63 Works

Museum epigenomics: characterizing cytosine methylation in historic museum specimens

Tricia Rubi, L. Lacey Knowles & Ben Dantzer
Museum genomics has transformed the field of collections-based research, opening up a range of new research directions for paleontological specimens as well as natural history specimens collected over the past few centuries. Recent work demonstrates that it is possible to characterize epigenetic markers such as DNA methylation in well preserved ancient tissues. This approach has not yet been tested in traditionally prepared natural history specimens such as dried bones and skins, the most common specimen...

Great smoky mountain ant community composition

Nathan J. Sanders, Jean-Philippe Lessard & Robert R. Dunn
Disentangling the drivers of diversity gradients can be challenging. The Measurement of Biodiversity (MoB) framework decomposes scale-dependent changes in species diversity into three components of community structure: the species abundance distribution (SAD), the total community abundance, and the within-species spatial aggregation. Here we extend MoB from categorical treatment comparisons to quantify variation along continuous geographic or environmental gradients. Our approach requires sites along a gradient, each consisting of georeferenced plots of abundance-based species composition data....

Longitudinal white-matter abnormalities in sports-related concussion: a diffusion MRI study of the NCAA-DoD CARE Consortium

Yu-Chien Wu, Jaroslaw Harezlak, Nahla Elsaid, Zikai Lin, Qiuting Wen, Sourajit Mustafi, Larry Riggen, Kevin Koch, Andrew Nencka, Timothy Meier, Andrew Mayer, Yang Wang, Christopher Giza, John DiFiori, Kevin Guskiewicz, Jason Mihalik, Stephen LaConte, Stefan Duma, Steven Broglio, Andrew Saykin, Michael McCrea & Thomas McAllister
Objective To study longitudinal recovery trajectories of white-matter after sports-related concussion (SRC), we performed diffusion tensor imaging (DTI) on collegiate athletes who sustained SRC. Methods Collegiate athletes (n=219, 82 concussed athletes, 68 contact-sport controls, and 69 non-contact-sport controls) were included from the Concussion Assessment, Research and Education (CARE) Consortium. The participants completed clinical assessments and DTI at four time points: 24-48-hours post-injury, asymptomatic state, seven days following return-to-play, and six-months post-injury. Tract-based spatial statistics were...

Diversification history of clown tree frogs in Neotropical rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group)

Renata Pirani, Pedro Peloso, Joyce Prado, Érico Polo, Lacey Knowles, Santiago Ron, Miguel Rodrigues, Marcelo Sturaro & Fernanda Werneck
General consensus emphasizes that no single biological process can explain the patterns of species’ distributions and diversification in the Neotropics. Instead, the interplay of several processes across space and time must be taken into account. Here we investigated the phylogenetic relationships and biogeographic history of tree frogs in the Dendropsophus leucophyllatus species group (Amphibia: Hylidae), which is distributed across Amazonia and the Atlantic rainforests. Using Next Generation Sequencing (NGS) and double digest restriction-site associated DNA...

Genomic insights into the origin of trans-Mediterranean disjunct distributions: The case of the saltmarsh band-winged grasshopper (Mioscirtus wagneri)

Víctor Noguerales, Pedro J. Cordero, L. Lacey Knowles & Joaquín Ortego
Aim: Two main biogeographic hypotheses have been proposed to explain the Mediterranean-Turanian disjunct distributions exhibited by numerous steppe-dwelling organisms, namely (i) dispersal during the Messinian salinity crisis (∼5.96-5.33 Ma) followed by range fragmentation and vicariance, and (ii) Pleistocene colonization and recent processes of population subdivision (<2 Ma). Despite the two hypotheses postulate the role of climatic alterations and changes in landmass configuration on determining such disjunct distributions, estimates of the timing of lineage diversification have...

Data from: Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems

Michael H. Cortez & Meghan Duffy
DataS1 These files are Maple and Matlab scripts for analyzing the predator-prey and host-pathogen models in "Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems" and generating the figures in that study.

