189 Works

Disentangling lousy relationships: Comparative phylogenomics of two sucking louse lineages parasitizing chipmunks

Kayce Bell, Julie M. Allen, Kevin P. Johnson, John R. Demboski & Joseph A. Cook
The evolution of obligate parasites is often interpreted in light of their hosts’ evolutionary history. An expanded approach is to examine the histories of multiple lineages of parasites that inhabit similar environments on a particular host lineage. Western North American chipmunks (genus Tamias) have a broad distribution, a history of divergence with gene flow, and host two species of sucking lice (Anoplura), Hoplopleura arboricola and Neohaematopinus pacificus. From total genomic sequencing, we obtained sequences of...

Artificial nightlight alters the predator-prey dynamics of an apex carnivore

Mark Ditmer, David Stoner, Clinton D. Francis, Jesse Barber, James Forester, David Choate, Kirsten Ironside, Kathleen Longshore, Kent Hersey, Randy Larsen, Brock McMillan, Daniel Olson, Alyson Andreasen, Jon Beckmann, Brandon Holton, Terry Messmer & Neil Carter
Artificial nightlight is increasingly recognized as an important environmental disturbance that influences the habitats and fitness of numerous species. However, its effects on wide-ranging vertebrates and their interactions remain unclear. Light pollution has the potential to amplify land-use change, and as such, answering the question of how this sensory stimulant affects behavior and habitat use of species valued for their ecological roles and economic impacts is critical for conservation and land-use planning. Here, we combined...

Audio recordings of Atelpus varius calls from Panama

Justin Kitzes, Samuel Lapp, Corinne Richards-Zawacki, Jamie Voyles, Keely Michelle Rodriguez & Tianhao Wu
Anurans (frogs and toads) are among the most globally threatened taxonomic groups. Successful conservation of anurans will rely on improved data on the status and changes in local populations, particularly for rare and threatened species. Automated sensors, such as acoustic recorders, have the potential to provide such data by massively increasing the spatial and temporal scale of population sampling efforts. We used AudioMoth autonomous recorders to survey for the critically endangered Harlequin toad (Atelopus varius)...

Stress in paradise: effects of elevated corticosterone on immunity and avian malaria resilience in a Hawaiian passerine

Gabrielle Names, Elizabeth Schultz, Jesse Krause, Thomas Hahn, John Wingfield, Molly Heal, Jamie Cornelius, Kirk Klasing & Kathleen Hunt
Vertebrates confronted with challenging environments often experience an increase in circulating glucocorticoids, which result in morphological, physiological, and behavioral changes that promote survival. However, chronically elevated glucocorticoids can suppress immunity, which may increase susceptibility to disease. Since the introduction of avian malaria to Hawaii a century ago, low elevation populations of Hawaii Amakihi (Chlorodrepanis virens) have undergone strong selection by avian malaria and evolved increased resilience (the ability to recover from infection), while populations at...

Data from: Passeridae and Cyanocitta stelleri teleport to my deck from other areas

Aaron Goetz
In neither the teleporting or the lab are they actually migrating. Yet, in the lab, they do it anyway, and the way their species does it, without having done it before. Passeridae and Cyanocitta stelleri teleport to my deck from other areas adds to the genetic difference hypothesis by saying migrating doesn’t matter, just that they have the genetic (and maybe neural) structure needed for migration, and is used for teleporting.

A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?

Lars Jermiin, John Robinson, Victor Vera-Ruiz, Victor A Vera-Ruiz & Lars S Jermiin
Abstract In molecular phylogenetics, it is typically assumed that the evolutionary process for DNA can be approximated by independent and identically distributed Markovian processes at the variable sites and that these processes diverge over the edges of a rooted bifurcating tree. Sometimes the nucleotides are transformed from a 4-state alphabet to a 3- or 2-state alphabet by a procedure that is called recoding, lumping, or grouping of states. Here, we introduce a likelihood-ratio test for...

