebastian Hohna, Jacob E. Crawford, Bruce J. Turner, Emilie J. Richards & Lee H. Simons
Our recent estimation of the divergence time and isolation of Death Valley pupfishes, including the iconic Devil’s Hole pupfish (DHP), rewrote widespread assumptions about this group. These species were previously assumed to be relic populations isolated over millions of years; our genomic analyses indicated recent colonization of Devil’s Hole within the past 105–830 years and frequent gene flow among Death Valley populations [1]. These results understandably attracted substantial attention given the iconic battle for conservation...

Data from: Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

Ethan B. Linck, Zachary R. Hanna, Anna Sellas & John P. Dumbacher
Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site-associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site-associated double digestion as the basis for probes that capture orthologous loci...

Data from: Comparative experimental taphonomy of eight marine arthropods indicates distinct differences in preservation potential

Adiël A. Klompmaker, Roger W. Portell & Michael G. Frick
Global biodiversity patterns in deep time can only be understood fully when the relative preservation potential of each clade is known. The relative preservation potential of marine arthropod clades, a diverse and ecologically important component of modern and past ecosystems, is poorly known. We tackled this issue by carrying out a 205-day long comprehensive, comparative, taphonomic experiment in a laboratory by scoring up to ten taphonomic characters for multiple specimens of seven crustacean and one...

Data from: Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

Dario Copetti, Alberto Burquez, Enriquena Bustamante, Joseph L. M. Charboneau, Kevin L. Childs, Luis E. Eguiarte, Seunghee Lee, Tiffany L. Liu, Michelle M. McMahon, Noah K. Whiteman, Rod A. Wing, Martin F. Wojciechowski & Michael J. Sanderson
Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We...

Data from: Carnivore carcasses are avoided by carnivores

Marcos Moleon, Carlos Martínez-Carrasco, Oliver Muellerklein, Wayne Getz, Carlos Muñoz-Lozano, José Antonio Sánchez-Zapata & Wayne M. Getz
1. Ecologists have traditionally focused on herbivore carcasses as study models in scavenging research. However, some observations of scavengers avoiding feeding on carnivore carrion suggest that different types of carrion may lead to differential pressures. Untested assumptions about carrion produced at different trophic levels could therefore lead ecologists to overlook important evolutionary processes and their ecological consequences. 2. Our general goal was to investigate the use of mammalian carnivore carrion by vertebrate scavengers. In particular,...

Data from: Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming

Erin Conlisk, Cristina Castanha, Matthew J. Germino, Thomas T. Veblen, Jeremy M. Smith & Lara M. Kueppers
1. Species distribution shifts in response to climate change require that recruitment increase beyond current range boundaries. For trees with long lifespans, the importance of climate-sensitive seedling establishment to the pace of range shifts has not been demonstrated quantitatively. 2. Using spatially explicit, stochastic population models combined with data from long-term forest surveys, we explored whether the climate-sensitivity of recruitment observed in climate manipulation experiments was sufficient to alter populations and elevation ranges of two...

GEOS-Chem output for \"Lightning NOx Emissions: Reconciling measured and modeled emissions estimates with updated NOx chemistry\"

Joshua Laughner, Ronald Cohen & Benjamin Nault
These GEOS-Chem simulations examine the effect of recent advances to our understanding of upper tropospheric chemistry on our ability to constrain lightning NOx emissions. These simulations examine the effect of the addition of methyl peroxy nitrate chemistry, as well as better constraints on the formation of pernitric acid, dinitrogen pentoxide, and nitric acid at the temperatures and pressures of the upper troposphere. These simulations include a base case, simulations implementing each change individually, all four...

Demonstration retrievals from \"Quantification of the effect of modeled lightning NO2 on UV-visible air mass factors\"

Joshua Laughner & Ronald Cohen
Space-borne measurements of tropospheric nitrogen dioxide (NO2) are up to 10x more sensitive to upper tropospheric NO2 than near-surface NO2 over low reflectivity surfaces. This make the modeling of lightning NO2 in the a priori profiles imperative to accurately retrieve NO2 over regions with significant lightning activity. This is quantified in our work "Quantification of the effect of modeled lightning NO2 on UV-visible air mass factors." This dataset contains the NO2 retrievals used in Section...

Vegetation Change in the Natural Reserve of Orange County

Katherine Suding, Sara Jo Dickens & Samuel Bedgood
This data set describes vegetation change in 109 areas in the Nature Reserve of Orange County. The authors of this data were mainly interested in the success of artichoke thistle (Cynara cardunculus) control, but it could be approached in many different ways. Surveyors identified and recorded more than 375 plant species from the years 1998, 2008, and 2013.

Code review regression analysis of open source GitHub projects

Christopher Thompson & David Wagner
This dataset contains the repository data used for our study "A Large-Scale Study of Modern Code Review and Security in Open Source Projects". This dataset was collected from GitHub, and includes 3,126 projects in 143 languages, with 489,038 issues and 382,771 pull requests. We also include the regression analysis notebooks for reproducing our results from this data.

Causal Evidence for Lateral Prefrontal Cortex Dynamics Supporting Cognitive Control

Derek Nee & Mark D'Esposito
The lateral prefrontal cortex (LPFC) is essential for higher-level cognition, but how its interactions support cognitive control remains elusive. Previously (Nee and D'Esposito, 2016), dynamic causal modeling (DCM) indicated that mid LPFC integrates abstract, rostral and concrete, caudal influences to inform context-appropriate action. Here, we use continuous theta-burst transcranial magnetic stimulation (cTBS) to causally test this model. cTBS was applied to three LPFC sites and a control site in counterbalanced sessions. Behavioral modulations resulting from...

