502 Works

Data from: Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)

Michael R. McKain, Norman Wickett, Yeting Zhang, Saravanaraj Ayyampalayam, W. Richard McCombie, Mark W. Chase, J. Chris Pires, Claude W. DePamphilis, Jim Leebens-Mack & Claude W. De Pamphilis
PREMISE OF THE STUDY: The stability of the bimodal karyotype found in Agave and closely related species has long interested botanists. The origin of the bimodal karyotype has been attributed to allopolyploidy, but this hypothesis has not been tested. Next Generation transcriptome sequence data were used to test whether a paleopolyploid event occurred on the same branch of the Agavoideae phylogenetic tree as the origin of the Yucca-Agave bimodal karyotype. METHODS: Illumina RNAseq data were...

Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs

Douglas S. Glazier, Eric M. Butler, Sara A. Lombardi, Travis J. Deptola, Andrew J. Reese & Erin V. Satterthwaite
Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic...

Data from: Degradation of internal organic matter is the main control on pteropod shell dissolution after death

Rosie L. Oakes, Victoria L. Peck, Clara Manno & Timothy J. Bralower
The potential for preservation of thecosome pteropods is thought to be largely governed by the chemical stability of their delicate aragonitic shells in seawater. However, sediment trap studies have found that significant carbonate dissolution can occur above the carbonate saturation horizon. Here we present the results from experiments conducted on two cruises to the Scotia Sea to directly test whether the breakdown of the organic pteropod body influences shell dissolution. We find that, on the...

Data from: Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens

Etya Amsalem, David A. Galbraith, Jonathan Cnaani, Peter E. A. Teal & Christina M. Grozinger
Diapause is the key adaptation allowing insects to survive unfavorable conditions and inhabit an array of environments. Physiological changes during diapause are largely conserved across species, and are hypothesized to be regulated by a conserved suite of genes (a “toolkit”). Furthermore, it is hypothesized that in social insects, this toolkit was co-opted to mediate caste differentiation between long-lived, reproductive, diapause-capable queens and short-lived, sterile workers. Using Bombus terrestris queens we examined the physiological and transcriptomic...

Data from: Covariation in abscission force and terminal velocity of wind-borne sibling seeds alters long distance dispersal projections

Brittany J. Teller, James H. Marden & Katriona Shea
1. Despite the fact that seeds are unlikely to be identical—even among siblings within a maternal individual—dispersal models typically use one mean trait value to represent the ability of an entire species to disperse. Previous work has shown that the environmental conditions under which individuals leave the maternal site strongly affect how far seeds will travel. However, less is known about how trait variation within individuals contributes to dispersal or how such variation might interact...

Data from: Costs of injury for scent signalling in a strepsirrhine primate

Rachel L. Harris, Marylène Boulet, Kathleen E. Grogan & Christine M. Drea
Honesty is crucial in animal communication when signallers are conveying information about their condition. Condition dependence implies a cost to signal production; yet, evidence of such cost is scarce. We examined the effects of naturally occurring injury on the quality and salience of olfactory signals in ring-tailed lemurs (Lemur catta). Over a decade, we collected genital secretions from 23 (13 male, 10 female) adults across 34 unique injuries, owing primarily to intra-group fights. Using gas...

Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods

Kimberly Ballare, Nathaniel Pope, Antonio Castilla, Sarah Cusser, Richard Metz & Shalene Jha
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next-generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we...

Enhanced and unified anatomical labeling for a common mouse brain atlas

Uree Chon, Daniel Vanselow, Keith Cheng & Yongsoo Kim
Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin and Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, here we adopt the FP labels into the CCF to merge two labels in...

Identifying and classifying shared selective sweeps from multilocus data

Alexandre Harris & Michael DeGiorgio
Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can...

Data from: The contribution of host cell-directed vs. parasite-directed immunity to the disease and dynamics of malaria infections

Nina Wale, Matthew J. Jones, Derek G. Sim, Andrew F. Read & Aaron A. King
Hosts defend themselves against pathogens by mounting an immune response. Fully understanding the immune response as a driver of host disease and pathogen evolution requires a quantitative account of its impact on parasite population dynamics. Here, we use a data-driven modeling approach to quantify the birth and death processes underlying the dynamics of infections of the rodent malaria parasite, Plasmodium chabaudi, and the red blood cells (RBCs) it targets. We decompose the immune response into...

Disentangling the mechanisms underpinning disturbance-mediated invasion data

Luke Lear, Elze Hesse, Katriona Shea & Angus Buckling
Disturbances can play a major role in biological invasions: by destroying biomass, they alter habitat and resource abundances. Previous field studies suggest that disturbance-mediated invader success is a consequence of resource influxes, but the importance of other potential covarying causes, notably the opening up of habitats, have yet to be directly tested. Using experimental populations of the bacterium Pseudomonas fluorescens we determined the relative importance of disturbance-mediated habitat opening and resource influxes, plus any interaction...

