110 Works

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...

Intraspecific genetic variation underlying postmating reproductive barriers between species in the wild tomato clade (Solanum sect. Lycopersicon)

Cathleen Jewell, Simo Zhang, Matthew Gibson, Alejandro Tovar-Mendez, Bruce McClure & Leonie Moyle
A goal of speciation genetics is to understand how the genetic components underlying interspecific reproductive barriers originate within species. Unilateral incompatibility (UI) is a postmating prezygotic barrier in which pollen rejection in the female reproductive tract (style) occurs in only one direction of an interspecific cross. Natural variation in the strength of UI has been observed among populations within species in the wild tomato clade. In some cases, molecular loci underlying self-incompatibility (SI) are associated...

Data from: Cell signaling-based classifier predicts response to induction therapy in elderly patients with acute myeloid leukemia

Alessandra Cesano, Cheryl L. Willman, Kenneth J. Kopecky, Urte Gayko, Santosh Putta, Brent Louie, Matt Westfall, Norman Purvis, David C. Spellmeyer, Carol Marimpietri, Aileen C. Cohen, James Hackett, Jing Shi, Michael G. Walker, Zhuoxin Sun, Elisabeth Paietta, Martin S. Tallman, Larry D. Cripe, Susan Atwater, Frederick R. Appelbaum & Jerald P. Radich
Single-cell network profiling (SCNP) data generated from multi-parametric flow cytometry analysis of bone marrow (BM) and peripheral blood (PB) samples collected from patients >55 years old with non-M3 AML were used to train and validate a diagnostic classifier (DXSCNP) for predicting response to standard induction chemotherapy (complete response [CR] or CR with incomplete hematologic recovery [CRi] versus resistant disease [RD]). SCNP-evaluable patients from four SWOG AML trials were randomized between Training (N = 74 patients...

Data from: In a variable thermal environment selection favors greater plasticity of cell membranes in Drosophila melanogaster

Brandon S. Cooper, Loubna A. Hammad, Nicholas P. Fisher, Jonathan A. Karty & Kristi L. Montooth
Theory predicts that developmental plasticity, the capacity to change phenotypic trajectory during development, should evolve when the environment varies sufficiently among generations, owing to temporal (e.g., seasonal) variation or to migration among environments. We characterized the levels of cellular plasticity during development in populations of Drosophila melanogaster experimentally evolved for over three years in either constant or temporally variable thermal environments. We used two measures of the lipid composition of cell membranes as indices of...

Data from: Resource and competitive dynamics shape the benefits of public goods cooperation in a plant pathogen

Thomas Gene Platt, Clay Fuqua & James D. Bever
Cooperative benefits depend on a variety of ecological factors. Many cooperative bacteria increase the population size of their groups by making a public good available. Increased local population size can alleviate the constraints of kin competition on the evolution of cooperation by enhancing the between-group fitness of cooperators. The cooperative pathogenesis of Agrobacterium tumefaciens causes infected plants to exude opines—resources that provide a nearly exclusive source of nutrient for the pathogen. We experimentally demonstrate that...

Data from: Sexual, fecundity, and viability selection on flower size and number in a sexually dimorphic plant

Lynda F. Delph & Christopher R. Herlihy
The evolution of sexual dimorphism will depend on how sexual, fecundity and viability selection act within each sex, with the different forms of selection potentially operating in opposing directions. We examined selection in the dioecious plant Silene latifolia using planted arrays of selection lines that differed in flower size (small vs. large). In this species a flower size/number tradeoff exists within each sex, and males produce smaller and more numerous flowers than females. Moreover, floral...

Data from: Validation of a rodent model of source memory

Jonathon Crystal, Wesley Alford, W. T. Alford & J. D. Crystal
Source memory represents the origin (source) of information. Recently, we proposed that rats (Rattus norvegicus) remember the source of information. However, an alternative to source memory is the possibility that rats selectively encoded some, but not all, information rather than retrieving an episodic memory. We directly tested this "encoding-failure" hypothesis. Here, we show that rats remember the source of information, under conditions that cannot be attributed to encoding failure. Moreover, source memory lasted at least...