Data from: Sea level, topography, and island diversity: phylogeography of the Puerto Rican Red-eyed Coquí, Eleutherodactylus antillensis

Brittany S. Barker, Javier A. Rodríguez-Robles, Vani S. Aran, Ashley Montoya, Robert B. Waide & Joseph A. Cook
Quaternary climatic oscillations caused changes in sea level that altered the size, number, and degree of isolation of islands, particularly in land-bridge archipelagoes. Elucidating the demographic effects of these oscillations increases our understanding of the role of climate change in shaping evolutionary processes in archipelagoes. The Puerto Rican Bank (Puerto Rico and the Eastern Islands, which comprise Vieques, Culebra, the Virgin Islands, and associated islets) in the eastern Caribbean Sea periodically coalesced during glaciations and...

Data from: Host conservatism, geography, and elevation in the evolution of a Neotropical moth radiation

Joshua P. Jahner, Matthew L. Forister, Thomas L. Parchman, Angela M. Smilanich, James S. Miller, Joseph S. Wilson, Thomas R. Walla, Eric J. Tepe, Lora A. Richards, Mario A. Quijano-Abril, Andrea E. Glassmire & Lee A. Dyer
The origins of evolutionary radiations are often traced to the colonization of novel adaptive zones, including unoccupied habitats or unutilized resources. For herbivorous insects, the predominant mechanism of diversification is typically assumed to be a shift onto a novel lineage of host plants. However, other drivers of diversification are important in shaping evolutionary history, especially for groups residing in regions with complex geological histories. We evaluated the contributions of shifts in host plant clade, bioregion,...

Data from: Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid

Subhash Rajpurohit, Cassia C. Oliveira, William J. Etges & Allen G. Gibbs
We used whole transcriptome microarrays to assess changes in gene expression and monitored mortality rates and epicuticular hydrocarbons (CHCs) in response to desiccation stress in four natural populations of Drosophila mojavensis from Baja California and mainland Mexico. Desiccation had the greatest effect on gene expression, followed by biogeographical variation at regional and population levels. Genes involved in environmental sensing and cuticular structure were up-regulated in dry conditions, while genes involved in transcription itself were down-regulated....

Data from: Highly variable reproductive isolation among pairs of Catostomus species

Elizabeth G. Mandeville, Thomas L. Parchman, David B. McDonald & C. Alex Buerkle
Hybridization between diverged taxa tests the strength of reproductive isolation and can therefore reveal mechanisms of reproductive isolation. However, it remains unclear how consistent reproductive isolation is across species' ranges and to what extent reproductive isolation might remain polymorphic as species diverge. To address these questions, we compared outcomes of hybridization across species pairs of Catostomus fishes in three rivers in the Upper Colorado River basin, where an introduced species, C. commersoni, hybridizes with at...

Data from: A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

Patrick R. Lemons, Tristan C. Marshall, Sarah E. McCloskey, Suresh A. Sethi, Joel A. Schmutz & Jim S. Sedinger
Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artefacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated...

Data from: A pollen fatty acid enhances learning and survival in bumblebees

Felicity Muth, Phillip R. Breslow, Pavel Masek & Anne S. Leonard
Learning associations between food-related stimuli and nutrients allows foragers to collect resources efficiently. In turn, the nutrients foragers consume can themselves affect learning performance, through innate preferences for pre-ingestive stimuli, as well as post-ingestive reinforcement. Bees are insect models of learning and memory, yet the vast majority of this research concerns nectar (carbohydrate) rather than pollen (protein/lipid) rewards, despite the fact that many bees collect both simultaneously. We asked how one component of pollen surface...

Data from: Genomic evidence of genetic variation with pleiotropic effects on caterpillar fitness and plant traits in a model legume

Zachariah Gompert, Megan Brady, Farzaneh Chalyavi, Tara C. Saley, Casey S. Philbin, Matthew J. Tucker, Matthew L. Forister & Lauren K. Lucas
Plant-insect interactions are ubiquitous, and have been studied intensely because of their relevance to damage and pollination in agricultural plants, and to the ecology and evolution of biodiversity. Variation within species can affect the outcome of these interactions. Specific genes and chemicals that mediate these interactions have been identified, but studies of genome- or metabolome-wide intraspecific variation might be necessary to better explain patterns of host-plant use and adaptation in the wild. Here, we present...

