111 Works

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...

Molecular assays of pollen use consistently reflect pollinator visitation patterns in a system of flowering plants

Aubrie James, Monica Geber & David Toews
Determining how pollinators visit plants versus how they carry and transfer pollen is an ongoing project in pollination ecology. The current tools for identifying the pollens that bees carry have different strengths and weaknesses when used for ecological inference. In this study we use three methods to better understand a system of congeneric, co-flowering plants in the genus Clarkia and their bee pollinators: observations of plant-pollinator contact in the field, and two different molecular methods...

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...

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...

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 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...

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...

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)...

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...

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.

PSU DEP Topographic Wetness Index (TWI)

C. Fernandez
GIS raster datasets displaying Topographic Wetness Index (TWI) for Pennsylvania by County. TWI raster datasets were derived from 2006-2008 LiDAR (Light Detection and Ranging) elevation points produced by the PAMAP Program. The coordinate system for blocks in the northern half of the state is Pennsylvania State Plane North (datum: NAD83, units: feet); blocks in the southern half are in Pennsylvania State Plane South. Raster spatial resolution is 9.6 ft (approximately 3 m). The TWI, also...

Value of Curation Survey, January 2021

Lisa R Johnston, Renata Gonçalves Curty, Sophia Lafferty-Hess, Hannah Hadley, Jonathan Petters, Hoa Luong, Susan Braxton, Jake Carlson & Wendy A Kozlowski
This dataset includes the raw and augmented survey results from the January 2021 Value of Curation survey run by the Data Curation Network. Distributed to US data repository staff and directors via email listservs the survey received a total of 120 responses. 22 responses were for non-US repositories and three did not provide a repository of reference. A majority of the participants self-identified as staff members with 52 staff and 34 repository directors. The remaining...

Data and Analysis in Support of “Methane Fluxes in a Region Containing Shale Gas Wells Cited with Cementing and Casing Issues”

L.E. Dennis, S.J. Richardson, N.L. Miles, J. Woda & K.J. Davis
We quantified atmospheric methane emissions from a subsurface source in the vicinity of a shale gas well that was cited for casing and cementing issues. We measured the magnitude and spatial and temporal variability of emissions in a farm field where patches of dead vegetation and methane bubbling from a nearby stream were observed. The methane emissions were quantified using an eddy covariance flux tower, chamber flux measurements, and a survey of near-surface methane mole...

The influence of maternal glucocorticoids on offspring phenotype in high- and low-risk environments

Kirsty J. MacLeod, Tracy Langkilde, Cameron Venable, David Ensminger & Michael Sheriff
Elevated maternal glucocorticoid levels during gestation can lead to phenotypic changes in offspring via maternal effects. Although such effects have traditionally been considered maladaptive, maternally derived glucocorticoids may adaptively prepare offspring for their future environment depending upon the correlation between maternal and offspring environments. Nevertheless, relatively few studies test the effects of prenatal glucocorticoid exposure across multiple environments. We tested the potential for ecologically relevant increases in maternal glucocorticoids in the eastern fence lizard (Sceloporus...

Prediction of intrahepatic cholestasis of pregnancy in the first 20 weeks of pregnancy

Xinyuan Zhang, Yu Chen, Stephen Salerno, Yi Li, Libin Zhou, Xiaoxi Zeng & Huafeng Li
Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disease associated with a significant risk of fetal complications including pre-term delivery and fetal death. Typically, it was diagnosed in the third trimester of pregnancy. This study utilized characteristics from routine maternal examinations in the first 20 weeks’ gestation to predict ICP in pregnant women. This is a retrospective case-control study. 13,329 medical records were collected on pregnant women presenting to the West China Second University...

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...

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...

Datasets associated with: Late Holocene spread of pastoralism coincides with endemic megafaunal extinction on Madagascar

Sean Hixon, Kristina Douglass, Brooke Crowley, Lucien Rakotozafy, Geoffrey Clark, Atholl Anderson, Simon Haberle, Jean Freddy Ranaivoarisoa, Mike Buckley, Salomon Fidiarisoa, Balzac Mbola & Douglas Kennett
Recently expanded estimates for when humans arrived on Madagascar (up to ~10,000 years ago) highlight questions about the causes of the island’s relatively late megafaunal extinctions (~2000-500 years ago). Introduced domesticated animals could have contributed to extinctions, but the arrival times and past diets of exotic animals are poorly known. To conduct the first explicit test of the potential for competition between introduced livestock and extinct endemic megafauna in southern and western Madagascar, we generated...

Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress

Viridiana Avila-Magaña, Bishoy Kamel, Michael DeSalvo, Kelly Gómez-Campo, Susana Enríquez, Hiroaki Kitano, Rori Rohlfs, Roberto Iglesias-Prieto & Mónica Medina
As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities...

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....

Registration Year

  • 2021

Resource Types

  • Dataset


  • Pennsylvania State University
  • University of Massachusetts Amherst
  • University of Arizona
  • Roger Williams University
  • University of Michigan-Ann Arbor
  • University of Michigan–Ann Arbor
  • Duke University
  • Fudan University
  • University of Minnesota
  • Potsdam Institute for Climate Impact Research