105 Works

Data from: Zooming in on mechanistic predator-prey ecology: integrating camera traps with experimental methods to reveal the drivers of ecological interactions

Justine Smith, Justin Suraci, Jennifer Hunter, Kaitlyn Gaynor, Carson Keller, Meredith Palmer, Justine Atkins, Irene Castañeda, Michael Cherry, Patrick Garvey, Sarah Huebner, Dana Morin, Lisa Teckentrup, Martijn Weterings & Lydia Beaudrot
1. Camera trap technology has galvanized the study of predator-prey ecology in wild animal communities by expanding the scale and diversity of predator-prey interactions that can be analyzed. While observational data from systematic camera arrays have informed inferences on the spatiotemporal outcomes of predator-prey interactions, the capacity for observational studies to identify mechanistic drivers of species interactions is limited. 2. Experimental study designs that utilize camera traps uniquely allow for testing hypothesized mechanisms that drive...

Data from: Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships

Matthew Campbell, Thaddaeus Buser, Michael Alfaro & J. Andres Lopez
Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or of an evolutionary history that did not generate the signal traits needed for its eventual reconstruction. Relationships within the euteleost fish family Salmonidae have proven...

NCST Caltrans project on sensor data error estimation

Yueyue Fan & Saurabh Maheshwari
The aim of this script is to automate the process of directed network graph formation, i.e., creation of incidence matrix, node adjacency matrix, and map the sensors to appropriate links. The data used for creating the freeway network is obtained from open street maps, whereas, the data for sensors is obtained from PeMS. The results of the algorithm will later be fed to the network sensor error estimation algorithm, that quantifies the erroneous sensors using...

Data from: Body shape diversification along the benthic-pelagic axis in marine fishes

Sarah Friedman, Samantha Price, Katherine Corn, Olivier Larouche, Christopher Martinez & Peter Wainwright
Colonization of novel habitats can result in marked phenotypic responses to the new environment that include changes in body shape and opportunities for further morphological diversification. Fishes have repeatedly transitioned along the benthic-pelagic axis, with varying degrees of association with the substrate. Previous work focusing on individual lineages shows that these transitions are accompanied by highly predictable changes in body form. Here, we generalize expectations drawn from this literature to study the effects of habitat...

Effects of low-carbon energy adoption on airborne particulate matter concentrations with feedbacks to future climate over California

Anikender Kumar, Christina Zapata, Sonia Yeh, Chris Yang, Joan Ogden, Hsiang-He Lee, ShuHua Chen & Michael Kleeman
California plans to reduce emissions of long-lived greenhouse gases (GHGs) through adoption of new energy systems that will also lower concentrations of short-lived absorbing soot contained in airborne particulate matter (PM). Here we examine the direct and indirect effects of reduced PM concentrationsunder a low-carbon energy (GHG-Step) scenario on radiative forcing in California. Simulations were carried out using the source-oriented WRF/Chem (SOWC) model over California with 12 km spatial resolutionfor the year 2054. The avoided...

Wildfire alters the disturbance impacts of an emerging infectious disease via changes to host occurrence and demographic structure

Allison Simler-Williamson, Margaret Metz, Kerri Frangioso & David Rizzo
1. Anthropogenic activities have altered historical disturbance regimes, and understanding the mechanisms by which these shifting perturbations interact is essential to predicting where they may erode ecosystem resilience. Emerging infectious plant diseases, caused by human translocation of nonnative pathogens, can generate ecologically-damaging forms of novel biotic disturbance. Further, abiotic disturbances, such as wildfire, may influence the severity and extent of disease-related perturbations via their effects on the occurrence of hosts, pathogens, and microclimates; however, these...

Early maternal separation is not associated with changes in telomere length in domestic kittens (Felis catus)

Mikel Delgado, C.A.T. Tony Buffington, Melissa Bain & Karen Vernau
Objective The objective of this study was to determine if premature separation from the mother affected telomere length in domestic kittens (Felis catus) at one and eight weeks of life. Subjects were 42 orphaned kittens and 10 mother-reared kittens from local animal rescue groups and shelters. Blood (200 µl) was collected from kittens at 1 and 8 weeks of age via jugular venipuncture. Telomere length was assessed by qPCR (quantitative polymerase chain reaction) from 86...

Equate SENAS and IVD cognitive measure: Summary of methods and results

Dan Mungas, Ji Won Han, Pauline Maillard, Danielle Harvey, Evan Fletcher, Oliver Martinez, David Johnson, John Olichney, Sarah Farias, Sylvia Villeneuve, William Jagust & Charles DeCarli
Conceptually similar measures of episodic memory and executive function have been derived from different tests that compose the SENAS (Spanish and English Neuropsychological Assessment Scale) and IVD-PPG (ischemic vascular contributions to cognitive decline and dementia) neuropsychological test batteries. The purpose of this project was to create equated episodic memory and executive scores from these two batteries that are on the same measurement metric and can be combined in analyses using data from both projects. This...

