87 Works

Parasite exposure and host susceptibility jointly drive the emergence of epidemics

Tara Stewart Merrill, Spencer Hall & Carla Cáceres
Parasite transmission is thought to depend on both parasite exposure and host susceptibility to infection; however, the relative contribution of these two factors to epidemics remains unclear. We used interactions between an aquatic host and its fungal parasite to evaluate how parasite exposure and host susceptibility interact to drive epidemics. In six lakes, we tracked the following factors from pre-epidemic to epidemic emergence: 1) parasite exposure (measured observationally as fungal spores attacking wild-caught hosts), 2)...

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: Little giants: a rapidly invading seagrass alters ecosystem functioning relative to native foundation species

Ranjan Muthukrishnan, Kelcie L. Chiquillo, Candice Cross, Peggy Fong, Thomas Kelley, C. Anna Toline, Regina Zweng & Demian A. Willette
The spread of invasive species is a major component of global ecological change and how and when to manage particular species is a diicult empirical question. Ideally, these decisions should be based on the speciic impacts of invading species including both their efects on native competitors and how they may or may not play similar roles in broader ecosystem functioning. Halophila stipulacea is an invasive seagrass currently spreading through the Caribbean, and as seagrasses are...

Evolution in novel environments: do restored prairie populations experience strong selection?

Susan Magnoli & Jennifer Lau
When populations colonize new habitats, they are likely to experience novel environmental conditions, and as a consequence may experience strong selection. While selection and the resulting evolutionary responses may have important implications for establishment success in colonizing populations, few studies have estimated selection in such scenarios. Here we examined evidence of selection in recently established plant populations in two prairie restorations in close proximity (< 15 km apart) using two approaches: 1) we tested for...

Shedding light on environmentally transmitted parasites: darker conditions within lakes promote larger epidemics

Clara Shaw, Spencer Hall, Erin Overholt, Carla Cáceres, Craig Williamson & Meghan Duffy
Parasite fitness depends on a successful journey from one host to another. For parasites that are transmitted environmentally, abiotic conditions might modulate the success of this journey. Here we evaluate how light, a key abiotic factor, influences spatiotemporal patterns of zooplankton disease where light varies seasonally, across lakes, and with depth in a lake. In an in situ experiment using those three sources of variation, we tested the sensitivity of spores of two parasites to...

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...

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: Early predictors of outcomes of hospitalization for cirrhosis and assessment of the impact of race and ethnicity at safety-net hospitals

, Samuel Akinyeye, Zachary Fricker, Moinuddin Syed, Eric Orman, Lauren Nephew, Eduardo Vilar Gomez, James Slaven, Naga Chalasani, Maya Balakrishnan, Michelle Long, Bashar Attar & Marwan Ghabril
Background. Safety-net hospitals provide care for racially/ethnically diverse and disadvantaged urban populations. Their hospitalized patients with cirrhosis are relatively understudied and may be vulnerable to poor outcomes and racial/ethnic disparities. Aims. To examine the outcomes of patients with cirrhosis hospitalized at regionally diverse safety-net hospitals and the impact of race/ethnicity. Methods. A study of patients with cirrhosis hospitalized at 4 safety-net hospitals in 2012 was conducted. Demographic, clinical factors, and outcomes were compared between centers...

Data from: Patterns of reproductive isolation in Nolana (Chilean Bellflower)

Cathleen Jewell, Amy Douglas Papineau, Rosanna Freyre & Leonie Clare Moyle
We examined reproductive isolating barriers at four postmating stages among 11 species from the morphologically diverse genus Nolana (Solanaceae). At least one stage was positively correlated with both genetic and geographic distance between species. Postzygotic isolation was generally stronger and faster evolving than postmating prezygotic isolation. In addition, there was no evidence for mechanical isolation or for reproductive character displacement in floral traits that can influence pollinator isolation. In general, among the potential isolating stages...

Data from: Mate choice in the eye and ear of the beholder? Female multimodal sensory configuration influences her preferences

Kelly Ronald, Esteban Fernandez-Juricic, Jeffrey Lucas, Jeffrey R. Lucas & Kelly L. Ronald
A common assumption in sexual selection studies is that receivers decode signal information similarly. However, receivers may vary in how they rank signallers if signal perception varies with an individual’s sensory configuration. Furthermore, receivers may vary in their weighting of different elements of multimodal signals based on their sensory configuration. This could lead to complex levels of selection on signalling traits. We tested whether multimodal sensory configuration could affect preferences for multimodal signals. We used...

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...

Data from: Reconciling extremely strong barriers with high levels of gene exchange in annual sunflowers

Julianno Bergoch Monteiro Sambatti, Jared L. Strasburg, Daniel Ortiz-Barrientos, Eric J. Baack & Loren Henry Rieseberg
In several cases, estimates of gene flow between species appears to be higher than predicted given the strength of interspecific barriers. However, as far as we are aware, detailed measurements of reproductive isolation have not previously been compared with a coalescent-based assessment of gene flow. Here, we contrast these two measures in two species of sunflower, Helianthus annuus and Helianthus petiolaris. We quantified the total reproductive barrier strength between these species by compounding the contributions...

Data from: Joint effects of habitat, zooplankton, host stage structure and diversity on amphibian chytrid

Jessica L. Hite, Jaime Bosch, Saioa Fernández-Beaskoetxea, Daniel Medina & Spencer R. Hall
Why does the severity of parasite infection differ dramatically across habitats? This question remains challenging to answer because multiple correlated pathways drive disease. Here, we examined habitat–disease links through direct effects on parasites and indirect effects on parasite predators (zooplankton), host diversity and key life stages of hosts. We used a case study of amphibian hosts and the chytrid fungus, Batrachochytrium dendrobatidis, in a set of permanent and ephemeral alpine ponds. A field experiment showed...

