79 Works

Solutions to BAS-PRO model runs for Modelling 1-10MeV Proton Phase Space Density

Alexander Lozinski, Richard Horne, Sarah Glauert, Giulio Del Zanna & Seth Claudepierre
This dataset contains solution data produced by the BAS-PRO proton radiation belt model for the study "Modelling Inner Proton Belt Variability at Energies 1 to 10MeV using BAS-PRO". The solution data is in the form of 3D grids describing phase space density computed during dynamic simulations of Earth's proton belt over the modelling period 2014 to 2018. Three model runs are included: SA19, J81 and S16. Files were produced in May 2021. This work was...

Precipitation and vegetation shape patterns of genomic and craniometric variation in the Central African rodent Praomys misonnei

Katy Morgan, Jean Francois Mboumba, Stephan Ntie, Patrick Mickala, Courtney A. Miller, Ying Zhen, Ryan J. Harrigan, Vinh Le Underwood, Kristen Ruegg, Eric B. Fokam, Geraud C. Tasse Taboue, Paul R. Sesink Clee, Trevon Fuller, Thomas B. Smith & Nicola M. Anthony
Predicting species capacity to respond to climate change is an essential first step in developing effective conservation strategies. However, conservation prioritization schemes rarely take evolutionary potential into account. Ecotones provide important opportunities for diversifying selection and may thus constitute important reservoirs of standing variation, increasing the capacity for future adaptation. Here we map patterns of environmentally-associated genomic and craniometric variation in the central African rodent Praomys misonnei to identify areas with the greatest turnover in...

Individual variation in tolerance of human activity by urban dark-eyed juncos (Junco hyemalis) 2021 Stansell et al data file

Peter Nonacs, Pamela Yeh, Daniel Blumstein & Hayley Stansell
An important goal of urban ecology is determining what differentiates urban-tolerant populations of birds from their non-urban ancestors and urban-intolerant species. One key to urban success may be reacting appropriately to human activity, and the degree to which birds view humans as threats can be quantified by their escape behavior. Understanding individual-level plasticity, however, requires the tracking of known individuals. We compared flight-initiation distances (FID) and distances fled (DF) from approaches by a human between...

Lack of synchronized breeding success in a seabird community: extreme events, niche separation, and environmental variability

Casey Youngflesh, Yun Li, Heather Lynch, Karine Delord, Christophe Barbraud, Rubao Ji & Stephanie Jenouvrier
Synchrony in ecological systems, the degree to which elements respond similarly over time or space, can inform our understanding of how ecosystems function and how they are responding to global change. While studies of ecological synchrony are often focused on within-species dynamics, synchrony among species may provide important insights into how dynamics of one species are indicative of conditions relevant to the larger community, with both basic and applied implications. Ecological theory suggests there may...

Data from: Virulent disease epidemics can increase host density by depressing foraging of hosts

Rachel Penczykowski, Marta Shocket, Jessica Housley Ochs, Brian Lemanski, Hema Sundar, Meghan Duffy & Spencer Hall
All else equal, parasites that harm host fitness should depress densities of their hosts. However, parasites that alter host traits may increase host density via indirect ecological interactions. Here, we show how depression of foraging rate of infected hosts can produce such a hydra effect. Using a foraging assay, we quantified reduced foraging rates of a zooplankton host infected with a virulent fungal parasite. We then parameterized a dynamical model of hosts, parasites, and resources...

Bats partition activity in space and time in a large, heterogeneous landscape

Elizabeth Beilke, Rachel Blakey & Joy O'Keefe
Diverse species assemblages theoretically partition along multiple resource axes to maintain niche separation between all species. Temporal partitioning has received less attention than spatial or dietary partitioning but may facilitate niche separation when species overlap along other resource axes. We conducted a broad-scale acoustic study of the diverse and heterogeneous Great Smoky Mountains National Park in the Appalachian Mountains. Between 2015 and 2016, we deployed acoustic bat detectors at 50 sites (for a total of...

Woody encroachment happens via intensification, not extensification, of species ranges in an African savanna

Yong Zhou, Morgan Tingley, Madelon Case, Corli Coetsee, Gregory Kiker, Rheinhardt Scholtz, Freek Venter & Carla Staver
Widespread woody encroachment is a prominent concern for savanna systems as it is often accompanied by losses in productivity and biodiversity. Extensive ecosystem-level work has advanced our understanding of its causes and consequences. However, there is still debate over whether local management can override regional and global drivers of woody encroachment, and it remains largely unknown how encroachment influences woody community assemblages. Here, we examined species-level changes in woody plant distributions and size structure from...