Data from: Community functional trait composition at the continental scale: the effects of non-ecological processes

A. Michelle Lawing, Jussi T. Eronen, Jessica L. Blois, Catherine H. Graham & P. David Polly
Ecological communities and their response to environmental gradients are increasingly being described by measures of trait composition at the community level – the trait-based approach. Whether ecological or non-ecological processes influence trait composition between communities has been debated. Understanding the processes that influence trait composition is important for reconstructing paleoenvironmental conditions from fossil deposits and for understanding changes in community functionality through time. Here, we assess the influence of ecological and non-ecological processes on the...

Incucyte data for infected cell colonized with Wolbachia or uncolonized

Irene Newton, Tamanash Bhattacharya & Richard Hardy
The ability of the endosymbiont Wolbachia pipientis to restrict RNA viruses is presently being leveraged to curb global transmission of arbovirus-induced diseases. Past studies have shown that virus replication is limited early in arthropod cells colonized by the bacterium, although it is unclear if this phenomenon is replicated in mosquito cells that first encounter viruses obtained through a vertebrate blood meal. Furthermore, these cellular events neither explain how Wolbachia limits dissemination of viruses between mosquito...

Experimentally elevated testosterone shortens telomeres across years in a free-living songbird

Britt Heidinger, Samuel Slowiniski, Aubrey Sirman, Nicole Gerlach & Ellen Ketterson
Reproductive investment often comes at a cost to longevity, but the mechanisms that underlie these long-term effects are not well understood. In male vertebrates, elevated testosterone has been shown to increase reproductive success, but simultaneously decrease survival. One factor that may contribute to or serve as a biomarker of these long-term effects of testosterone on longevity is telomeres, which are often positively related to lifespan and have been shown to shorten in response to reproduction....

Data from: Testing potential mechanisms of conspecific sperm precedence in Drosophila pseudoobscura

Brooke Peckenpaugh, Dean M. Castillo & Leonie C. Moyle
Drosophila pseudoobscura females that co-occur with sister species D. persimilis show elevated fertilization by conspecific sperm when they mate with both a heterospecific and a conspecific male. This phenomenon, known as conspecific sperm precedence (CSP), has evolved as a mechanism to avoid maladaptive hybridization with D. persimilis. In this study, we assessed pericopulatory (during mating) and postcopulatory (after mating) traits in crosses with sympatric or allopatric D. pseudoobscura females and conspecific or heterospecific males to...

Sequencing data and normalized counts for tripartite RNAseq of Drosophila, Wolbachia, and SINV virus

Irene Newton
Wolbachia is a maternally transmitted bacterium that manipulates arthropod and nematode biology in myriad ways. The Wolbachia strain colonizing Drosophila melanogaster creates sperm-egg incompatibilities and protects its host against RNA viruses, making it a promising tool for vector control. Despite successful trials using Wolbachia-transfected mosquitoes for Dengue control, knowledge of how Wolbachia and viruses jointly affect insect biology remains limited. Using the Drosophila melanogaster model, transcriptomics and gene expression network analyses revealed pathways with altered...

Invasive species and biotic homogenization in temperate aquatic plant communities

Ranjan Muthukrishnan & Daniel Larkin
Aim: Biotic homogenization (BH), a reduction in the distinctness of species composition between geographically separated ecological communities in a region, is an important but underappreciated potential consequence of biological invasions. While BH theory has always considered invasions, it has generally been in a relatively narrow context, i.e., that the cosmopolitan nature of invasive species increases BH because of their shared presence across many locations. We sought to evaluate this component of BH as well as...

