84 Works

Integrative taxonomic analysis to reveal the species status of Bombus flavidus, combining COI and nuclear sequencing, wing morphometrics and secretions used for mate attraction as well as patterns of color polymorphism

Patrick Lhomme, Sarah D. Williams, Guillaume Ghisbain, Baptiste Martinet, Maxence Gérard & Heather H. Hines
Bumble bees, due to their morphological monotony and color diversity, have presented difficulties with species delimitation. Recent bumble bee declines have made it ever more imperative to resolve the status of species to address conservation concerns. Some of the taxa found to be most threatened are the often-rare socially parasitic bumble bees, which have additional trophic requirements. Among the socially parasitic bumble bees, Bombus flavidus Eversmann has contentious species status. While multiple separate species allied...

Mine Maps as Grey Literature

Linda Musser
Mine maps are extremely useful resources for determining regional and local hydrogeologic conditions as well as mineral resources and reserves. Users include mining companies, property owners concerned about risk factors related to mining activities, government inspectors, engineers and planners. Hundreds of thousands of mine maps exist yet how many are collected or cataloged by libraries or archives? This paper examines the characteristics of mine maps, how they are published, their value, and describes some efforts...

Are polycultures for silage pragmatic medleys or gallimaufries?: Silage polyculture data 2016 to 2018

A.B. Burton, G.W. Roth, A. R. Kemanian, J. Baniszewski & J.F. Tooker
This dataset and accompanying supplemental materials are companion pieces to the journal article “Are polycultures for silage pragmatic medleys or gallimaufries?” published in Agronomy Journal in 2021 by Burton et al. Maize silage is a particularly important dairy crop in Pennsylvania and across the US, but abiotic stress stemming from climate change can cause yearly variation in yield. Polycultures are mixtures of species that are grown together in the same field at the same time;...

Bottom-up coarse-grained models for external fields and interfaces

M.R. DeLyser & W.G. Noid
These simulations were used to parameterize coarse-grained models of interfacial systems of methanol subject to an external potential and to evaluate these models.

The Paris Climate Agreement and future sea level rise from Antartica

Robert M. DeConto, David Pollard, Richard B. Alley, Isabella Velicogna, Edward Gasson, Natalya Gomez, Shaina Sadai, Alan Condron, Daniel M. Gilford, Erica L. Ashe, Robert E. Kopp, Dawei Li & Andrea Dutton

Data from: Application of a novel haplotype-based scan for local adaptation to study high-altitude adaptation in rhesus macaques

Zachary Szpiech, Taylor Novak, Nick Bailey & Laurie Stevison
When natural populations split and migrate to different environments, they may experience different selection pressures that can lead to local adaptation. To capture the genomic patterns of a local selective sweep, we develop XP-nSL, a genomic scan for local adaptation that compares haplotype patterns between two populations. We show that XP-nSL has power to detect ongoing and recently completed hard and soft sweeps, and we then apply this statistic to search for evidence of adaptation...

Idealized atmospheric boundary layer simulations for Wang et al. (2021) WENO-scheme study

A. Wang, Y. Pan & P. Markowski
This dataset contains the numerical simulations used in the Wang et al. (2021) study of WENO schemes in an idealized atmospheric boundary layer. That work explores the influence of Weighted Essentially Non-Oscillatory (WENO) schemes on Cloud Model 1 (CM1) large-eddy simulation (LES) of a quasi-steady, horizontally homogeneous, fully developed atmospheric boundary layer (ABL). An advantage of applying WENO schemes to scalar advection is the elimination of acoustic-wave propagation generated by solving the compressible fluid equations...

Sociability increases survival of adult female giraffes

Monica Bond, Derek Lee, Damien Farine, Arpat Ozgul & Barbara Koenig
Studies increasingly show that social connectedness plays a key role in determining survival, in addition to natural and anthropogenic environmental factors. Few studies, however, integrated social, non-social, and demographic data to elucidate what components of an animal’s socio-ecological environment are most important to their survival. Female giraffes (Giraffa camelopardalis) form structured societies with highly dynamic group membership but stable long-term associations. We examined the relative contributions of sociability (relationship strength, gregariousness, and betweenness), together with...

Impact of Helicoverpa zea salivary GOX on stomatal conductance and volatile emission of host plants

Po-An Lin, Yintong Chen, Duverney Chaverra-Rodriguez, Chan Chin Heu, Nursyafiqi Bin Zainuddin, Jagdeep Singh Sidhu, Michelle Peiffer, Ching-Wen Tan, Anjel Helms, Donghun Kim, Jared Ali, Jason Rasgon, Jonathan Lynch, Charles Anderson & Gary Felton
This data set contain raw data associated with the manuscript titled "Silencing the alarm: An insect salivary enzyme closes plant stomata and inhibits volatile release". Herbivore-induced plant volatiles (HIPVs) are widely recognized as ecologically important to plant. While the majority of studies focused on the induction of this “cry for help”, little is known about whether insect herbivores have evolved mechanisms to reduce the release of HIPVs. Here we show that a caterpillar (Helicoverpa zea)...

Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping

D.Y. Goldrich, B. LaBarge, S. Chartrand, L. Zhang, S.B. Sadowski, Y. Zhang, K. Pham, H. Way, C. Lai, A.W.C. Pang, B. Clifford, A.R. Hastie, M. Oldakowski, D. Goldenberg & J. Broach
Genomic structural variants comprise a significant fraction of somatic mutations driving cancer onset and progression. However, such variants are not readily revealed by standard next-generation sequencing. Optical genome mapping (OGM) surpasses short-read sequencing in detecting large (>500 bp) and complex structural variants (SVs) but requires isolation of ultra-high-molecular-weight DNA from the tissue of interest. We have successfully applied a protocol involving a paramagnetic nanobind disc to a wide range of solid tumors. Using as little...

The geography of parasite local adaptation to host communities

Emily Bellis, Chloee McLaughlin, Claude DePamphilis & Jesse Lasky
Fitness responses to environment can shape species distributions, though opposing eco-evolutionary processes can obscure environmental effects. For example, host specificity influences parasite dynamics, but is unclear how adaptation of parasites to local host communities may scale up to continental distributions. Here, we develop a macroecological framework to determine how host community structure affects the distribution of specialist and generalist populations of Striga hermonthica, an African parasitic plant of cereal crops. Combining data from global crop...

Patterns of recent natural selection on genetic loci associated with sexually differentiated human body size and shape phenotypes

Audrey M. Arner, Kathleen E. Grogan, Mark Grabowski, Hugo Reyes-Centeno & George H. Perry
Levels of sex differences for human body size and shape phenotypes are hypothesized to have adaptively reduced following the agricultural transition as part of an evolutionary response to relatively more equal divisions of labor and new technology adoption. In this study, we tested this hypothesis by studying genetic variants associated with five sexually differentiated human phenotypes: height, body mass, hip circumference, body fat percentage, and waist circumference. We first analyzed genome-wide association (GWAS) results for...

Supplementary data and code for ‘Oscillatory Spatiotemporal Signal Detection in Climate Studies: A Multiple-Taper Spectral Domain Approach’ (Mann and Park 1999)

M.E. Mann & J. Park
This chapter introduces a methodology for signal detection and reconstruction of irregular spatiotemporal oscillatory signals—the multiple-taper spectrum estimation method (MTM)–singular-value decomposition (SVD) methodology. This methodology is offered as an alternative technique which avoids most of the problems encountered in traditional techniques and provides an efficient exploratory method for climate signal detection. The associated signal-detection parameter—the local fractional variance spectrum (LFV) spectrum—yields the correct null distribution for a very general class of spatiotemporal climate noise processes...

Supplementary data, code, and information for ‘Atlantic Hurricane Trends linked to Climate Change’ (Mann et al. 2006)

M.E. Mann & K. Emanuel
Increases in key measures of Atlantic hurricane activity over recent decades are believed to reflect, in large part, contemporaneous increases in tropical Atlantic warmth [e.g., Emanuel, 2005]. Some recent studies [e.g., Goldenberg et al., 2001] have attributed these increases to a natural climate cycle termed the Atlantic Multidecadal Oscillation (AMO), while other studies suggest that climate change may instead be playing the dominant role [Emanuel, 2005; Webster et al., 2005]. Using a formal statistical analysis...

Inbreeding depression in artificial selection lines of Ipomoea purpurea

Megan Van Etten, Anah Soble & Regina Baucom
Inbreeding depression is a central parameter underlying mating system variation in nature and one that can be altered by environmental stress. Although a variety of systems show that inbreeding depression tends to increase under stressful conditions, we have very little understanding across most organisms how the level of inbreeding depression may change as a result of adaptation to stressors. In this work we examined the potential that inbreeding depression varied among lineages of Ipomoea purpurea...

Balancing selection and drift in a polymorphic salamander metapopulation

Sean Giery, Marketa Zimova, Dana Drake & Mark Urban
Understanding how genetic variation is maintained in a metapopulation is a longstanding problem in evolutionary biology. Historical resurveys of polymorphisms have offered efficient insights about evolutionary mechanisms, but are often conducted on single, large populations, neglecting the more comprehensive view afforded by considering all populations in a metapopulation. Here, we resurveyed a metapopulation of spotted salamanders (Ambystoma maculatum) to understand the evolutionary drivers of frequency variation in an egg mass colour polymorphism. We found that...