Interpreting morphological adaptations associated with viviparity in the Tsetse fly (Glossina morsitans) by three-dimensional analysis

Geoffrey Attardo
Tsetse flies (genus Glossina), the sole vectors of African trypanosomiasis, are distinct from other disease vectors, and most other insects, due to dramatic evolutionary adaptations required to support their unique life history. These morphological and physiological adaptations are driven by demands associated with their strict dietary and reproductive requirements. Tsetse reproduce by obligate viviparity which entails obligate intrauterine larval development and provisioning of nutrients for the developing larvae. Viviparous reproduction reduces reproductive capacity/rate which also...

Implications of genetic heterogeneity for plant translocation during ecological restoration

Taylor Crow
Ecological restoration often requires translocating plant material from distant sites. Importing suitable plant material is important for successful establishment and persistence. Yet published guidelines for seed transfer are available for very few species. Accurately predicting how transferred plants will perform requires multi-year and multi-environment field trials and comprehensive follow-up work, and is therefore infeasible given the number of species used in restoration programs. Alternative methods to predict the outcomes of seed transfer are valuable for...

Unraveling the complex hybrid ancestry and domestication history of cultivated strawberry

Michael Hardigan, Anne Lorant, Dominique Pincot, Mitchell Feldmann, Randi Famula, Charlotte Acharya, Seonghee Lee, Sujeet Verma, Vance Whitaker, Nahla Bassil, Jason Zurn, Glenn Cole, Kevin Bird, Patrick Edger & Steven Knapp
Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (F. chiloensis and F. virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease...

Insect diversity over 36 years at a protected Sierra Nevada (California) site

Jay Rosenheim & Philip Ward
Recent authors have suggested that declines of insect abundance or diversity, documented first for particular insect taxa of high interest (e.g., butterflies, bees), may apply to insect diversity more generally. This has led to an urgent call for analysis of additional longitudinal datasets to examine trends in general insect diversity. Here we present a dataset gathered from 1982-2018 by advanced undergraduate students and graduate students enrolled in a taxonomy course that involved collecting as many...

Transportation Network Company (TNC) taxes/fees by state/city in the United States

Sam Fuller & Austin Brown
Cities and states across the U.S. are assessing fees or taxes on transportation network company (TNC) platforms, such as Uber and Lyft. The goals of these policies include traffic and emissions mitigation, as well as revenue generation, among other objectives. Our research aims to assess the goals and effectiveness of these fees in achieving some of these policy objectives, primarily congestion and emissions mitigation. The analysis addresses a core difficulty in comparing TNC fees—some fees...

Predator group composition indirectly influences food web dynamics through predator growth rates

Kate Laskowski, Marta Alirangues Nunez, Sabine Hilt, Mark Gessner & Thomas Mehner
Considerable theoretical work predicts that intraspecific trait variation can have profound ecological consequences by altering species interactions. Because of their high flexibility, behavioral traits may be especially relevant in mediating how species respond to one another, thus affecting food web dynamics and ecosystem functioning. However, empirical evidence supporting this idea is limited. Here we generated predator groups where we manipulated the composition of behavioral types within the groups to assess effects on predator growth rates,...

Landscape simplification increases vineyard pest outbreaks and insecticide use

Daniel Paredes, Jay Rosenheim, Rebecca Chaplin-Kramer, Silvia Winter & Daniel Karp
Diversifying agricultural landscapes may mitigate biodiversity declines and improve pest management. Yet landscapes are rarely managed to suppress pests, in part because researchers seldom measure key variables related to pest outbreaks and insecticides that drive management decisions. We used a 13-year government database to analyze landscape effects on European grapevine moth (Lobesia botrana) outbreaks and insecticides across ~400 Spanish vineyards. At harvest, we found pest outbreaks increased four-fold in simplified, vineyard-dominated landscapes compared to complex...

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Anneliek Ter Horst, Christian Santos-Medellín, Jackson Sorensen, Laura Zinke, Rachel Wilson, Eric Johnston, Gareth Trubl, Jennifer Pett-Ridge, Steven Blazewicz, Paul Hanson, Jeffrey Chanton, Christopher Schadt, Joel Kostka & Joanne Emerson
Background: Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in thawing permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland...

Dataset for the transcriptome analysis of hippocampal subfields identifies gene expression profiles associated with long-term active place avoidance memory

Rayna Harris, Hsin-Yi Kao, Juan Marcos Alarcon, André Fenton & Hans Hofmann
The hippocampus plays a critical role in storing and retrieving spatial information. By targeting the dorsal hippocampus and manipulating specific “candidate” molecules using pharmacological and genetic manipulations, we have previously discovered that long-term active place avoidance memory requires transient activation of particular molecules in dorsal hippocampus. These molecules include amongst others, the persistent kinases Ca-calmodulin kinase II (CaMKII) and the atypical protein kinase C isoform PKC iota/lambda for acquisition of the conditioned behavior, whereas persistent...