Origins of 1/f-like tissue oxygenation fluctuations in the murine cortex

Qingguang Zhang, Kyle Gheres & Patrick Drew
The concentration of oxygen in the brain spontaneously fluctuates, and the distribution of power in these fluctuations has a 1/f-like spectra, where the power present at low frequencies of the power spectrum is orders of magnitude higher than at higher frequencies. Though these oscillations have been interpreted as being driven by neural activity, the origins of these 1/f-like oscillations is not well understood. Here, to gain insight of the origin of the 1/f-like oxygen fluctuations,...

Data from: Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis

Ángel Ferrero-Serrano, Megan M. Sylvia, Peter C. Forstmeier, Andrew J. Olson, Doreen Ware, Philip C. Bevilacqua & Assmann Sarah M.
BackgroundGenome-Wide Association Studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Single nucleotide variants (SNVs) within transcripts may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions and translation. However, no plant genomes have been yet assessed for the presence of these structure-altering polymorphisms or “riboSNitches”.ResultsWe experimentally demonstrate the presence of riboSNitches in transcripts of two Arabidopsis genes, ZINC RIBBON 3 (ZR3) and COTTON GOLGI-RELATED 3 (CGR3), which are associated with continentality...

Oak galls exhibit ant-dispersal convergent with myrmecochorous seeds

Robert Warren, Antoine Guiguet, Chloe Mokadam, John Tooker & Andrew Deans
Ants disperse oak galls of some cynipid wasp species similarly to how they disperse seeds with elaiosomes. We conducted choice assays in field and lab settings, with ant-dispersed seeds and wasp-induced galls found in ant nests and found that seed-dispersing ants retrieve these galls as they do myrmecochorous seeds. We also conducted manipulative experiments in which we removed the putative ant-attracting appendages (“kapéllos”) from galls and found ants are specifically attracted to kapéllos. Finally, we...

Data from: Friction of Longmaxi shale gouges and implications for seismicity during hydraulic fracturing

Mengke An, Fengshou Zhang, Derek Elsworth, Zhengyu Xu, Zhaowei Chen & Lianyang Zhang
Longmaxi formation shales are the major target reservoir for shale gas extraction in the Sichuan Basin, southwest China. Swarms of earthquakes accompanying hydraulic fracturing are observed at depths typified by the Longmaxi formation. Mineral composition varies broadly through the stratigraphic section due to different depositional environments. The section is generally tectosilicate-poor and phyllosilicate-rich with a minor portion (~5 wt.%) the converse. We measure the frictional and stability properties of shale gouges taken from the full...

Substantial genetic divergence and lack of recent gene flow support cryptic speciation in a colour polymorphic bumble bee (Bombus bifarius) species complex

Guillaume Ghisbain, Jeffrey D. Lozier, Sarthok Rasique Rahman, Briana D. Ezray, Li Tian, Jonah M. Ulmer, Sam D. Heraghty, James P. Strange, Pierre Rasmont & Heather M. Hines
Phenotypic polymorphism can constitute an inherent challenge for species delimitation. This issue is exemplified in bumble bees (Bombus), where species can exhibit high colour variation across their range, but otherwise exhibit little morphological variation to distinguish them from close relatives. We examine the species status of one of the most abundant North American bumble bees, Bombus bifarius Cresson, which historically was comprised of two major taxa, bifarius s.s. (sensu stricto) and nearcticus. These sublineages are...

Configurational crop heterogeneity increases within-field plant diversity

Audrey Alignier, Xavier Solé-Senan, Irene Robleño, Barbara Baraibar, Fahrig Lenore, David Giralt, Nicolas Gross, Jean-Louis Martin, Jordi Recasens, Clelia Sirami, Gavin Siriwardena, Aliette Bosem Baillod, Colette Bertrand, Romain Carrie, Annika Hass, Laura Henckel, Paul Miguet, Isabelle Badenhausser, Jacques Baudry, Gerard Bota, Vincent Bretagnolle, Lluis Brotons, Francoise Burel, François Calatayud, Yann Clough … & Péter Batáry
1. Increasing landscape heterogeneity by restoring semi-natural elements to reverse farmland biodiversity declines is not always economically feasible or acceptable to farmers due to competition for land. We hypothesized that increasing the heterogeneity of the crop mosaic itself, hereafter referred to as crop heterogeneity, can have beneficial effects on within-field plant diversity. 2. Using a unique multi-country dataset from a cross-continent collaborative project covering 1451 agricultural fields within 432 landscapes in Europe and Canada, we...

Selection on a small genomic region underpins differentiation in multiple color traits between two warbler species

Silu Wang, Sievert Rohwer, Devin De Zwaan, David Toews, Irby Lovette, Jacqueline Mackenzie & Darren Irwin
Speciation is one of the most important processes in biology, yet the study of the genomic changes underlying this process is in its infancy. North American warbler species Setophaga townsendi and S. occidentalis hybridize in a stable hybrid zone, following a period of geographic separation. Genomic differentiation accumulated during geographic isolation can be homogenized by introgression at secondary contact, while genetic regions that cause low hybrid fitness can be shielded from such introgression. Here we...

