280 Works

Shrubland vegetation topographic facets of Southern California

Allan Hollander & Emma Underwood
To approximate the distribution of shrubland species based on their postfire reproductive strategy (resprouter, seeder, and facultative seeder) across Southern California, we created a raster layer subdividing the landscape into a number of different facet classes. This raster dataset is at 30 meters pixel resolution and contains 12 different landscape facet classes based on vegetation and physiography. Specifically, the facets included several different vegetation types based on the California Wildlife Habitat Relations (WHR) classification (three...

Drosophila enhancer adult bristle expression assay using UAS sv-RNAi

David Luecke
Data from manuscript "Sex-specific evolution of a Drosophila sensory system via interacting cis- and trans-regulatory changes" by D Luecke, G Rice, and A Kopp. This study examines the regulation of expression for the chemosensory bristle specifier gene Pox neuro, which has expanded expression into ancestrally mechanosensory bristles in male D. prolongata. Flourescent assays show qualitativetly expanded expression driven by the D. prolongata allele relative to enhancers from sister species in the developing pupal leg. Adult...

Phylogeny, Evolution, and Biogeography of the North American Trapdoor Spider family Euctenizidae (Araneae: Mygalomorphae) and the discovery of a new ‘Endangered Living Fossil’ along California’s Central Coast

Jason E. Bond, Chris A. Hamilton, Rebecca L. Godwin, Joel M. Ledford & James. Starrett
We report here the discovery of a remarkable new monotypic mygalomorph spider genus, known only from one geographical location along the central coast of California. The single relict species comprising Cryptocteniza kawtakn. gen. n. sp., is morphologically distinct and geographically isolated from other related genera, with its closest phylogenetic relatives found much further to the east in New Mexico and Arizona. Using a phylogenomic approach employing anchored hybrid enrichment, we reconstruct the evolutionary history of...

Data From: Polygenic basis and the role of genome duplication in adaptation to similar selective environments

Matthew Campbell, Eric Anderson, John Carlos Garza & Devon Pearse
Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean access and compared them to each other and to an anadromous below-barrier population representing their ancestral source to search for signatures of both parallel and...

Hyaluronic acid-binding, anionic, nanoparticles inhibit ECM degradation and restore compressive strength in aggrecan-depleted articular cartilage explants

Marcus Deloney, Alyssa Panitch, Blaine Christiansen, Parssa Garoosi & Vanessa Dartoura
Joint trauma results in the production of inflammatory cytokines that stimulate the secretion of catabolic enzymes which degrade articular cartilage. Molecular fragments of the degraded articular cartilage further stimulate inflammatory cytokine production with this process eventually resulting in post-traumatic osteoarthritis (PTOA). The loss of aggrecan is considered an early step in the progression of PTOA. Aggrecan, composed of a core protein linked to sulfated glycosaminoglycans (GAGs), associates with hyaluronic acid (HA) via a link protein....

Cargo routing and disadvantaged communities

Anmol Pahwa & Miguel Jaller
Freight is fundamental to economic growth, however, the trucks that haul this freight are pollution intensive, emitting criteria pollutants and greenhouse gases at high rates. The increasing volume and time-sensitivity of freight demand over the past decade has encouraged carriers to take the fastest route, which is often not an eco-friendly route. The increase in urban freight movement has thus brought along negative externalities such as congestion, emissions, and noise into cities. Alternative fuel technologies,...

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...

Data from: Attacks on genetic privacy via uploads to genealogical databases

Doc Edge & Graham Coop
Direct-to-consumer (DTC) genetics services are increasingly popular for genetic genealogy, with tens of millions of customers as of 2019. Several DTC genealogy services allow users to upload their own genetic datasets in order to search for genetic relatives. The statement that a user's uploaded genome shares one or more segments in common with that of a target person in the database---that is, that the two genomes share one or more regions identical by state (IBS)---reveals...

Correlated evolution of sex allocation and mating system in wrasses and parrotfishes

Jennifer Hodge, Francesco Santini & Peter Wainwright
In accordance with predictions of the size-advantage model, comparative evidence confirms that protogynous sex change is lost when mating behavior is characterized by weak size advantage. However, we lack comparative evidence supporting the adaptive significance of sex change. Specifically, it remains unclear whether increasing male size advantage induces transitions to protogynous sex change across species, as it can within species. We show that in wrasses and parrotfishes (Labridae), the evolution of protogynous sex change is...

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...

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...

