78 Works

Data from: Genomic analysis of MHC-based mate choice in the monogamous California mouse

Jesyka Meléndez-Rosa, Ke Bi, Elieen A. Lacey & Eileen A Lacey
Variation at Major Histocompatibility Complex (MHC) genes is thought to be an important mechanism underlying mate choice in vertebrates, with individuals typically predicted to prefer MHC-dissimilar reproductive partners. However, analyses based on individual MHC loci have generated contradictory results regarding the role of these genes in mate choice decisions. To provide a more comprehensive assessment of relationships between MHC variation and mating behavior, we used an exome capture strategy to characterize variability at 13 MHC...

Data from: Microbiome interactions shape host fitness

Alison L. Gould, Vivian Zhang, Lisa Lamberti, Eric W. Jones, Benjamin Obadia, Nikolaos Korasidis, Alex Gavryushkin, Jean M. Carlson, Niko Beerenwinkel & William B. Ludington
Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host, in turn, shapes the gut microbiome. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here, we combinatorially dissect the natural microbiome of Drosophila melanogaster and reveal that interactions between bacteria shape host fitness through life history tradeoffs. Empirically, we made germ-free flies colonized with each...

Data from: Native grass ground covers provide multiple ecosystem services in Californian vineyards

Kent M. Daane, Brian N. Hogg, Houston Wilson & Glenn Y. Yokota
1. The mechanisms responsible for the success or failure of agricultural diversification are often unknown. Most studies of arthropod pest management focus on enhancing the effectiveness of natural enemies, but non-crop plants can also improve or hamper pest suppression by changing the host quality of crop plants by reducing or adding available soil nutrients or water. Native perennial ground covers may provide resources and long-term habitat to resident natural enemies and be more compatible than...

Data from: Natural selection interacts with recombination to shape the evolution of hybrid genomes

Molly Schumer, Chenling Xu, Daniel L Powell, Arun Durvasula, Laurits Skov, Chris Holland, John C Blazier, Sriram Sankararaman, Peter Andolfatto, Gil G Rosenthal & Molly Przeworski
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the “minor” parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human...

Data from: Bayesian vector transmission model detects conflicting interactions from transgenic disease‐resistant grapevines

Adam R. Zeilinger, Daniel Turek, Daniele Cornara, Anne Sicard, Steven E. Lindow & Rodrigo P. P. Almeida
Effective management of vector-borne plant pathogens often relies on disease-resistant cultivars. While heterogeneity in host resistance and in pathogen population density at the host population level play important and well-recognized roles in epidemiology, the effects of resistance traits on pathogen distribution at the individual host level, and the epidemiological consequences in turn, are poorly understood. Transgenic disease-resistant plants that produce bacterial Diffusible Signaling Factor (DSF) could provide resistance to the vector-borne bacterium Xylella fastidiosa by...

Data from: Rapid divergence of mussel populations despite incomplete barriers to dispersal

Diede L. Maas, Stefan Prost, Ke Bi, Lydia L. Smith, Ellie E. Armstrong, Ludi P. Aji, Abdul H.A. Toha, Rosemary G. Gillespie & Leontine E. Becking
Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment, and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to...

Data from: The Metapopulation Microcosm Plate: a modified 96-well plate for use in microbial metapopulation experiments

Helen Kurkjian & Helen M. Kurkjian
1. Researchers in many sub-fields of ecology and evolutionary biology test hypotheses relating to metapopulation dynamics and landscape spatial structure. Key aspects of these hypotheses are often (a) large numbers of subpopulations and dispersal corridors and (b) their positions relative to each other. Testing such spatial hypotheses using traditional lab equipment and methods can be impractical, unwieldy, expensive, or impossible. 2. The Metapopulation Microcosm Plate (MMP) overcomes these difficulties. This device resembles a 96-well microtiter...

Data from: Animals alter precipitation legacies: trophic and ecosystem engineering effects on plant community temporal dynamics

Joshua B. Grinath, Nicolas Deguines, John W. Chesnut, Laura R. Prugh, Justin S. Brashares & Katharine N. Suding
1. Multi-year precipitation ‘legacies’ can have stronger effects on plant community composition than rainfall in the current growing season, but variation in the magnitude of these effects is not fully understood. Direct interactions between plants and animals, such as herbivory, and indirect interactions, such as ecosystem engineering (via changes in the physical environment), may influence precipitation legacies by altering mechanisms of lagged effects. However, the role of direct and indirect plant-animal interactions in determining the...

Data from: Glucocorticoid-environment relationships align with responses to environmental change in two co-occurring congeners

Talisin T. Hammond, Rupert Palme & Eileen A. Lacey
As more species undergo range shifts in response to climate change, it is increasingly important to understand the factors that determine an organism’s realized niche. Physiological limits imposed by abiotic factors constrain the distributions of many species. Because glucocorticoids are essential to the maintenance of physiological homeostasis, identifying glucocorticoid-environment relationships may generate critical insights into both limits on species distributions and potential responses to environmental change. We explored relationships between variability in baseline glucocorticoids and...

