87 Works

Data from: The influence of size on body shape diversification across Indo-Pacific shore fishes

Sarah T. Friedman, Christopher M. Martinez, Samantha Ann Price & Peter C. Wainwright
Understanding the causes of body shape variability across the tree of life is one of the central issues surrounding the origins of biodiversity. One potential mechanism driving observed patterns of shape disparity is a strongly conserved relationship between size and shape. Conserved allometry has been shown to account for as much as 80% of shape variation in some vertebrate groups. Here, we quantify the amount of body shape disparity attributable to changes in body size...

Data from: Historical population size change and differentiation of relict populations of the endangered giant kangaroo rat

Mark J. Statham, William T. Bean, Nathan Alexander, Michael F. Westphal & Benjamin N. Sacks
From a conservation management perspective it is important to understand how genetic diversity is partitioned across a species’ range, including (1) identification of evolutionarily distinct units versus those recently isolated through anthropogenic activities and (2) the relative genetic contributions among components of fragmented (meta)populations. To address these questions, we investigated the phylogeography and metapopulation structure among relict populations of the endangered giant kangaroo rat (Dipodomys ingens) in the highly altered San Joaquin Desert Ecosystem. This...

Signatures of Environmental Adaptation During Range Expansion of Wild Common Bean (Phaseolus vulgaris)

Paul Gepts
Landscape genomics integrates population genetics with landscape ecology, allowing the identification of putative molecular determinants involved in environmental adaptation across the natural geographic and ecological range of populations. Wild Phaseolus vulgaris, the progenitor of common bean (P. vulgaris), has a remarkably extended distribution over 10,000 km from northern Mexico to northwestern Argentina. Earlier research has shown that this distribution represents a range expansion from Mesoamerica to the southern Andes through several discrete migration events and...

Data from: Noninvasive sampling reveals short-term genetic rescue in an insular red fox population

Cate B. Quinn, Preston B. Alden & Benjamin N. Sacks
Genetic factors in the decline of small populations are extremely difficult to study in nature. We leveraged a natural experiment to investigate evidence of inbreeding depression and genetic rescue in a remnant population of subalpine-specialized Sierra Nevada red foxes (Vulpes vulpes necator) using noninvasive genetic monitoring during 2010–2017. Only 7 individuals were detected in the first 2 years. These individuals assigned genetically to the historical population and exhibited genetic hallmarks of inbreeding and no evidence...

Bacteria isolated from bengal cat (Felis catus × Prionailurus bengalensis) anal sac secretions produce volatile compounds associated with animal signaling

Mei Yamaguchi, Guillaume Jospin, Holly Ganz, David Coil, Jonathan Eisen, Adrienne Cho, Thant Zaw, Mitchell McCartney & Cristina Davis
Anal sacs are an important odor producing organ found across the mammalian Order Carnivora. Secretions from the anal sac may be used as chemical signals by animals for behaviors ranging from defense to species recognition to signaling reproductive status. In addition, a recent study suggests that domestic cats utilize short-chain free fatty acids in anal sac secretions for individual recognition. The fermentation hypothesis is the idea that symbiotic microorganisms living in association with animals contribute...

Data from: Genetic variation and possible origins of weedy rice found in California

Teresa B. De Leon, Elizabeth Karn, Kassim Al-Khatib, Luis Espino, Timothy Blank, Cynthia B. Andaya, Virgilio C. Andaya & Whitney Brim-DeForest
Control of weeds in cultivated crops is a pivotal component in successful crop production allowing higher yield and higher quality. In rice‐growing regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed related to cultivated rice which infests rice fields. With populations across the globe evolving a suite of phenotypic traits characteristic of weeds and of cultivated rice, varying hypotheses exist on the origin of weedy rice. Here, we investigated the genetic diversity...

Data from: Assessing thermal adaptation using family-based association and FST-outlier tests in a threatened trout

Stephen J. Amish, Omar Ali, Mary Peacock, Michael Miller, Morgan Robinson, Seth Smith, Gordon Luikart & Helen Neville
Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full‐sibling families from...