Male-like female morphs in hummingbirds: the evolution of a widespread sex-limited plumage polymorphism

Eleanor Diamant, Jay J. Falk & Dustin R. Rubenstein
Differences in the way males and females look or behave are common in animals. However, discrete variation within sexes (sex-limited polymorphism) also occurs in several vertebrate and invertebrate lineages. In birds, female-limited polymorphism (FLP) in which some females resemble males in coloration is most prominent in hummingbirds, a group known for its morphological and behavioural sexual dimorphism. Yet, it remains unclear whether this intrasexual colour variation in hummingbirds arises through direct selection on females, or...

Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation

Yei-Chen Lai, Ziwei Liu & Irene Chen
Functional biomolecules, such as RNA, encapsulated inside a protocellular membrane are believed to have comprised a very early, critical stage in the evolution of life, since membrane vesicles allow selective permeability and create a unit of selection enabling cooperative phenotypes. The biophysical environment inside a protocell would differ fundamentally from bulk solution, due to the microscopic confinement. However, the effect of the encapsulated environment on ribozyme evolution has not been previously studied experimentally. Here we...

Environmental DNA in a global biodiversity hotspot: Lessons from coral reef fish diversity across the Indonesian archipelago

Onny Marwayana, Zachary Gold, Christopher Meyer & Paul Barber
Indonesia is the heart of the Coral Triangle, the world’s most diverse marine ecosystem. Preserving the biological and economic value of this marine biodiversity requires efficient and economical ecosystem monitoring, yet our understanding of marine biodiversity in this region remains limited. Towards this end, this study uses environmental DNA (eDNA) to survey fish communities across a well-documented biodiversity gradient in Indonesia. A total of 6,608,693 sequence reads of MiFish 12S rRNA from 39 sites spanning...

Data from: Modularity and connectivity of nest structure scale with colony size

Julie Miller, Noa Pinter-Wollman, Sean O'Fallon & Emma Wan
The files contained in this repository include data files and code used for analysis and figure creation in the article "Modularity and connectivity of nest structure scale with colony size". Data include csv files of edge-lists that are network representations of each nest, measures of chamber width for each nest, colony size data for each species, and ant length measures. These data are used in five sets of analyses, for which we include the R...

Faster evolution of a premating reproductive barrier is not associated with faster speciation rates in New World passerine birds

Benjamin Freeman, Jonathan Rolland, Graham Montgomery & Dolph Schluter
Why are speciation rates so variable across the tree of life? One hypothesis is that this variation is explained by how rapidly reproductive barriers evolve. We tested this hypothesis by conducting a comparative study of the evolution of bird song, a premating barrier to reproduction. Speciation in birds is typically initiated when geographically isolated (allopatric) populations evolve reproductive barriers. We measured the strength of song as a premating barrier between closely related allopatric populations by...

Marmot mass gain rates relate to their group’s social structure

Conner S. Philson, Sophia Todorov & Daniel T. Blumstein
Mass gain is an important fitness correlate for survival in highly seasonal species. While many physiological, genetic, life history, and environmental factors can influence mass gain, more recent work suggests the specific nature of an individual’s own social relationships also influences mass gain. However, less is known about consequences of social structure for individuals. We studied the association between social structure, quantified via social network analysis, and annual mass gain in yellow-bellied marmots (Marmota flaviventer)....

Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery

Patrice Salomé & Sabeeha Merchant
The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a...

Data from: Accelerated diversification explains the exceptional species richness of tropical characoid fishes

Bruno Melo, Brian Sidlauskas, Thomas Near, Fabio Roxo, Ava Ghezelayagh, Luz Ochoa, Melanie Stiassny, Jairo Arroyave, Jonathan Chang, Brant Faircloth, Daniel MacGuigan, Richard Harrington, Ricardo Benine, Michael Burns, Kendra Hoekzema, Natalia Sanches, Javier Maldonado-Ocampo, Ricardo Castro, Fausto Foresti, Michael Alfaro & Claudio Oliveira
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1288 ultraconserved element loci spanning 293 species, 211...

Do early life experiences predict variation in the general factor of personality (GFP)?

Joseph Manson, Kristine Joy Chua & Aaron Lukaszewski
Evolutionary approaches to examine human personality variation have used the Big Five as given, tested higher order latent structures like the Big Two or the General Factor of Personality (GFP), or applied domain-specific psychological adaptations. Yet, debates regarding the adaptive significance of personality variation are ongoing. We focus on latent factor models and test adaptationist hypotheses linking facultative responses of the GFP, its subparts (i.e., metatrait alpha), and extraversion to early life experiences in 366...

Data from: Evaluating the tradeoff between offspring number and survivorship across fishes, amphibians, reptiles and mammals

David Anderson
Species differ widely in their strategies of resource allocation to offspring size and number, ranging from teleost fishes and amphibians that produce many tiny offspring to reptiles and mammals that produce relatively few large offspring. Trade-offs between offspring survivorship and fecundity are thought to limit the success of any particular reproductive strategy, but these trade-offs have not been evaluated quantitatively across the full range of variability in offspring size and number. Here we examine the...