Supplementary data, code, and information for ‘Atlantic and Pacific multidecadal oscillations and Northern Hemisphere temperatures’ (Science, Steinman et al. 2015)

B.A. Steinman, M.E. Mann & S.K. Miller
The recent slowdown in global warming has brought into question the reliability of climate model projections of future temperature change and has led to a vigorous debate over whether this slowdown is the result of naturally occurring, internal variability or forcing external to Earth’s climate system. To address these issues, we applied a semi-empirical approach that combines climate observations and model simulations to estimate Atlantic- and Pacific-based internal multidecadal variability (termed “AMO” and “PMO,” respectively)....

Factors Impacting Food Away from Home (FAFH) Spending in the United States: A Macroeconomic Perspective

Michael S. Lin, Inhaeng N. Jung & Yidan Huang

Investigating the Impact of Racial Diversity in Decision‐making Groups: The Moderating Role of Relationship Conflict

Brian Manata

Developmental transcriptomics reveals a gene network driving mimetic color variation in a bumble bee

Sarthok Rasique Rahman, Tatiana Terranova, Li Tian & Heather Hines
A major goal of evolutionary genetics and evo-devo is to understand how changes in genotype manifest as changes in phenotype. Bumble bees display remarkable color pattern diversity while converging onto numerous regional Müllerian mimicry patterns, thus enabling exploration of the genetic mechanisms underlying convergent phenotypic evolution. In western North America, multiple bumble bee species converge onto local mimicry patterns through parallel shifts of midabdominal segments from red to black. It was previously demonstrated that a...

Supplementary data, code, and information for ‘Atlantic hurricanes and climate over the past 1,500 years’ (Mann et al. 2009)

M.E. Mann
Atlantic tropical cyclone activity, as measured by annual storm counts, reached anomalous levels over the past decade. The short nature of the historical record and potential issues with its reliability in earlier decades, however, has prompted an ongoing debate regarding the reality and significance of the recent rise. Here we place recent activity in a longer-term context by comparing two independent estimates of tropical cyclone activity over the past 1,500 years. The first estimate is...

Supplementary data, code, and information for ‘Smoothing of Climate Time Series Revisited’ (Mann 2008)

M.E. Mann
We present an easily implemented method for smoothing climate time series, generalizing upon an approach previously described by Mann (2004). The method adaptively weights the three lowest order time series boundary constraints to optimize the fit with the raw time series. We apply the method to the instrumental global mean temperature series from 1850 – 2007 and to various surrogate global mean temperature series from 1850 – 2100 derived from the CMIP3 multimodel intercomparison project....

On bridging paired-end RNA-seq data

X. Li, Q. Shi & M. Shao
The widely-used high-throughput RNA-sequencing technologies (RNA-seq) usually produce paired-end reads. We explore if full fragments can be computationally reconstructed from the sequenced two ends—a problem here we refer to as bridging. Solving this problem provides longer, more informative RNA-seq reads, and hence benefits downstream RNA-seq analysis such as transcriptome assembly and expression quantification. However, bridging is a challenging and complicated task owing to alternative splicing, transcript noises, and sequencing errors. It remains unclear if the...

Organic fertility inputs synergistically increase denitrification-derived nitrous oxide emissions in agroecosystems

D. Saha, J.P. Kaye, A. Bhowmik, M. Bruns, J.M. Wallace & A.R. Kemanian
Organic fertility inputs synergistically increase denitrification-derived nitrous oxide emissions in agroecosystems.

Threading the needle: how humans influence predator-prey spatiotemporal interactions in a multiple-predator system

Asia Murphy, Duane Diefenbach, Mark Ternent, Matt Lovallo & David Miller
Perceived predation risk and the resulting antipredator behavior varies across space, time, and predator identity. Communities with multiple predators that interact and differ in their use of space, time of activity, and hunting mode create a complex landscape for prey to avoid predation. Anthropogenic presence and disturbance have the potential to shift interactions among predators and prey and the where and when encounters occur. We examined how spatiotemporal antipredator behavior of white-tailed deer fawns (Odocoileus...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Text
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  • Journal Article
  • Model
  • Software


  • Pennsylvania State University
  • Roger Williams University
  • University of Massachusetts Amherst
  • University of Connecticut
  • United States Geological Survey
  • Potsdam Institute for Climate Impact Research
  • University of Arizona
  • Yale University
  • University of Pennsylvania
  • University of Michigan-Ann Arbor