Long-term evidence shows crop-rotation diversification increases agricultural resilience to adverse growing conditions in North America

Timothy Bowles, Maria Mooshammer, Yvonne Socolar, Franciso Calderón, Michel Cavigelli, Steve Culman, William Dean, Axel Garcia Y Garcia, Amélie Gaudin, W Scott Harkom, Michael Lehman, Shannon Osborne, G Philip Robertson, Jonathan Salerno, Marty Schmer, Jeffrey Strock, A Stuart Grandy & Craig Drury
A grand challenge facing humanity is how to produce food for a growing population in the face of a changing climate and environmental degradation. Though empirical evidence remains sparse, management strategies that increase environmental sustainability, like increasing agroecosystem diversity through crop rotations, may also increase resilience to weather extremes without sacrificing yields. We used multilevel regression analyses of long-term crop yield datasets across a continental precipitation gradient to assess how temporal crop diversification affects maize...

The influence of feeding behaviour and temperature on the capacity of mosquitoes to transmit malaria

Eunho Suh, Marissa Grossman, Jessica Waite, Nina Dennington, Ellie Sherrard-Smith, Thomas Churcher & Matthew Thomas
Insecticide-treated bed nets reduce malaria transmission by limiting contact between mosquito vectors and human hosts when mosquitoes feed during the night. However, malaria vectors can also feed in the early evening and in the morning when people are not protected. Here, we explored how timing of blood feeding interacts with environmental temperature to influence the capacity of Anopheles mosquitoes to transmit the human malaria parasite, Plasmodium falciparum. In laboratory experiments, we found no effect of...

Supplementary data, code, and information for ‘The Influence of Climate State Variables on Atlantic Tropical Cyclone Occurrence Rates’ (Sabbatelli and Mann 2007)

T.A. Sabatelli & M.E. Mann
We analyzed annual North Atlantic tropical cyclone (TC) counts from 1871-2004, considering three climate state variables—the El Niño/Southern Oscillation (ENSO), peak (August-October or ‘ASO’) Sea Surface Temperatures (SST) over the main development region (‘MDR’: 6-18N latitude, 20-60W), and the North Atlantic Oscillation (NAO)—thought to influence variations in annual TC counts on interannual and longer timescales. The unconditional distribution of TC counts is observed to be inconsistent with the null hypothesis of a fixed rate random...

Supplementary data, code, and information for ‘Robustness of Proxy-Based Climate Field Reconstruction Methods’ (Mann et al. 2007)

M.E. Mann, S. Rutherford, E. Wahl & C. Ammann
We present results from continued investigations into the fidelity of covariance-based climate field reconstruction (CFR) approaches used in proxy-based climate reconstruction. Our experiments employ synthetic ‘‘pseudoproxy’’ data derived from simulations of forced climate changes over the past millennium. Using networks of these pseudoproxy data, we investigate the sensitivity of CFR performance to signal-to-noise ratios, the noise spectrum, the spatial sampling of pseudoproxy locations, the statistical representation of predictors used, and the diagnostic used to quantify...

Supplementary data, code, and information for ‘Assessing Climate Change Impacts on Extreme Weather Events: The Case For an Alternative (Bayesian) Approach’ (Mann et al. 2017)

M.E. Mann, E.A. Lloyd & N. Oreskes
The conventional approach to detecting and attributing climate change impacts on extreme weather events is generally based on frequentist statistical inference wherein a null hypothesis of no influence is assumed, and the alternative hypothesis of an influence is accepted only when the null hypothesis can be rejected at a sufficiently high (e.g., 95% or p = 0.05) level of confidence. Using a simple conceptual model for the occurrence of extreme weather events, we show that...

Supplementary data, code, and information for ‘Long-term variability in the El Niño/Southern Oscillation and associated teleconnections’

M.E. Mann, R.S. Bradley & M.K. Hughes
We analyze global patterns of reconstructed surface temperature for insights into the behavior of the El Niño/Southern Oscillation (ENSO) and related climatic variability during the past three centuries. The global temperature reconstructions are based on calibrations of a large set of globally distributed proxy records, or “multiproxy” data, against the dominant patterns of surface temperature during the past century. These calibrations allow us to estimate large-scale surface temperature patterns back in time. The reconstructed eastern...

Model Input, Analysis Code, and Select Model Output for the Murdzek et al. (2021) Inflow Layer Study

S. Murdzek, P. Markowski, Y.P. Richardson & M.R. Kumjian
This dataset contains all relevant Cloud Model 1 (CM1) input files, python analysis code, and select CM1 output for the Murdzek et al. (2021, JAS) study that examines whether reversible or pseudoadiabatic convective inhibition should be used when determining the effective inflow layer of a convective storm. Enough CM1 output is provided to recreate all the figures from Murdzek et al. (2021), and the rest of the output can be recreated using the supplied input...

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