Data from: Evaluating community effects of a keystone ant, Azteca sericeasur, on Inga micheliana leaf litter decomposition in a shaded coffee agro-ecosystem

Lauren Schmitt & Bolivar Aponte-Rolon
Our research examined the effect of Azteca sericeasur, a keystone arboreal ant, on the decomposition of leaf litter of the shade tree, Inga micheliana, in coffee agro-ecosystems. This interaction is important in understanding the spatial heterogeneity in decomposition. We hypothesized that A. sericeasur could affect leaf litter decomposition by excluding other ants, which could release decomposers, like collembolans, from predation pressure. Determining the relative strengths of these interactions can illuminate the importance of A. sericeasur...

Data from: Social bonds do not mediate the relationship between early adversity and adult glucocorticoids in wild baboons

Stacy Rosenbaum, Shuxi Zeng, Fernando Campos, Laurence Gesquiere, Jeanne Altmann, Susan Alberts, Fan Li & Elizabeth Archie
In humans and other animals, harsh conditions in early life can have profound effects on adult physiology, including the stress response. This relationship may be mediated by a lack of supportive relationships in adulthood. That is, early life adversity may inhibit the formation of supportive social ties, and weak social support is itself often linked to dysregulated stress responses. Here we use prospective, longitudinal data from wild baboons in Kenya to test the links between...

Tree phenology and abiotic variables 1998-2017 at Ngogo, Kibale National Park, Uganda

Kevin Potts, David Watts, Kevin Langergraber & John Mitani
Fruit production in tropical forests varies considerably in space and time, with important implications for frugivorous consumers. Characterizing temporal variation in forest productivity is thus critical for understanding adaptations of tropical forest frugivores, yet long-term phenology data from the tropics, in particular from African forests, are still scarce. Similarly, as the abiotic factors driving phenology in the tropics are predicted to change with a warming climate, studies documenting the relationship between climatic variables and fruit...

Logical inferences from visual and auditory information in ruffed lemurs and sifakas

Francesca De Petrillo & Alexandra Rosati
Inference by exclusion, or the ability to select a correct course of action by systematically excluding other potential alternatives, is a form of logical inference that allow individuals to solve problems without complete information. Current comparative research shows that several bird, mammal, and primate species can find hidden food through inference by exclusion. Yet there is also wide variation in how successful different species are, as well kinds of sensory information they can use to...

Antibiotic interactions shape short-term evolution of resistance in Enterococcus faecalis

Ziah Dean, Jeff Maltas & Kevin Wood
Antibiotic combinations are increasingly used to combat bacterial infections. Multidrug therapies are a particularly important treatment option for E. faecalis, an opportunistic pathogen that contributes to high-inoculum infections such as infective endocarditis. While numerous synergistic drug combinations for E. faecalis have been identified, much less is known about how different combinations impact the rate of resistance evolution. In this work, we use high-throughput laboratory evolution experiments to quantify adaptation in growth rate and drug resistance...

Data from: Co-evolving wing spots and mating displays are genetically separable traits in Drosophila

Jonathan H. Massey & Patricia Wittkopp
The evolution of sexual traits often involves correlated changes in morphology and behavior. For example, in Drosophila, divergent mating displays are often accompanied by divergent pigment patterns. To better understand how such traits co-evolve, we investigated the genetic basis of correlated divergence in wing pigmentation and mating display between the sibling species Drosophila elegans and D. gunungcola. Drosophila elegans males have an area of black pigment on their wings known as a wing spot and...

Redescription of the cranial skeleton of the Early Devonian (Emsian) sarcopterygian Durialepis edentatus Otto, 2007 (Dipnomorpha; Porolepiformes)

Sam Giles, Jorge Mondéjar-Fernández & Matt Friedman
Porolepiforms represent a clade of Devonian stem lungfishes, divided into the cosmine-bearing and likely paraphyletic ‘Porolepidae’ (e.g., Porolepis, Heimenia) and the cosmine-free and stratigraphically younger Holoptychiidae (e.g., Holoptychius, Glyptolepis, Laccognathus). Data on the dermoskeleton are available for both groups, but are more limited for ‘porolepids’. Here we present new information on the ‘porolepid’ Durialepis edentatus from the Emsian (Early Devonian) of Germany based on micro-CT scanning. The material comprises an articulated skull of a single...