Data from: Seed ingestion and germination in rattlesnakes: overlooked agents of rescue and secondary dispersal

Randall S. Reiserer, Gordon W. Schuett & Harry W. Greene
Seed dispersal is a key evolutionary process and a central theme in the population ecology of terrestrial plants. The primary producers of most land-based ecosystems are propagated by and maintained through various mechanisms of seed dispersal that involve both abiotic and biotic modes of transportation. By far the most common biotic seed transport mechanism is zoochory, whereby seeds, or fruits containing them, are dispersed through the activities of animals. Rodents are one group of mammals...

Supporting data for \"Evaluation of version 3.0B of the BEHR OMI NO2 product\"

Joshua Laughner, Qindan Zhu & Ronald Cohen
This dataset contains supporting data for the paper "Evaluation of version 3.0B of the BEHR OMI NO2 product" by Laughner, Zhu, and Cohen. Evaluation of new satellite trace gas products is an important step in proving their usefulness, and, in the case of NO2, is typically done by comparing the satellite-observed vertical column densities to independent measurements taken by aircraft or ground-based spectrometers. Input data required by the satellite retrieval may also be directly compared...

2D attenuation model of Long Valley (CA)

Janire Prudencio, Michael Manga & Taka'aki Taira
We image seismic intrinsic (Qi-1) and scattering (Qs-1) attenuation in Long Valley caldera, California, by analyzing more than 1700 vertical-component waveforms from local earthquakes. Observed energy envelopes are fit to the diffusion model (data files) and seismic attenuation images (anomalies files) are produced using two-dimensional space-weighting functions.

Restoration of incomplete oceanographic datasets

Siavash Ameli & Shawn Shadden
Remote sensing of oceanographic data often yields incomplete coverage of the measurement domain. This can limit interpretability of the data and identification of coherent features informative of ocean dynamics. Several methods exist to fill gaps of missing oceanographic data, and are often based on projecting the measurements onto basis functions or a statistical model. Herein, we use an information transport approach inspired from an image processing algorithm. This approach aims to restore gaps in data...

Thermal and energetic ion dynamics in Ganymede's magnetosphere

This dataset accompanies the manuscript "Thermal and energetic dynamics in Ganymede's magnetosphere", JGR Space Physics, 2018.

Data from: Mutual fitness benefits arise during coevolution in a nematode-defensive microbe model

Charlotte Rafaluk-Mohr, Ben Ashby, Dylan A. Dahan & Kayla C. King
Species interactions can shift along the parasitism-mutualism continuum. However, the consequences of these transitions for coevolutionary interactions remain unclear. We experimentally coevolved a novel species interaction between Caenorhabditis elegans hosts and a mildly parasitic bacterium, Enterococcus faecalis, with host-protective properties against virulent Staphylococcus aureus. Coinfections drove the evolutionary transition of the C.elegans-E. faecalis relationship towards a reciprocally beneficial interaction. As E. faecalis evolved to protect nematodes against S. aureus infection, hosts adapted by accommodating greater...

Data from: Validating dispersal distances inferred from autoregressive occupancy models with genetic parentage assignments

Laurie A. Hall, Nathan D. Van Schmidt & Steven R. Beissinger
1.Dispersal distances are commonly inferred from occupancy data but have rarely been validated. Estimating dispersal from occupancy data is further complicated by imperfect detection and the presence of unsurveyed patches. 2.We compared dispersal distances inferred from seven years of occupancy data for 212 wetlands in a metapopulation of the secretive and threatened California black rail (Laterallus jamaicensis coturniculus) to distances between parent-offspring dyads identified with 16 microsatellites. 3.We used a novel autoregressive multi-season occupancy model...

Data from: Legume abundance along successional and rainfall gradients in neotropical forests

Maga Gei, Danaë M. A. Rozendaal, Lourens Poorter, Frans Bongers, Janet I. Sprent, Mira D. Garner, T. Mitchell Aide, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Pedro H.S. Brancalion, George A. L. Cabral, Ricardo Gomes César, Robin L. Chazdon, Rebecca J. Cole, Gabriel Dalla Colletta, Ben De Jong, Julie S. Denslow, Daisy H. Dent, Saara J. DeWalt, Juan Manuel Dupuy, Sandra M. Durán, Mário Marcos Do Espírito Santo, G. Wilson Fernandes, Yule Roberta Ferreira Nunes … & Jennifer S. Powers
The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen (N)-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest-inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area...

Data from: Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests

Bonnie G. Waring, Rachel Adams, Sara Branco & Jennifer S. Powers
Rates of ecosystem nitrogen (N) cycling may be mediated by the presence of ectomycorrhizal fungi, which compete directly with free‐living microbes for N. In the regenerating tropical dry forests of Central America, the distribution of ectomycorrhizal trees is affected by succession and soil parent material, both of which may exert independent influence over soil N fluxes. In order to quantify these interacting controls, we used a scale‐explicit sampling strategy to examine soil N cycling at...

