25 Works

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...

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....

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...

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...

Data from: Non-invasive stratification of non-alcoholic fatty liver disease by whole-transcriptome cell-free mRNA characterization

Naga Chalsani, Shusuke Toden, John Sninsky, Richard Rava, Jerome Braun, Samer Gawrieh, Jiali Zhuang, Michael Nerenberg, Stephen Quake & Tara Maddala
Hepatic fibrosis stage is the most important determinant of outcomes in patients with non-alcoholic fatty liver disease (NAFLD). There is an urgent need for non-invasive tests that can accurately stage fibrosis and determine efficacy of interventions. Here we describe a novel cf-mRNA-Sequencing approach that can accurately and reproducibly profile low levels of circulating mRNAs and evaluate the feasibility of developing a cf-mRNA-based NAFLD fibrosis classifier. Using separate discovery and validation cohorts with biopsy-confirmed NAFLD (n=176...

Data from: Nanotransfection-based vasculogenic cell reprogramming drives functional recovery in a mouse model of ischemic stroke

Luke Lemmerman, Maria Balch, Jordan Moore, Diego Alzate-Correa, Maria Rincon-Benavides, Ana Salazar-Puerta, Surya Gnyawali, Hallie Harris, William Lawrence, Lilibeth Ortega-Pineda, Lauren Wilch, Ian Risser, Aidan Maxwell, Silvia Duarte-Sanmiguel, Daniel Dodd, Gina Guio-Vega, Dana McTigue, William Arnold, Shahid Nimjee, Chandan Sen, Savita Khanna, Cameron Rink, Natalia Higuita-Castro & Daniel Gallego-Perez
Ischemic stroke causes vascular and neuronal tissue deficiencies that could lead to significant functional impairment and/or death. Although progenitor-based vasculogenic cell therapies have shown promise as a potential rescue strategy following ischemic stroke, current approaches face major hurdles. Here we used fibroblasts nanotransfected with Etv2, Foxc2, and Fli1 (EFF), to drive reprogramming-based vasculogenesis, intracranially, as a potential therapy for ischemic stroke. Perfusion analyses suggest that intracranial delivery of EFF-nanotransfected fibroblasts led to a dose-dependent increase...

Data from: Ecological and evolutionary significance of primates’ most consumed plant families

Jun Ying Lim, Michael D. Wasserman, Jorin Veen, Marie-Lynne Despres-Einspenner & W. Daniel Kissling
Angiosperms have been essential components of primate diet for millions of years, but the relative importance of different angiosperm families in primate diets and their influence on primate evolution and ecology remains unclear. Here, we assess the contribution and ecological and evolutionary significance of plant families to the diets of wild primates based on an unprecedented dietary dataset of over 8,000 dietary records, compiled from 140 primary sources encompassing 109 primate species. Out of the...

Wing and bill measurements of Tyrannus round specimens identified to subspecies

Maggie MacPherson, Alejandro Jahn & Nicholas Mason
Morphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb-morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviors also interact with diet, such that migratory animals tend to be dietary generalists, while sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. We tested for evolutionary associations between migratory status and...

Testing hormonal responses to real and simulated social challenges in a competitive female bird

Elizabeth George, Sarah Wolf, Alexandra Bentz & Kimberly Rosvall
Competitive interactions often occur in series; therefore animals may respond to social challenges in ways that prepare them for success in future conflict. Changes in the production of the steroid hormone testosterone (T) are thought to mediate phenotypic responses to competition, but research over the past few decades has yielded mixed results, leading to several potential explanations as to why T does not always elevate following a social challenge. Here, we measured T levels in...

Supplemental material for: NINDS consensus diagnostic criteria for Traumatic Encephalopathy Syndrome

Douglas Katz, Charles Bernick, David Dodick, Jesse Mez, Megan Mariani, Charles Adler, Michael Alosco, Laura Balcer, Sarah Banks, William Barr, David Brody, Robert Cantu, Kristen Dams-O'Connor, Yonas Geda, Barry Jordan, Thomas McAllister, Elaine Peskind, Ronald Petersen, Jennifer Wether, Ross Zafonte, Eimear Foley, Debra Babcock, Walter Koroshetz, Ann McKee, Martha Shenton … & Robert Stern
Objective: To develop evidence-informed, expert consensus research diagnostic criteria for Traumatic Encephalopathy Syndrome (TES), the clinical disorder associated with neuropathologically diagnosed Chronic Traumatic Encephalopathy (CTE). Methods: A panel of 20 expert clinician-scientists in neurology, neuropsychology, psychiatry, neurosurgery, and physical medicine and rehabilitation, from 11 academic institutions, participated in a modified Delphi procedure to achieve consensus, initiated at the First NINDS Consensus Workshop to Define the Diagnostic Criteria for TES, April, 2019. Prior to consensus, panelists...