Nanitic scan sample data for division of labor in incipient Pogonomyrmex rugosus colonies

Peter Nonacs & Brittany Enzmann
Division of labor (DOL) is a principal characteristic of workers in mature colonies of many social insect species. In newly initiated ant colonies, however, the first workers (called nanitics) are few in number and much smaller in size than workers of mature colonies. This limited workforce must nevertheless perform most of the tasks of a mature colony, and it is unknown if they also exhibit DOL. In this study, we tracked several inside-nest and outside-nest...

Mechanisms of reduced interspecific interference between territorial species

Shawn McEachin, Jonathan P. Drury, Christopher N. Anderson & Gregory F. Grether
Interspecific territoriality has complex ecological and evolutionary consequences. Species that interact aggressively often exhibit spatial or temporal shifts in activity that reduce the frequency of costly encounters. We analyzed data collected over a 13-year period on 50 populations of rubyspot damselflies (Hetaerina spp.) to examine how rates of interspecific fighting covary with fine-scale habitat partitioning and to test for agonistic character displacement in microhabitat preferences. In most sympatric species, interspecific fights occur less frequently than...

Example measurements of electron energy and pitch angle distributions from Venus Express

Shaosui Xu, Rudy Frahm, Yingjuan Ma, Janet Luhmann & David Mitchell
Venus has negligible intrinsic magnetic fields to the first order, such that its ionosphere (the charged part of the atmosphere) interacts directly with the solar wind plasma and magnetic field. Therefore, magnetic connectivity to the ionosphere and/or solar wind is an important piece of information for understanding the near-Venus space environment and the Sun-Venus interaction. We utilize measurements from the Venus Express to determine magnetic connectivity, or magnetic topology, for the first time. We find...

Harnessing clinical annotations to improve deep learning performance in prostate segmentation

Karthik V. Sarma, Alex G. Raman, Nikhil J. Dhinagar, Alan M. Priester, Stephanie Harmon, Thomas Sanford, Sherif Mehralivand, Baris Turkbey, Leonard S. Marks, Steven S. Raman, William Speier & Corey W. Arnold
Purpose Developing large-scale datasets with research-quality annotations is challenging due to the high cost of refining clinically generated markup into high precision annotations. We evaluated the direct use of a large dataset with only clinically generated annotations in development of high-performance segmentation models for small research-quality challenge datasets. Materials and methods We used a large retrospective dataset from our institution comprised of 1,620 clinically generated segmentations, and two challenge datasets (PROMISE12: 50 patients, ProstateX-2: 99...

Predicting intraspecific trait variation among California’s grasses

Brody Sandel, Claire Pavelka, Thomas Hayashi, Lachlan Charles, Jennifer Funk, Fletcher Halliday, Gaurav Kandlikar, Andrew Kleinhesslink, Nathan Kraft, Loralee Larios, Tesa Madsen-McQueen & Marko Spasojevic
1. Plant species can show considerable morphological and functional variation along environmental gradients. This intraspecific trait variation (ITV) can have important consequences for community assembly, biotic interactions, ecosystem functions and responses to global change. However, directly measuring ITV across many species and wide geographic areas is often infeasible. Thus, a method to predict spatial variation in a species’ functional traits could be valuable. 2. We measured specific leaf area (SLA), height and leaf area (LA)...

Environmental map layers for Los Angeles environmental assessment project

Ariel Simons
In an increasingly urbanized world, there is a need to study urban areas as their own class of ecosystems as well as assess the impacts of anthropogenic impacts on biodiversity. However, collecting a sufficient number of species observations to estimate patterns of biodiversity in a city can be costly. Here we investigated the use of community science-based data on species occurrences, combined with species distribution models (SDMs), built using MaxEnt and remotely-sensed measures of the...

Data from: The utility of environmental DNA from sediment and water samples for recovery of observed plant and animal species from four Mojave Desert springs

MAURA PALACIOS MEJIA, Emily Curd, Kiumars Edalati, Mark Renshaw, Roy Dunn, Daniel Potter, Naomi Fraga, Jenna Moore, Justin Saiz, Robert Wayne & Sophie Parker
Background: Mojave Desert springs are fragile ecosystems, hosting endemic plants and animals, which are threatened by the increasing human demand for water and climate change. To develop management practices that will protect the groundwater-dependent ecosystems at Mojave Desert springs, real-time, low cost biodiversity monitoring and assessments are required. Environmental DNA (eDNA) metabarcoding uses DNA shed from organisms (e.g. skin cells, feces, pollen, etc.) that is present in water, air, soil, or sediment samples to assess...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Text


  • University of California Los Angeles
  • University of California, Los Angeles
  • University of Sao Paulo
  • Yale University
  • University of California, Irvine
  • University of California, Berkeley
  • University of Connecticut
  • University of California, Santa Barbara
  • National Park Service
  • Columbia University