Trans-specific polymorphism and the convergent evolution of supertypes in MHC class II genes in Darters (Etheostoma)

Kara Million & Curt Lively
Major Histocompatibility Complex (MHC) genes are one of the most polymorphic gene groups known in vertebrates. MHC genes also exhibit allelic variants that are shared among taxa, referred to as trans-specific polymorphism (TSP). The role that selection plays in maintaining such high diversity within species, as well as TSP, is an ongoing discussion in biology. In this study we used deep-sequencing techniques to characterize MHC class IIb gene diversity in three sympatric species of darters....

Histological and life history data for small-bodied mammals from: Multituberculate mammals show evidence of a life history strategy similar to that of placentals, not marsupials

Lucas Weaver, Henry Fulghum, David Grossnickle, William Brightly, Zoe Kulik, Gregory Wilson Mantilla & Megan Whitney
The remarkable evolutionary success of placental mammals has been partly attributed to their reproductive strategy of prolonged gestation and birthing of relatively precocial, quickly weaned neonates. Although this strategy was conventionally considered derived relative to that of marsupials with highly altricial neonates and long lactation periods, mounting evidence has challenged this view. Until now, the fossil record has been relatively silent on this debate, but here we find that proportions of different bone tissue microstructures...

Cross-biome synthesis of source vs sink limits to tree growth

Antoine Cabon, Steven Kannenberg, Flurin Babst, Dennis Baldocchi, Soumaya Belmecheri, Nicolas Delpierre, Rossella Guerrieri, Justin Maxwell, Shawn McKenzie, Chritoforos Pappas, Adrian Rocha, Paul Szejner, Masahito Ueyama, Danielle Ulrich, Caroline Vincke, Jingshu Wei, David Woodruff, Altaf Arain, Rick Meinzer, David J. P. Moore, Steven L. Voelker & William R. L. Anderegg
Uncertainties surrounding tree carbon allocation to growth are a major limitation to projections of forest carbon sequestration and response to climate change. The prevalence and extent to which carbon assimilation (source) or cambial activity (sink) mediate wood production is fundamentally important and remains elusive. Here we quantify source-sink relations across biomes by combining eddy-covariance gross primary production with extensive on-site and regional tree-ring observations. We find widespread temporal decoupling between carbon assimilation and tree growth,...

Molecular basis for the evolved instability of a human G-protein coupled receptor

Laura Chamness, Nathan Zelt, Charles Kuntz, Brian Bender, Wesley Penn, Joshua Ziarek, Jens Meiler, Jonathan Schlebach & Haley Harrington
Membrane proteins are prone to misfolding and degradation. This is particularly true for mammalian forms of the gonadotropin-releasing hormone receptor (GnRHR). Although they function at the plasma membrane, mammalian GnRHRs accumulate within the secretory pathway. Their apparent instability is believed to have evolved through selection for attenuated GnRHR activity. Nevertheless, the molecular basis of this adaptation remains unclear. We show that adaptation coincides with a C-terminal truncation that compromises the translocon-mediated membrane integration of its...

Manduca sexta experience high parasitoid pressures in the field but minor fitness costs of consuming plant secondary compounds

Deidra Jacobsen
Plant-herbivore co-evolutionary interactions have led to a range of plant defenses that minimize insect damage and a suite of counter-adaptations that allow herbivores to feed on defended plants. Consuming plant secondary compounds results in herbivore growth and developmental costs but can have beneficial effects such as deterrence or harm of parasitoid enemies. Therefore, the role of secondary compounds on herbivore fitness must be considered in the context of the abundance and level of harm from...

Data from: Surprising complexity of the ancestral apoptosis network

Christian M. Zmasek, Qing Zhang, Yuzhen Ye & Adam Godzik
Apoptosis, one of the main types of programmed cell death, is regulated and performed by a complex protein network. Studies in model organisms, mostly in the nematode C. elegans, identified a relatively simple apoptotic network consisting of only a few proteins. However, analysis of several recently sequenced invertebrate genomes, ranging from the cnidarian sea anemone Nematostella vectensis, representing one of the morphologically simplest metazoans, to the deuterostomes sea urchin and amphioxus, contradicts the current paradigm...