Data from: The relationship between native species richness and exotic species richness or occurrence will always be negative when the total number of species is accounted for in statistical models: A response to Beaury et al.

Ranjan Muthukrishnan
Beaury et al. (2020) attempt to address the scale dependence of evidence for biotic resistance by including environmental covariates that can account for total species richness. However, this approach will incorrectly estimate relationships, driven by the accuracy of the covariates rather than the true relationship between native and non-native species.

Warming during maternal generations delays offspring germination in native and nonnative species

Meredith Zettlemoyer & Jennifer Lau
As environmental conditions shift due to global warming and other human-caused environmental changes, plastic responses in phenological traits like germination or flowering time may become increasingly important. While phenological plasticity is a common response to global warming, with many populations exhibiting earlier germination or flowering in warmer years, warming may also result in transgenerational plasticity, especially on early life stages. In other words, seeds produced by mothers inhabiting warmer environments may germinate faster (or slower)...

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...

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...

Genotypic variation in an ecologically important parasite is associated with host species, lake, and spore size

Clara Shaw, Rebecca Bilich, Bruce O'Brien, Carla Cáceres, Spencer Hall, Timothy James & Meghan Duffy
Genetic variation in parasites has important consequences for host-parasite interactions. Prior studies of the ecologically important parasite Metschnikowia bicuspidata have suggested low genetic variation in the species. Here, we collected M. bicuspidata from two host species (Daphnia dentifera and Ceriodaphnia dubia) and two regions (Michigan and Indiana, USA). Within a lake, outbreaks tended to occur in one host species but not the other. Using microsatellite markers, we identified six parasite genotypes grouped within three distinct...

Observational evidence of herbivore-specific associational effects between neighboring conspecifics in natural, dimorphic populations of Datura wrightii

Jay Goldberg, Sonya Sternlieb, Genevieve Pintel & Lynda Delph
Associational effects – in which the vulnerability of a plant to herbivores is influenced by its neighbors – have been widely implicated in mediating plant-herbivore interactions. Studies of associational effects typically focus on interspecific interactions or pest-crop dynamics. However, associational effects may also be important for species with intraspecific variation in defensive traits. In this study, we observed hundreds of Datura wrightii – which exhibits dimorphism in its trichome phenotype – from over 30 dimorphic...

Supporting information for: The frequency and topology of pseudoorthologs

Megan Smith & Matthew Hahn
Phylogenetics has long relied on the use of orthologs, or genes related through speciation events, to infer species relationships. However, identifying orthologs is difficult because gene duplication can obscure relationships among genes. Researchers have been particularly concerned with the insidious effects of pseudoorthologs—duplicated genes that are mistaken for orthologs because they are present in a single copy in each sampled species. Because gene tree topologies of pseudoorthologs may differ from the species tree topology, they...

Data from: Signatures of north-eastern expansion and multiple refugia: Genomic phylogeography of the Pine Barrens Treefrog, Hyla andersonii (Anura: Hylidae)

Alexa Warwick, Lisa Barrow, Megan Smith, D. Bruce Means, Alan Lemmon & Emily Lemmon
Range fragmentation poses challenges for species persistence over time and may be caused by both historical and contemporary processes. We combined genomic data, phylogeographic model testing, and paleoclimate niche modeling to infer the evolutionary history of the Pine Barrens Treefrog (Hyla andersonii), a seepage bog specialist, in eastern North America to better understand the historical context of its fragmented distribution. We sampled H. andersonii populations across the three disjunct regions of the species’ range: Alabama/Florida...