Data from: Synthesizing the effects of large, wild herbivore exclusion on ecosystem function

Elizabeth S. Forbes, J. Hall Cushman, Deron E. Burkepile, Truman P. Young, Maggie Klope & Hillary S. Young
1. Wild large herbivores are declining worldwide. Despite extensive use of exclosure experiments to investigate herbivore impacts, there is little consensus on the effects of wild large herbivores on ecosystem function. 2. Of the ecosystem functions likely impacted, we reviewed the five most-studied in exclosure experiments: ecosystem resilience/resistance to disturbance, nutrient cycling, carbon cycling, plant regeneration, and primary productivity. 3. Experimental data on large wild herbivores’ effects on ecosystem functions were predominately derived from temperate...

Data from: Impacts of inference method and dataset filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini)

Bryan S. McLean, Kayce C. Bell, Julia M. Allen, Kristofer M. Helgen, Joseph A. Cook & Julie M Allen
Phylogenomic datasets are illuminating many areas of the Tree of Life. However, the large size of these datasets alone may be insufficient to resolve problematic nodes in the most rapid evolutionary radiations, because inferences in zones of extraordinarily low phylogenetic signal can be sensitive to the model and method of inference, as well as the information content of loci employed. We used a dataset of >3,950 ultraconserved element (UCE) loci from a classic mammalian radiation,...

Data from: Leaf-cutter ants engineer large nitrous oxide hot spots in tropical forests

Fiona M. Soper, Benjamin W. Sullivan, Brooke B. Osborne, Alanna N. Shaw, Laurent Philippot & Cory C. Cleveland
Though tropical forest ecosystems are among the largest natural sources of the potent greenhouse gas nitrous oxide (N2O), the spatial distribution of emissions across landscapes is often poorly resolved. Leaf-cutter ants (LCA, Atta and Acromyrmex, Myrmicinae) are dominant herbivores throughout Central and South America and influence multiple aspects of forest structure and function. In particular, their foraging creates spatial heterogeneity by concentrating large quantities of organic matter (including nitrogen, N) from the surrounding canopy into...

Data from: Specificity, rank preference and the colonization of a non-native host plant by the Melissa blue butterfly

Matthew L. Forister, Cynthia F. Scholl, Josh P. Jahner, Joseph S. Wilson, James A. Fordyce, Zach Gompert, Divya R. Narala, C. Alex Buerkle & Chris C. Nice
Animals often express behavioral preferences for different types of food or other resources, and these preferences can evolve or shift following association with novel food types. Shifts in preference can involve at least two phenomena: a change in rank preference or a change in specificity. The former corresponds to a change in the order in which hosts are preferred, while a shift in specificity can be an increase in the tendency to utilize multiple hosts....

Data from: Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars

Andrea E. Glassmire, Christopher S. Jeffrey, Matthew L. Forister, Thomas L. Parchman, Chris C. Nice, Joshua P. Jahner, Joseph S. Wilson, Thomas R. Walla, Lora A. Richards, Angela M. Smilanich, Michael D. Leonard, Colin R. Morrison, Wilmer Simbaña, Luis A. Salagaje, Craig D. Dodson, Jim S. Miller, Eric J. Tepe, Santiago Villamarin-Cortez & Lee A. Dyer
Chemically mediated plant–herbivore interactions contribute to the diversity of terrestrial communities and the diversification of plants and insects. While our understanding of the processes affecting community structure and evolutionary diversification has grown, few studies have investigated how trait variation shapes genetic and species diversity simultaneously in a tropical ecosystem. We investigated secondary metabolite variation among subpopulations of a single plant species, Piper kelleyi (Piperaceae), using high-performance liquid chromatography (HPLC), to understand associations between plant phytochemistry...