Data from: Social group signatures in hummingbird displays provide evidence of co-occurrence of vocal and visual learning

Marcelo Araya-Salas, Grace Smith-Vidaurre, Daniel J. Mennill, Paulina L. González-Gómez, James Cahill & Timothy F. Wright
Vocal learning, in which animals modify their vocalizations based on social experience, has evolved in several lineages of mammals and birds, including humans. Despite much attention, the question of how this key cognitive trait has evolved remains unanswered. The motor theory for the origin of vocal learning posits that neural centers specialized for vocal learning arose from adjacent areas in the brain devoted to general motor learning. One prediction of this hypothesis is that visual...

Data from: A Bayesian approach for inferring the impact of a discrete character on rates of continuous-character evolution in the presence of background-rate variation

Michael R May & Brian R Moore
Understanding how and why rates of character evolution vary across the Tree of Life is central to many evolutionary questions; e.g., does the trophic apparatus (a set of continuous characters) evolve at a higher rate in fish lineages that dwell in reef versus non-reef habitats (a discrete character)? Existing approaches for inferring the relationship between a discrete character and rates of continuous-character evolution rely on comparing a null model (in which rates of continuous-character evolution...

Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution

Michael Hardigan, Mitchell Feldmann, Anne Lorant, Kevin Bird, Steven Knapp, Patrick Edger, Glenn Cole, Charlotte Acharya & Randi Famula
Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a...

Data from: Anthropogenic Basin Closure and Groundwater Salinization (ABCSAL)

Richard Pauloo
Global food systems rely on irrigated agriculture, and most of these systems in turn depend on fresh sources of groundwater. In this study, we demonstrate that groundwater development, even without overdraft, can transform a fresh, open basin into an evaporation dominated, closed-basin system, such that most of the groundwater, rather than exiting via stream baseflow and lateral subsurface flow, exits predominantly by evapotranspiration from irrigated lands. In these newly closed hydrologic basins, just as in...

Exploring the role of attitude in the acceptance of self-driving shuttles

YAN XING, Susan Handy, Giovanni Circella, Yunshi Wang & Farzad Alemi
Self-driving vehicles, as a revolution in mobility, are emerging and developing rapidly. However, public attitudes toward this new unproven technology are still uncertain. Given the significant influence of attitude toward a new technology on the intention to use it, the question arises as to why some people are in favor of this technology whereas others are not. Additionally, questions about the key attitudes influencing self-driving technology acceptance, where these attitudes come from, and how they...

Multi-scale landscape genetics of American marten at their southern range periphery

Cody Aylward, James Murdoch & C. William Kilpatrick
American marten (Martes americana) are a conservation priority in many forested regions of North America. Populations are fragmented at the southern edge of their distribution due to suboptimal habitat conditions. Facilitating gene flow may improve population resilience through genetic and demographic rescue. We used a multi-scale approach to estimate the relationship between genetic connectivity and landscape characteristics among individuals at three scales in the northeastern United States: regional, subregional, and local. We integrated multiple modeling...

One-dimensional models of radiation transfer in heterogeneous canopies: a review, re-evaluation, and improved model

Brian Bailey, María Ponce De León & E. Scott Krayenhoff
This dataset contains the project files and data output for the publication: Bailey, Brian; Ponce de León, María; Krayenhoff, E. Scott (2019), One-dimensional models of radiation transfer in heterogeneous canopies: A review, re-evaluation, and improved model. The file main.cpp contains the main program that sets up and runs the simulations. Output files are stored in the 'output' directory. The current version of the Helios source code can be downloaded at https://www.github.com/PlantSimulationLab/Helios

Data from: Evolution of sexually dimorphic pheromone profiles coincides with increased number of male-specific chemosensory organs in Drosophila prolongata

Yige Luo, Yuewei Zhang, Jean-Pierre Farine, Jean-François Ferveur, Santiago Ramírez & Artyom Kopp
Binary communication systems that involve sex-specific signaling and sex-specific signal perception play a key role in sexual selection and in the evolution of sexually dimorphic traits. The driving forces and genetic changes underlying such traits can be investigated in systems where sex-specific signaling and perception have emerged recently and show evidence of potential coevolution. A promising model is found in Drosophila prolongata, which exhibits a species-specific increase in the number of male chemosensory bristles. We...