The probability of being infected with haemosporidian parasites increases with host age

Samuel Slowinski, Aidan Geissler, Nicole Gerlach, Britt Heidinger & Ellen Ketterson
In vertebrates, disease susceptibility often varies with age. Older individuals may be more susceptible than younger individuals due to senescent declines in immune function. Alternatively, disease susceptibility may decrease with age if older individuals are more likely to have had prior exposures to parasites and acquired adaptive immune responses that allowed them to resist future infections. Disease susceptibility can also vary with reproductive state, and reproductive hormones have been shown to increase infection susceptibility. Here...

A shift to shorter cuticular hydrocarbons accompanies sexual isolation among Drosophila americana group populations

Jeremy S Davis, Matthew Pearcy, Joanne Yew & Leonie Moyle
Because sensory signals often evolve rapidly, they could be instrumental in the emergence of reproductive isolation between species. However, pinpointing their specific contribution to isolating barriers, and the mechanisms underlying their divergence, remains challenging. Here we demonstrate sexual isolation due to divergence in chemical signals between two populations of Drosophila americana (SC and NE) and one population of D. novamexicana, and dissect its underlying phenotypic and genetic mechanisms. Mating trials revealed strong sexual isolation between...

Compartmentalization of cerebrospinal fluid inflammation across the spectrum of HIV infection

Richard Price, Magnus Gisslen, Sheila Keating, Serena Spudich, Victor Arechiga, Sophie Stephenson, Henrik Zetterberg, Clara Di Germanio, Kaj Blennow, Lars Hagberg, Philip Norris, Julia Peterson, Barbara Shacklett & Constantin Yiannoutsos
Objective: To characterize the evolution of central nervous system (CNS) inflammation in HIV-1 infection applying a panel of cerebrospinal fluid (CSF) inflammatory biomarkers to grouped subjects representing a broad spectrum of systemic HIV-1 immune suppression, CNS injury and viral control. Methods: This is a cross-sectional analysis of archived CSF and blood samples, assessing concentrations of 10 functionally diverse soluble inflammatory biomarkers by immunoassays in 143 HIV-1-infected subjects divided into 8 groups: untreated primary HIV-1 infection...

Mycorrhizal effects on decomposition and soil CO2 flux depend on changes in nitrogen availability during forest succession

Ruiqiang Liu, Yanghui He, Guiyao Zhou, Junjiong Shao, Lingyan Zhou, Huimin Zhou, Nan Li, Bingqian Song, Chao Liang, Enrong Yan, Xiao-Yong Chen, Xihua Wang, Minhuang Wang, Shahla Hosseini Bai, Xuhui Zhou & Richard Phillips
Mycorrhizal fungi play a central role in plant nutrition and nutrient cycling, yet our understanding on their effects on free-living microbes, soil carbon (C) decomposition and soil CO2 fluxes remains limited. Here we used trenches lined with mesh screens of varying sizes to isolate mycorrhizal hyphal effects on soil C dynamics in subtropical successional forests. We found that the presence of mycorrhizal hyphae suppressed soil CO2 fluxes by 17% in early-successional forests, but enhanced CO2...

Data from: Causation without correlation: parasite-mediated frequency-dependent selection and infection prevalence

Curtis Lively, Frida Ben-Ami & Julie Xu
Parasite-mediated selection is thought to maintain genetic diversity for resistance in natural host populations. We might thus expect to find a strong positive correlation between host genetic diversity and infection prevalence across field populations. Here we used computer simulations to examine host-parasite coevolution in 20 simi-isolated populations, using a broad range of values for both parasite virulence and parasite fecundity. We found that the correlation between host genetic diversity and infection prevalence can be significantly...

Ionic amplifying circuits inspired by electronics and biology

Zuzanna Siwy, Rachel Lucas, Lane Baker & Chih-Yuan Lin
Integrated circuits are present in all electronic devices, and enable signal amplification, modulation, and relay. Nature uses another type of circuits composed of channels in a cell membrane, which regulate and amplify transport of ions, not electrons and holes as is done in electronic systems. Here we show an abiotic ionic circuit that is inspired by concepts from electronics and biology. The circuit amplifies small ionic signals into ionic outputs, and its operation mimics the...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Indiana University
  • University of Florida
  • Pennsylvania State University
  • North Dakota State University
  • Michigan State University
  • Sun Yat-sen University
  • University of Washington
  • Stanford University
  • University of Michigan-Ann Arbor
  • The Ohio State University