Data from: Woodland resilience to regional drought: Dominant controls on tree regeneration following overstorey mortality

Miranda D. Redmond, Peter J. Weisberg, Neil S. Cobb & Michael J. Clifford
Drought events occurring under warmer temperatures (i.e. “hotter droughts”) have resulted in widespread tree mortality across the globe, and may result in biome-level vegetation shifts to alternate vegetation types if there is a failure of trees to regenerate. We investigated how overstorey trees, understorey vegetation, and local climatic and edaphic conditions interact to influence tree regeneration, a key prerequisite for resilience, in a region that has experienced severe overstorey tree mortality due to hotter droughts...

Data from: Chronotype variation drives night-time sentinel-like behaviour in hunter–gatherers

David Samson, Alyssa Crittenden, Ibrahim Mabulla, Audax Mabulla, Charles Nunn, Charles L. Nunn, David R. Samson, Audax Z. P. Mabulla, Ibrahim A. Mabulla & Alyssa N. Crittenden
Sleep is essential for survival, yet it also represents a time of extreme vulnerability to predation, hostile conspecifics, and environmental dangers. To reduce the risks of sleeping, the sentinel hypothesis proposes that group-living animals share the task of vigilance during sleep, with some individuals sleeping while others are awake. To investigate sentinel-like behaviour in sleeping humans, we investigated activity patterns at night among Hadza hunter-gatherers of Tanzania. Using actigraphy, we discovered that all subjects were...

Hydrology, geochemistry, and microbiology data from meter-scale infiltration experiments exploring the impact of a woodchip soil amendment on nitrate removal during infiltration

Sarah Beganskas, Galen Gorski, Tess Weathers, Andrew Fisher, Calla Schmidt, Chad Saltikov, Kaitlyn Redford, Brendon Stoneburner, Ryan Harmon & Walker Weir
We present results from field experiments linking hydrology, geochemistry, and microbiology during infiltration at a field site that is used for managed aquifer recharge (MAR). These experiments measured how a horizontal permeable reactive barrier (PRB) made of woodchips impacted subsurface nitrate removal and microbial ecology. Concentrations of dissolved organic carbon consistently increased in infiltrating water below the PRB, but not in un-amended native soil. The average nitrate removal rate in soils below the PRB was...

The geographic distribution of rodent granivory and cheek pouches across North America

Jacob Dittel & Stephen Vander Wall
Seeds are an important food resource for many rodents. One of the specializations that many granivorous rodents exhibit to increase their efficiency in harvesting seeds is cheek pouches. However, many rodent species lack cheek pouches. We propose that the presence or absence of cheek pouches is related to seed size and the productivity of the habitat where those rodents reside. Location North America – United States and Canada. Taxon Granivorous rodents. We divided granivorous rodents...

Data from: Piping Plover population increase after Hurricane Sandy mediated by immigration and reproductive output

Samantha Robinson, Daniel Gibson, Thomas Riecke, James Fraser, Henrietta Bellman, Audrey DeRose-Wilson, Sarah Karpanty & Katie Walker
Evaluating population-level responses to conservation action following large-scale disturbance can improve the efficacy of future habitat conservation measures. In October 2012, Hurricane Sandy storm surges cleared vegetation and opened inlets through the barrier islands, Fire Island and Westhampton Island, New York, creating Piping Plover (Charadrius melodus) habitat. Storm effects prompted an island-wide stabilization project, which had the potential to negatively affect novel Piping Plover habitat. Certain sections of Fire Island were designed to create and/or...

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...

Data from: Evidence of widespread topoclimatic limitation for lower treelines of the Intermountain West, U.S.A.

Alexandra Urza, Peter Weisberg & Thomas Dilts
Many forests in dry mountain regions are characterized by a lower elevational treeline. Understanding the controls on the position of lower treeline is important for predicting future forest distributional shifts in response to global environmental change. Lower treelines currently at their climate limit are expected to be more sensitive to changing climate, whereas lower treelines constrained by non-climatic factors are less likely to respond directly to climate change but may be sensitive to other global...

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