Data from: Target Sequence Capture of Nuclear-Encoded Genes for Phylogenetic Analysis in Ferns

Paul G. Wolf, Tanner A. Robison, Matthew G. Johnson, Michael A. Sundue, Weston L. Testo & Carl J. Rothfels
Premise of the study: Until recently, most phylogenetic studies of ferns were based on chloroplast genes. Evolutionary inferences based on these data can be incomplete because the characters are from a single linkage group and are uniparentally inherited. These limitations are particularly acute in studies of hybridization, which is prevalent in ferns; fern hybrids are common and ferns are able to hybridize across highly diverged lineages, up to 60 million years since divergence in one...

Data from: Parallel Pleistocene amphitropical disjunctions in a parasitic plant and its host

Adam C. Schneider & Abigail J. Moore
PREMISE OF THE STUDY: Aphyllon is a clade of holoparasites that includes closely related North American and South American species parasitic on Grindelia. Both Aphyllon (Orobanchaceae) and Grindelia (Asteraceae) have amphitropical disjunctions between North America and South America; however, the timing of these patterns and the processes to explain them are unknown. METHODS: Chronograms for the Orobanchaceae and Grindelia and their relatives were constructed using fossil and secondary calibration points, one of which was based...

Data from: Adaptation of the pathogen, Pseudomonas syringae during experimental evolution on a native versus alternative host plant

Sean Meaden & Britt Koskella
The specialization and distribution of pathogens among species has substantial impact on disease spread, especially when reservoir hosts can maintain high pathogen densities or select for increased pathogen virulence. Theory predicts that optimal within-host growth rate will vary among host genotypes/species and therefore that pathogens infecting multiple hosts should experience different selection pressures depending on the host environment in which they are found. This should be true for pathogens with broad host ranges, but also...

Data from: Population genetic and field ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian

Ian J. Wang & H. Bradley Shaffer
The explosive growth of empirical population genetics has seen a proliferation of analytical methods leading to a steady increase in our ability to accurately measure key population parameters, including genetic isolation, effective population size, and gene flow in natural systems. Assuming they yield similar results, population genetic methods offer an attractive complement to, or replacement of, traditional field ecological studies. However, empirical assessments of the concordance between direct field ecological and indirect population genetic studies...

Data from: Stimulus discriminability may bias value-based probabilistic learning

Iris Schutte, Heleen A. Slagter, Anne G.E. Collins, Michael J. Frank, J. Leon Kenemans & Anne G. E. Collins
Reinforcement learning tasks are often used to assess participants' tendency to learn more from the positive or more from the negative consequences of one's action. However, this assessment often requires comparison in learning performance across different task conditions, which may differ in the relative salience or discriminability of the stimuli associated with more and less rewarding outcomes, respectively. To address this issue, in a first set of studies, participants were subjected to two versions of...

Data from: Tree-growth is more sensitive than species distributions to recent changes in climate and acidic deposition in the northeastern United States

Jay W. Wason, Martin Dovciak, Colin M. Beier & John J. Battles
Tree-growth responses to environmental change could provide early detection of shifts in forest composition and help facilitate ecosystem management and conservation. We studied forest tree responses to recent trends in climate and acidic deposition using analyses of tree rings and long-term climate, deposition and forest plot data along an elevational climatic gradient in the northeastern United States. We analyzed how (a) individual growth of dominant species (Picea rubens, Abies balsamea), and (b) spatial distributions of...

Data from: Transgenerational effects alter plant defense and resistance in nature

Jack Colicchio
Trichomes, or leaf hairs, are epidermal extensions that take a variety of forms and perform many functions in plants, including herbivore defense. In this study, I document genetically determined variation, within-generation plasticity, and a direct role of trichomes in herbivore defense for (Mimulus guttatus). After establishing the relationship between trichomes and herbivory, I test for transgenerational effects of wounding on trichome density and herbivore resistance. Patterns of inter-annual variation in herbivore density and the high...

Data from: The seasonal climate niche predicts phenology and distribution of an ephemeral annual plant, Mollugo verticillata

Joe Hereford, Johanna Schmitt & David D. Ackerly
1.Many short-lived species complete their life cycles during brief seasonal windows of favorable environmental conditions. Such species may persist in the face of climate warming by migration to track their seasonal climate niche in space and/or by phenological shifts to track favorable conditions in time within the year. To describe the seasonal climate niche of the short-lived annual Mollugo verticillata in California, we used data from herbarium specimens and historic climate records to estimate environmental...

Data from: Caching for where and what: evidence for a mnemonic strategy in a scatter-hoarder

Mikel M. Delgado & Lucia F. Jacobs
Scatter-hoarding animals face the task of maximizing retrieval of their scattered food caches while minimizing loss to pilferers. This demand should select for mnemonics, such as chunking, i.e. a hierarchical cognitive representation that is known to improve recall. Spatial chunking, where caches with the same type of content are related to each other in physical location and memory, would be one such mechanism. Here we tested the hypothesis that scatter-hoarding eastern fox squirrels (Sciurus niger)...

Data from: Trapped within the city: Integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization

André Lourenço, David Álvarez, Ian J. Wang & Guillermo Velo-Antón
Urbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments are poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders...

Registration Year

  • 2017
    76

Resource Types

  • Dataset
    76

Affiliations

  • University of California, Berkeley
    76
  • University of California System
    9
  • University of Colorado Boulder
    4
  • University of Washington
    3
  • The University of Texas at Austin
    3
  • University of Michigan-Ann Arbor
    3
  • University of North Carolina
    3
  • Australian National University
    3
  • California Academy of Sciences
    3
  • University of Florida
    3