Data from: A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait

Peter C. Zee, Helena Mendes-Soares, Yuen-Tsu Nicco Yu, Susanne A. Kraemer, Heike Keller, Stephan Ossowski, Korbinian Schneeberger & Gregory J. Velicer
While the importance of epistasis in evolution has long been recognized, remarkably little is known about the processes by which epistatic interactions evolve in real time in specific biological systems. Here, we have characterized how the epistatic fitness relationship between a social gene and an adapting genome changes radically over a short evolutionary time frame in the social bacterium Myxococcus xanthus. We show that a highly beneficial effect of this social gene in the ancestral...

Data from: Alternative paths to success in a parasite community: within-host competition can favor higher virulence or direct interference

Farrah Bashey-Visser, Hadas Hawlena & Curtis M. Lively
Selection imposed by coinfection may vary with the mechanism of within-host competition between parasites. Exploitative competition is predicted to favor more virulent parasites, while interference competition may result in lower virulence. Here, we examine whether exploitative or interference competition determines the outcome of competition between two nematode species (Steinernema spp.), which in combination with their bacterial symbionts (Xenorhabdus spp.), infect and kill insect hosts. Multiple isolates of each nematode species, carrying their naturally associated bacteria,...

Data from: The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen

Desiree E. Allen & Michael Lynch
Cyclical parthenogens are a valuable system in which to empirically test theoretical predictions as to the genetic consequences of sexual reproduction in natural populations, particularly if the frequency of sexual relative to asexual reproduction can be quantified. In this study we utilized a series of lake populations of the cyclical parthenogen, Daphnia pulicaria, that vary consistently in their investment in sexual reproduction, to address the questions of whether the ecological variation in investment in sex...

Data from: The roles of compensatory evolution and constraint in aminoacyl tRNA synthetase evolution

Jeffrey R. Adrion, P. Signe White & Kristi L. Montooth
Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their nuclear-encoded counterparts, the cytoplasmic tRNAs (cyt-tRNAs). This dynamic predicts elevated rates of compensatory evolution of mt-aaRS that interact with mt-tRNAs, relative to aaRS that interact with cyt-tRNAs (cyt-aaRS). We find that mt-aaRS do evolve...

Data from: Habitat heterogeneity, host population structure and parasite local adaptation

Curtis M. Lively
Reciprocal-transplant experiments have proven to be a powerful tool for detecting local adaptation (LA). More recently, reciprocal cross-inoculation experiments have been used to evaluate adaptation by parasites to their local host populations. These experiments are conceptually similar to reciprocal-transplant experiments, except that the "environment" (the host population) may have evolved in response to changes in the parasite population. Here, I use analytical tools and computer simulations to determine when parasites would be expected to be...

Data from: Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals

Gregg W. C. Thomas & Matthew W. Hahn
Convergent evolution occurs when the same trait arises independently in multiple lineages. In most cases of phenotypic convergence such transitions are adaptive, so finding the underlying molecular causes of convergence can provide insight into the process of adaptation. Convergent evolution at the genomic level also lends itself to study by comparative methods, though molecular convergence can also occur by chance, adding noise to this process. Parker et al. (2013) studied convergence across the genomes of...

Data from: Global database of matched Plasmodium falciparum and P. vivax incidence and prevalence records from 1985–2013

Katherine E. Battle, Carlos A. Guerra, Nick Golding, Kirsten A. Duda, Ewan Cameron, Rosalind E. Howes, Iqbal R. F. Elyazar, J. Kevin Baird, , Peter W. Gething, David L. Smith & Simon I. Hay
Measures of clinical incidence are necessary to help estimate the burden of a disease. Incidence is a metric not commonly measured in malariology because the longitudinal surveys required are costly and labour intensive. This database is an effort to collate published incidence records obtained using active case detection for Plasmodium falciparum and Plasmodium vivax malaria. The literature search methods, data abstraction procedures and data processing procedures are described here. A total of 1,680 spatio-temporally unique...

Data from: Wide variation in ploidy level and genome size in a New Zealand freshwater snail with coexisting sexual and asexual lineages

Maurine Neiman, Dorota Paczesniak, Deanna M Soper, Austin T Baldwin & Gery Hehman
Natural animal populations are rarely screened for ploidy-level variation at a scale that allows detection of potentially important aberrations of common ploidy patterns. This type of screening can be especially important for the many mixed sexual/asexual systems where sexuals are presumed to be dioecious diploids and asexuals are assumed to be triploid and all-female. For example, elevation of ploidy level above triploidy can be a source of genetic variation and raises the possibility of gene...

Data from: Population genomics of wild and laboratory zebrafish (Danio rerio)

Andrew R Whiteley, Anuradha Bhat, Emilia P Martins, Richard L Mayden, M Arunachalam, Silva Uusi-Heikkilä, A.T.A. Ahmed, Jiwan Shrestha, Matthew Clark, Derek Stemple & Louis Bernatchez
Understanding a wider range of genotype-phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1,832 polymorphic EST-based SNPs and the cytb mitochondrial gene in 13 wild populations and...

Data from: Gene-tree reconciliation with MUL-trees to resolve polyploidy events

Gregg W.C. Thomas, S. Hussain Ather & Matthew W. Hahn
Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids - autopolyploids and allopolyploids - differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together...

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...

Registration Year

  • 2022
  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2012

Resource Types

  • Dataset


  • Indiana University
  • Indiana University Bloomington
  • Stanford University
  • University of Michigan-Ann Arbor
  • University of Georgia
  • University of Minnesota
  • University of Melbourne
  • Indiana State University
  • Texas A&M University
  • Purdue University