Adaptive specialization and constraint in morphological defenses of planktonic larvae

Samuel Bashevkin, John Christy & Steven Morgan
Morphological defenses of plankton can include armor, spines, and coloration. Spines defend from gape-limited fish predators while pigmentation increases visibility to fishes but defends from ultraviolet radiation (UVR). Planktonic crab larvae (zoeae) exhibit inter- and intra-specific variability in the lengths of defensive spines, extent of pigmentation, and body size. The determinants of this variability and the relationships among these traits are largely unknown. Larvae may employ generalized defenses against the dual threats of UVR and...

Data from: Interest in nonsocial novel stimuli as a function of age in rhesus monkeys

Eliza Bliss-Moreau & Mark Baxter
Human cognitive and affective life changes with healthy aging; cognitive capacity declines while emotional life becomes more positive and social relationships are prioritized. This may reflect an awareness of limited lifetime unique to humans, leading to a greater interest in maintaining social relationships at the expense of the nonsocial world in the face of limited cognitive and physical resources. Alternately, fundamental biological processes common to other primate species may direct preferential interest in social stimuli...

Measurements from the Fire Influence on Regional and Global Environments Experiment (FIREX) Fire Lab Mini Chamber Experiment

Christopher Cappa, Christopher Lim, David Hagan & Jesse Kroll
All experiments were conducted during the Fire Influence on Regional to Global Environments Experiment (FIREX) lab study, which took place at the Missoula Fire Sciences Lab in Missoula, MT, USA during November, 2016. Experiments focused on refining our understanding of emissions and short timescale processing. The focus was on measuring fuels or combustion conditions that are characteristic of the western U.S. that may be under-sampled by the fire research community. Numerous types of biomass were...

Pharmaceutical Effects of Inhibiting the Soluble Epoxide Hydrolase in Canine Osteoarthritis

Cindy McReynolds, Sung Hee Hwang, Jun Yang, Debin Wan, Karen Wagner, Christophe Morisseau, Dongyang Li, William Schmidt & Bruce Hammock
Osteoarthritis (OA) is a degenerative joint disease that causes pain and bone deterioration driven by an increase in prostaglandins and inflammatory cytokines. Current treatments focus on inhibiting prostaglandin production, a pro-inflammatory lipid metabolite, with NSAID drugs; however, other lipid signaling targets could provide safer and more effective treatment strategies. Epoxides of polyunsaturated fatty acids are anti-inflammatory lipid mediators that are rapidly metabolized by the soluble epoxide hydrolase (sEH) into corresponding vicinal diols. sEH inhibitors (sEHI)...

Data from: Human-induced reductions in fish predator boldness decrease their predation rates on prey in kelp forests

O. Kennedy Rhoades, Steve I. Lonhart & John J. Stachowicz
Humans have restructured food webs and ecosystems by depleting biomass, reducing size structure, and altering traits of consumers. However, few studies have examined the ecological impacts of human-induced trait changes across large spatial and temporal scales and species assemblages. We compared behavioural traits and predation rates by predatory fishes on standard squid prey in protected areas of different protection levels and ages, and found that predation rates were 6.5 times greater at old, no-take (>...