Structure and distribution of chalky deposits in the Pacific oyster using x-ray computed tomography (CT)

Roxanne Banker & Dawn Sumner
Oysters are unusual among bivalves in that they possess chambers, often filled with soft, chalky calcite, that are irregularly scattered throughout the shell. Because the function of these so-called chalky deposits is still unclear, evaluating the growth and distribution of chalk is important for elucidating the ecological function of this unique shell trait. Specimens of the Pacific oyster Magallana gigas, an oyster well known for chalk expression, were grown in Bodega Harbor, Bodega Bay, CA....

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...

Data from \"Quantification of major particulate matter species from a single filter type using infrared spectroscopy – Application to a large-scale monitoring network\"

Ann Dillner, Bruno Debus, Andrew T. Weakley, Satoshi Takahama, Kathryn George, Bret Schichtel, Scott Copeland & Anthony Wexler
This data set contains FT-IR data obtained from spectra of PTFE filters routinely in IMPROVE network during the time period 2015-2017, as well as the corresponding routine IMPROVE data for all ( ~160) IMPROVE sites except Korea. The data include PM2.5 aerosol concentrations measurements for organic carbon (OC), elemental carbon (EC), total carbon (TC), sulfate, nitrate, silicon, aluminum, calcium, titanium, iron, mass and light absorption. The data are in ug/m3. Some samples are excluded based...

Penn World Table 8.1

Robert Inklaar Robert C. Feenstra

Example data for ERP Analysis Book

Steven J Luck

CNS isotope values in eye lenses for juvenile and adult Chinook Salmon

Miranda Bell Tilcock, Carson Jeffres, Andrew Rypel, Ted Sommer, Jacob Katz, George Whitman & Rachel Johnson
Tracking habitat use and dietary shifts in migratory species is vital to conservation and management. Yet conventional animal tracking often precludes tracking small juveniles at critical life-stages where recruitment bottlenecks often manifest. Stable isotope analysis (SIA) in consecutive laminae in eye lenses, a protein-rich depositional tissue, has emerged as a promising tool in fishes to develop long-term interpretive records of dietary histories using a single archival tissue. Currently, studies using fisheye lenses to study SIA...

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...

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,...

Age affects strain-rate dependence of the mechanical properties of kelp tissue

Nicholas Burnett & M.A.R. Koehl
Premise: The resistance of macroalgae to hydrodynamic forces imposed by ambient water motion depends in part on the mechanical properties of their tissues. In wave-swept habitats, tissues are stretched (strained) at different rates as hydrodynamic forces constantly change. Kelp have tissues of different ages, and mechanical properties of kelp tissue change with age. However, the effects of age on the strain-rate dependence of the mechanical behavior of kelp tissues is unknown. Methods: Using the kelp...

Retention of green leaves not brown leaves increases spring cynipid diversity on large valley oaks

Vincent Pan, Adam Pepi, Jake Goidell & Richard Karban
Plants can retain either physiologically active green leaves or inactive brown leaves over winter. Research has suggested that leaf retention incurs a cost due to higher herbivore load in the following year; however, no distinction has, thus, far been made between retention of green and brown leaves. We surveyed the over-winter retention of physiologically active green and inactive brown leaves of valley oaks (Quercus lobata) and examined their relationship with the diversity and density of...

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...

Dispersal of nectar microbes in California flowering communities

Rachel Vannette, Griffin Hall, Ivan Munkres, Marshall McMunn, Douglas Perry & Tobias Mueller
Variation in dispersal ability among taxa affects community assembly and biodiversity maintenance within metacommunities. Although fungi and bacteria frequently coexist, their relative dispersal abilities are poorly understood. Nectar-inhabiting microbial communities affect plant reproduction and pollinator behavior, and are excellent models for studying dispersal of bacteria and fungi in a metacommunity framework. Here, we assay dispersal ability of common nectar bacteria and fungi in an insect-based dispersal experiment. We then compare these results to the incidence...

Transgenerational plasticity and the capacity to adapt to low salinity in the eastern oyster, Crassostrea virginica

Joanna Griffiths, Kevin Johnson, Kyle Sirovy, Mark Yeats, Francis Pan, Jerome La Peyre & Morgan Kelly
Salinity conditions in oyster breeding grounds in the Gulf of Mexico are expected to drastically change due to increased precipitation from climate change and anthropogenic changes to local hydrology. We determined the capacity of the eastern oyster, Crassostrea virginica, to adapt via standing genetic variation or acclimate through transgenerational plasticity. We outplanted oysters to either a low or medium salinity site in Louisiana for two years. We then crossed adult parents using a North Carolina...

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