Data from: Conspecific sperm precedence is reinforced, but postcopulatory sexual selection weakened, in sympatric populations of Drosophila

Dean M. Castillo & Leonie C. Moyle
Sexual selection can accelerate speciation by driving the evolution of reproductive isolation, but forces driving speciation could also reciprocally feedback on sexual selection. This might be particularly important in the context of ‘reinforcement’, where selection acts directly to increase prezygotic barriers to reduce the cost of heterospecific matings. Using assays of sperm competition within and between two sister species, we show a signature of reinforcement where these species interact: populations of Drosophila pseudoobscura that co-occur...

Data from: Differential changes in bone strength of two inbred mouse strains following administration of a sclerostin-neutralizing antibody during growth

Noah J. Mathis, Emily N. Adaniya, Lauren M. Smith, Alexander G. Robling, Karl J. Jepsen & Stephen H. Schlecht
Administration of sclerostin-neutralizing antibody (Scl-Ab) treatment has been shown to elicit an anabolic bone response in growing and adult mice. Prior work characterized the response of individual mouse strains but did not establish whether the impact of Scl-Ab on whole bone strength would vary across different inbred mouse strains. Herein, we tested the hypothesis that two inbred mouse strains (A/J and C57BL/6J (B6)) will show different whole bone strength outcomes following sclerostin-neutralizing antibody (Scl-Ab) treatment...

Data from: Longitudinal cognitive and biomarker changes in dominantly inherited Alzheimer disease

Eric McDade, Guoqiao Wang, Brian Andrew Gordon, Jason Hassenstab, Tammie L.S. Benzinger, Virginia Buckles, Anne M. Fagan, David M. Holtzman, Nigel J. Cairns, Alison M. Goate, Daniel S. Marcus, John C. Morris, Katrina Paumier, Chengjie Xiong, Ricardo Allegri, Sarah B. Berman, William Klunk, James Nobel, John Ringman, Bernardino Ghetti, Martin Farlow, Reisa Anne Sperling, Jasmeer Chhatwal, Stephen Salloway, Neil R. Graff-Radford … & Randall J. Bateman
Objective: To assess the onset, sequence and rate of progression of comprehensive biomarker and clinical measures across the spectrum of Alzheimer disease using the Dominantly Inherited Alzheimer Network (DIAN) study and compare these to cross-sectional estimates. Methods: We conducted longitudinal clinical, cognitive, cerebrospinal fluid (CSF) and neuroimaging assessments (mean of 2.7 (+/- 1.1) visits) in 217 DIAN participants. Linear mixed effects models were used to assess changes in each measure relative to individuals’ estimated years...

Recombination data for Wolbachia and Spiroplasma infected flies

Irene Newton & Kaeli Bryant
Wolbachia pipientis is an intracellular alphaproteobacterium that infects 40-60% of insect species and is well known for host reproductive manipulations. Although Wolbachia are primarily maternally transmitted, evidence of horizontal transmission can be found in incongruent host-symbiont phylogenies and recent acquisitions of the same Wolbachia strain by distantly related species. Parasitoids and predator-prey interactions may indeed facilitate the transfer of Wolbachia between insect lineages but it is likely that Wolbachia are acquired via introgression in many...

Heating Arrays Aboveground Biomass Data

Louis Jochems, Jennifer Lau, Lars Brudvig & Emily Grman
Restoration in this era of climate change comes with a new challenge: anticipating how best to restore populations to persist under future climate conditions. Specifically, it remains unknown whether locally-adapted or warm-adapted seeds best promote native plant community restoration in the warmer conditions predicted in the future and whether local or warm-adapted soil microbial communities could mitigate plant responses to warming. This may be especially relevant for biomes spanning large climatic gradients, such as the...

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