Data from: Lions and leopards coexist without spatial, temporal or demographic effects of interspecific competition

Jennifer R.B. Miller, Ross T. Pitman, Gareth K.H. Mann, Angela K. Fuller, Guy A. Balme, Jennifer R. B. Miller & Gareth K. H. Mann
1. Although interspecific competition plays a principle role in shaping species behaviour and demography, little is known about the population-level outcomes of competition between large carnivores, and the mechanisms that facilitate coexistence. 2. We conducted a multi-landscape analysis of two widely distributed, threatened large carnivore competitors to offer insight into coexistence strategies and assist with species-level conservation. 3. We evaluated how interference competition affects occupancy, temporal activity and population density of a dominant competitor, the...

Data from: The return to water in ancestral Xenopus was accompanied by a novel mechanism for producing and shaping vocal signals

Ursula Kwong-Brown, Martha L. Tobias, Damian O. Elias, Ian C. Hall, Coen P.H. Elemans, Darcy B. Kelley & Coen PH Elemans
Listeners locate potential mates using species-specific vocal signals. As tetrapods transitioned from water to land, lungs replaced gills, allowing expiration to drive sound production. Some frogs then returned to water. Here we explore how air-driven sound production changed upon re-entry to preserve essential acoustic information on species identity in the secondarily aquatic frog genus Xenopus. We filmed movements of cartilage and muscles during evoked sound production in isolated larynges. Results refute the current theory for...

Data from: Black spot infection in juvenile steelhead trout increases with stream temperature in northern California

Cody J. Schaaf, Suzanne J. Kelson, Sébastien C. Nusslé & Stephanie M. Carlson
Climate change will increase water temperature in rivers and streams that provide critical habitat for imperiled species. Warmer water temperatures will influence the intensity and nature of biotic interactions, including parasitism. To better understand the factors influencing a neascus-type parasitic infection known as black spot disease, we examined the relationship between infection rate in juvenile steelhead trout (Oncorhynchus mykiss), abundance of another intermediate host (ramshorn snail, Planorbella trivolvis), and water temperature. We quantified infection patterns...

Data from: Stream flow alone does not predict population structure of diving beetles across complex tropical landscapes

Athena Lam, Emmanuel F. A. Toussaint, Carolin Kindler, Matthew H. Van Dam, Rawati Panjaitan, George K. Roderick & Michael Balke
Recent theoretical advances have hypothesized a central role of habitat persistence on population genetic structure and resulting biodiversity patterns of freshwater organisms. Here, we address the hypothesis that lotic species, or lineages adapted to comparably geologically stable running water habitats (streams and their marginal habitats), have high levels of endemicity and phylogeographic structure due to the persistent nature of their habitat. We use a nextRAD sequencing approach to investigate the population structure and phylogeography of...

Data from: Ecological specialization, variability in activity patterns, and response to environmental change

Talisin T. Hammond, Rupert Palme & Eileen A. Lacey
Differences in temporal patterns of activity can modulate the ambient conditions to which organisms are exposed, providing an important mechanism for responding to environmental change. Such differences may be particularly relevant to ecological generalists, which are expected to encounter a wider range of environmental conditions. Here, we compare temporal patterns of activity for partially sympatric populations of a generalist (the lodgepole chipmunk, Tamias speciosus) and a more specialized congener (the alpine chipmunk, T. alpinus) that...

ASHRAE Global Thermal Comfort Database II

Veronika Földváry Ličina, Toby Cheung, Hui Zhang, Richard De Dear, Thomas Parkinson, Edward Arens, Chungyoon Chun, Stefano Schiavon, Maohui Luo, Gail Brager, Peixian Li & Soazig Kaam
Recognizing the value of open-source research databases in advancing the art and science of HVAC, in 2014 the ASHRAE Global Thermal Comfort Database II project was launched under the leadership of University of California at Berkeley’s Center for the Built Environment and The University of Sydney’s Indoor Environmental Quality (IEQ) Laboratory. The exercise began with a systematic collection and harmonization of raw data from the last two decades of thermal comfort field studies around the...

The influence of dopamine on cognitive flexibility is mediated by functional connectivity in young but not older adults

Anne Berry
Dopaminergic signaling in striatum is strongly implicated in executive functions including cognitive flexibility. However, there is a paucity of multimodal research in humans defining the nature of relationships between endogenous dopamine, striatal network activity, and cognition. Here, we measured dopamine synthesis capacity in young and older adults using the PET tracer 6-[18F]fluoro-L-m-tyrosine, and examined its relationship with cognitive performance and functional connectivity during an fMRI study of task switching. Aging is associated with alteration in...

Registration Year

  • 2018
    78

Resource Types

  • Dataset
    78

Affiliations

  • University of California, Berkeley
    78
  • University of Minnesota
    4
  • University of Washington
    3
  • Columbia University
    3
  • University of California System
    3
  • Museum of Vertebrate Zoology
    3
  • Dayton Foundation
    3
  • Cornell University
    3
  • Stanford University
    2
  • University of California, San Diego
    2