Data from: Shifts in species interactions and farming contexts mediate net effects of birds in agroecosystems

Elissa Olimpi, Karina Garcia, Daniel Karp & David Gonthier
Some birds are viewed as pests and vectors of foodborne pathogens in farmlands, yet birds also benefit growers by consuming pests. While many growers seek to prevent birds from accessing their farms, few studies have attempted to quantify the net effects of bird services and disservices, let alone how net effects shift across farm management strategies. We quantified the net effect of birds on crop production across 20 California strawberry (Fragaria x ananassa) farms that...

Colour dimorphism in labrid fishes as an adaptation to life on coral reefs

Jennifer Hodge, Francesco Santini & Peter Wainwright
Conspicuous colouration displayed by animals that express sexual colour dimorphism is generally explained as an adaptation to sexual selection, yet the interactions and relative effects of selective forces influencing colour dimorphism are largely unknown. Qualitatively, colour dimorphism appears more pronounced in marine fishes that live on coral reefs where traits associated with strong sexual selection are purportedly more common. Using phylogenetic comparative analysis, we show that wrasses and parrotfishes exclusive to coral reefs are the...

Belize terrestrial mammal database from: An integrated approach to measure hunting intensity and assess its impacts on mammal populations

Michael Dobbins
1. Unsustainable hunting of wildlife is one of the greatest threats to diverse and healthy forests, yet our understanding of hunting activity is limited by our methods of accurately identifying its intensity and distribution. Several methods have been used to quantify hunting in past studies (e.g. interviews, ranger patrols, and camera traps). However, none of these alone have been able to produce precise spatiotemporal measures of hunting activity. 2. In this study, we used a...

Digitized pear and peach trees with fruits

Stavros Vougioukas & Rajkishan Arikapudi
The dataset contains files with sets of point coordinates derived via manual digitization of entire trees and all fruits on them. Twenty Bartlett pear and twenty cling-peach trees were digitized. Digitization was restricted to rigid, thick branches (> 2.5 cm) that present obstacles to machinery interacting with trees; robotic harvesting simulation and design were the targeted applications. Each branch segment that had small enough curvature was considered linear and was approximated by a conical frustum....

Greenhouse gas reduction opportunities for local governments: a quantification and prioritization framework

Alissa Kendall, John T. Harvey, Ali A. Butt, Mark T. Lozano, Arash Saboori & Changmo Kim
The goal of this research was to present a decision-making framework for greenhouse gas (GHG) mitigation strategy selection for local governments based on the development of life cycle GHG mitigation “supply curves”. This approach offers the ability to combine the impacts and cost-effectiveness measurements of numerous GHG mitigation options at the same time. Life cycle GHG emissions accounting considers emissions generated throughout the supply chain of a product or process, and also typically considers system-wide...

Data from: Cooling cows efficiently with sprinklers: physiological responses to water spray

Cassandra B. Tucker, Karin E. Schütz &
Dairies in the United States commonly cool cattle with sprinklers mounted over the feed bunk that intermittently spray the cows’ backs. These systems use potable water—an increasingly scarce resource—but there is little experimental evidence about how much is needed to cool cows or about droplet size, which is thought to affect hair coat penetration. Our objectives were to determine how sprinkler flow rate and droplet size affect physiological measures of heat load in a hot,...

Data from: Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex

Lacie Newton, James Starrett, Brent Hendrixson, Shahan Derkarabetian & Jason Bond
Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth’s quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, Antrodiaetus unicolor species complex which contains two sympatric species, exhibits this pattern of relative morphological stasis...

Data from: Gene flow in the anemone Anthopleura elegantissima limits signatures of local adaptation across an extensive geographic range

Brendan Cornwell
Species inhabiting marine environments face a wide range of environmental conditions that vary spatially across several orders of magnitude. The selective pressures that these conditions impose on marine organisms, in combination with potentially high rates of gene flow between distant populations, make it difficult to predict the extent to which these populations can locally adapt. Here, I identify how selection and gene flow influence the population genetic structure of the anemone Anthopleura elegantissima along the...

Registration Year

  • 2020

Resource Types

  • Dataset
  • Text
  • Software


  • University of California, Davis
  • University of California, Berkeley
  • United States Geological Survey
  • University of Minnesota
  • United States Department of Agriculture
  • University of Florida
  • University of California, Santa Cruz
  • Cornell University
  • SUNY Downstate Medical Center
  • California State University, Northridge