Genomes From Bacteria Associated with the Canine Oral Cavity: a Test Case for Automated Genome-Based Taxonomic Assignment

David Coil, Guillaume Jospin, Jonathan Eisen, Aaron Darling, Collin Wallis, Ian Davis, Stephen Harris, Lucy Holcombe & Ciaran O'Flynn
Taxonomy for bacterial isolates is commonly assigned via sequence analysis. However, the most common sequence-based approaches (e.g. 16S rRNA gene-based phylogeny or whole genome comparisons) are still labor intensive and subjective to varying degrees. Here we present a set of 33 bacterial genomes, isolated from the canine oral cavity. Taxonomy of these isolates was first assigned by PCR amplification of the 16S rRNA gene, Sanger sequencing, and taxonomy assignment using BLAST. After genome sequencing, taxonomy...

Data from: Loss of cytoplasmic incompatibility and minimal fecundity effects explain relatively low Wolbachia frequencies in Drosophila mauritiana

Megan K. Meany, William R. Conner, Sophia V. Richter, Jessica A. Bailey, Michael Turelli & Brandon S. Cooper
Maternally transmitted Wolbachia bacteria infect about half of all insect species. Many Wolbachia cause cytoplasmic incompatibility (CI), reduced egg hatch when uninfected females mate with infected males. Although CI produces a frequency-dependent fitness advantage that leads to high equilibrium Wolbachia frequencies, it does not aid Wolbachia spread from low frequencies. Indeed, the fitness advantages that produce initial Wolbachia spread and maintain non-CI Wolbachia remain elusive. wMau Wolbachia infecting Drosophila mauritiana do not cause CI, despite...

Data from: Species-specific responses to habitat conversion across scales synergistically restructure Neotropical bird communities

Luke O. Frishkoff & Daniel S. Karp
Ecologists are increasingly exploring methods for preserving biodiversity in agricultural landscapes. Yet because species vary in how they respond to habitat conversion, ecological communities in agriculture and more natural habitats are often distinct. Unpacking the heterogeneity in species responses to habitat conversion will be essential for predicting and mitigating community shifts. Here, we analyze two years of bird censuses at 150 sites across gradients of local land cover, landscape forest amount and configuration, and regional...

Data from: Organic functional group and organic matter concentrations from FT-IR measurements of particulate matter samples in the Southeastern Aerosol Research and Characterization (SEARCH) network from 2009-2016

Ann M. Dillner, Alexandra J. Boris, Satoshi Takahama, Andrew T. Weakley, Bruno Debus, Carley D. Frederickson, Martin Esparza-Sanchez, Charlotte Burke, Matteo Reggente, Stephanie L. Shaw & Eric S. Edgerton
This dataset contains organic functional group, organic matter (OM), organic carbon (OC) concentration measurements at five sites in the SEARCH network from 2009-2016. Spectra from each sample are included, in the format used in these papers. The sampling sites are urban Birmingham (BHM) and rural Centreville (CTR) in Alabama, urban Jefferson Street, Atlanta (JST) and rural Yorkville (YRK) in Georgia, and rural Outlying Landing Field (OLF) near Pensacola in Florida as well as a co-located...

Data from: Resource constraints highlight complex microbial interactions during lake biofilm development

Kevin H. Wyatt, Rody C. Seballos, Maria N. Shoemaker, Shawn P. Brown, Sudeep Chandra, Kevin A. Kuehn, Allison R. Rober & Steven Sadro
Abstract 1. This study evaluated how the availability of nutrients and organic carbon interact to influence the associations between autotrophic and heterotrophic microorganisms during lake biofilm development. Considering that decomposers are often better competitors for nutrients than producers in aquatic environments, we hypothesized that heterotrophs would outcompete autotrophs for available nutrients unless heterotrophs were limited by organic carbon provided by autotrophs. 2. To test our hypothesis, we evaluated autotrophic (algae) and heterotrophic (fungi, bacteria) biomass...

Registration Year

  • 2019
    87

Resource Types

  • Dataset
    87

Affiliations

  • University of California, Davis
    87
  • University of Montana
    3
  • University of Nevada Reno
    3
  • University of Washington
    2
  • Stanford University
    2
  • Lund University
    2
  • Fudan University
    2
  • University of Vermont
    2
  • University of California, Berkeley
    2
  • United States Department of Agriculture
    2