Historical biogeography of Vochysiaceae reveals an unexpected perspective of plant evolution in the Neotropics

Deise Josely Pereira Goncalves, Gustavo H. Shimizu, Edgardo M. Ortiz, Robert K. Jansen & Beryl B. Simpson
PREMISE OF THE STUDY: Despite the fast pace of exploration of the patterns and processes influencing Neotropical plant hyperdiversity, taxa explored are mostly from large groups that are widely distributed, morphologically diverse or economically important. Vochysiaceae is an example of an undersampled taxon, providing an excellent system for investigating Neotropical biogeography. We present a phylogenomic-based hypothesis of species relationships in Vochysiaceae to investigate its evolutionary history through space and time. METHODS: We inferred a phylogeny...

Prehistoric baseline reveals substantial decline of oyster reef condition in a Gulf of Mexico conservation priority area

Stephen Hesterberg, Gregory Herbert, Thomas Pluckhahn, Ryan Harke, Nasser Al-Qattan, C. Trevor Duke, Evan Moore, Megan Smith, Alexander Delgado & Christina Sampson
This dataset contains oyster shell height measurements for prehistoric and modern oysters collected near Crystal River, Florida, USA. Oxygen and carbon stable isotope values for large prehistoric and modern oysters are also reported.

Data from: Detecting aquatic invasive species in bait and pond stores with targeted environmental (e) DNA high-throughput sequencing metabarcode assays: angler, retailer, and manager implications

Matt Snyder, Carol Stepien, Nathaniel Marshall, Hannah Scheppler, Christopher Black & Kevin Czajkowski
Bait and pond stores comprise potential, yet poorly understood, vectors for aquatic invasive species (AIS). We tested for AIS and illegal native species in 51 bait and 21 pond stores from the central Great Lakes (Lake Erie, Ohio and Lake St. Clair, Michigan) and the adjacent Wabash River (Indiana) using environmental DNA (eDNA) metabarcode assays of water samples and morphological identifications. Retailers were questioned about supply chains, and anglers surveyed about baitfish use and disposal....

Data from: The evolutionary origins of natural pedagogy: Rhesus monkeys show sustained attention following nonsocial cues versus social communicative signals

Rosemary Bettle & Alexandra Rosati
The natural pedagogy hypothesis proposes that human infants preferentially attend to communicative signals from others, facilitating rapid cultural learning. In this view, sensitivity to such signals are a uniquely human adaptation and as such nonhuman animals should not produce or utilize these communicative signals. We test these evolutionary predictions by examining sensitivity to communicative cues in 206 rhesus monkeys (Macaca mulatta) using an expectancy looking time task modeled on prior work with infants. Monkeys observed...

Spatial variation in diet-microbe associations across populations of a generalist North American carnivore

A. Shawn Colborn, Corbin C. Kuntze, Gabriel I. Gadsden & Nyeema C. Harris
1. Generalist species, by definition, exhibit variation in niche attributes that promote survival in changing environments. Increasingly, phenotypes previously associated with a species, particularly those with wide or expanding ranges, are dissolving and compelling greater emphasis on population-level characteristics. 2. In the present study, we assessed spatial variation in diet characteristics, gut microbiome, and the association between these two ecological traits across populations of coyotes (Canis latrans). We highlight the influence of the carnivore community...

Data from: Large-bodied sabre-toothed anchovies reveal unanticipated ecological diversity in early Palaeogene teleosts

Alessio Capobianco, Hermione Beckett, Etienne Steurbaut, Philip Gingerich, Giorgio Carnevale & Matthew Friedman
Many modern groups of marine fishes first appear in the fossil record during the early Palaeogene (66–40 million years ago), including iconic predatory lineages of spiny-rayed fishes that appear to have originated in response to ecological roles left empty after the Cretaceous/Palaeogene extinction. The hypothesis of extinction-mediated ecological release likewise predicts that other fish groups have adopted novel predatory ecologies. Here we report remarkable trophic innovation in early Palaeogene clupeiforms (herrings and allies), a group...

Data-driven identification of reliable sensor species to predict regime shifts in ecological networks

Amin Ghadami, Shiyang Chen & Bogdan I. Epureanu
Signals of critical slowing down are useful for predicting impending transitions in ecosystems. However, in a system with complex interacting components not all components provide the same quality of information to detect system-wide transitions. Identifying the best indicator species in complex ecosystems is a challenging task when a model of the system is not available. In this paper, we propose a data-driven approach to rank the elements of a spatially-distributed ecosystem based on their reliability...

Elevated atmospheric concentrations of CO2 increase endogenous immune function in a specialist herbivore

Leslie Decker, Chris Jeffrey, Kaitlin Ochsenrider, Abigail Potts, Jaap De Roode, Angela Smilanich & Mark Hunter
1. Animals rely on a balance of endogenous and exogenous sources of immunity to mitigate parasite attack. Understanding how environmental context affects that balance is increasingly urgent under rapid environmental change. In herbivores, immunity is determined, in part, by phytochemistry which is plastic in response to environmental conditions. Monarch butterflies, Danaus plexippus, consistently experience infection by a virulent parasite, Ophryocystis elektroscirrha, and some medicinal milkweed (Asclepias) species, with high concentrations of toxic steroids (cardenolides), provide...

Within-host priority effects and epidemic timing determine outbreak severity in coinfected populations

Patrick Clay, Meghan Duffy & Volker Rudolf
Coinfections of hosts by multiple pathogen species are ubiquitous, but predicting their impact on disease remains challenging. Interactions between coinfecting pathogens within hosts can alter pathogen transmission, with the impact on transmission typically dependent on the relative arrival order of pathogens within hosts (within-host priority effects). However, it is unclear how these within-host priority effects influence multi-pathogen epidemics, particularly when the arrival order of pathogens at the host population scale varies. Here we combined models...

Higher rates of liana regeneration after canopy fall drives species abundance patterns in central Amazonia

Elisangela Rocha, Juliana Schietti, Caian Gerolamo, Robyn Burnham & Anselmo Nogueira
In tropical rainforest, most vascular plants have some capacity to resprout, and lianas are often effective resprouters after canopy fall. However, the diversity of resprouting responses of liana species and the consequence for plant persistence is poorly understood. We hypothesized that variation in regeneration among liana species causes differences in liana species abundance in tropical rainforest through differential resprouting capacity, such that liana species with higher densities produce more resprouts after canopy falls. We applied...

Risk factors for cardiovascular disease (CVD) in adults with type 1 diabetes: findings from prospective real-life T1D exchange registry

Nicole Foster, Viral N Shah, Ryan Bailey, Mengdi Wu, Rodica Pop-Busui, Michelle Katz, Jill Crandall, Fida Bacha, Kristen Nadeau, Ingrid Libman, Paul Hiers, Kara Mizokami-Stout, Linda A DiMeglio, Jennifer Sherr, Richard Pratley, Shivani Agarwal, Janet Snell-Bergeon, Eda Cengiz, Sarit Polsky & Sanjeev N Mehta
Context Cardiovascular disease (CVD) is a major cause of mortality in adults with type 1 diabetes. Objective We prospectively evaluated CVD risk factors in a large, contemporary cohort of adults with type 1 diabetes living in the United States. Design Observational study of CVD and CVD risk factors over a median of 5.3 years. Setting The T1D Exchange clinic network. Patients Adults (age ≥18 years) with type 1 diabetes and without known CVD diagnosed before...

Data from: The soil microbial community alters patterns of selection on flowering time and fitness related traits in Ipomoea purpurea

Lindsay Chaney & Regina S. Baucom
Premise of the study Plant flowering time plays an important role in plant fitness and thus evolutionary processes. Soil microbial communities are diverse and have a large impact, both positive and negative, on the host plant. However, owing to few available studies, how the soil microbial community may influence the evolutionary response of plant populations is not well understood. Here we sought to uncover if below-ground microbial communities act as an agent of selection on...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of Michigan-Ann Arbor
  • University of Michigan–Ann Arbor
  • University of Nevada Reno
  • University of Minnesota
  • University of Sao Paulo
  • Emory University
  • California Polytechnic State University
  • Estación Biológica de Doñana
  • Stanford University
  • University of Saskatchewan