69 Works

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...

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...

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...

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...

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...

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...

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...

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...

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...

Odor boosts visual object approach in flies

Karen Y. Cheng & Mark Frye
Multisensory integration is synergistic - input from one sensory modality might modulate the behavioral response to another. Work in flies has shown that a small visual object presented in the periphery elicits innate aversive steering responses in flight, likely representing an approaching threat. Object aversion is switched to approach when paired with a plume of food odor. The ‘open loop’ design of prior work facilitated the observation of changing valence. How does odor influence visual...

Local adaptation in thermal tolerance for a tropical butterfly across ecotone and rainforest habitats

Michel AK Dongmo, Rachid Hanna, Thomas B Smith, KKM Fiaboe, Abraham Fomena & Timothy C Bonebrake
Thermal adaptation to habitat variability can determine species vulnerability to environmental change. For example, physiological tolerance to naturally low thermal variation in tropical forests species may alter their vulnerability to climate change impacts, compared with open habitat species. However, the extent to which habitat-specific differences in tolerance derive from within-generation versus across-generation ecological or evolutionary processes are not well characterized. Here we studied thermal tolerance limits of a Central African butterfly (Bicyclus dorothea) across two...

Individual trial data on path choice in response to risk in Linepithema humile

Peter Nonacs & Emily Lessig
Ant colonies are likely able to access food locations by multiple paths that can vary predictably in length or mortality risk. To favor one path over another requires ants to perceive, communicate and act upon important differences in length and risk between paths. Here we present replicate Linepithema humile colonies with four equal-length paths to a sugar source. The paths vary in probabilities of encountering a risk cue that range from 0 to 100%. The...

Coexistence within an endangered predator–prey community in California vernal pools

Arianne F. Messerman, Adam G. Clause, Shantel V. L. Catania, H. Bradley Shaffer & Christopher A. Searcy
1. Globally endangered ecosystems, like ephemeral wetlands, are often critical habitat for multiple interacting imperiled species. To conserve this biodiversity, managers must consider both species-specific resource requirements and mechanisms for endangered species coexistence under variable habitat conditions. 2. We examined communities native to California playa pools, ephemeral wetlands that have declined by >90% from their historic extent. Specifically, we describe the diet of a federally Threatened amphibian (Ambystoma californiense), and characterize interactions between this amphibian...

Resolving the consequences of gradual phenotypic plasticity for populations in variable environments

Samuel Fey, Colin Kremer, Tamara Layden & David Vasseur
Phenotypic adjustments following environmental change are ubiquitous and trait changes arising through phenotypic plasticity often lag behind their environmental stimuli. Evolutionary biologists seeking to understand how adaptive plasticity can evolve have extensively studied this phenomenon. However, the ecological consequences of common features of plastic responses to environmental variability, including gradual phenotypic change (i.e., slower than the pace of environmental change), are underappreciated. We present a framework based on the unifying concept of phenotype x environment...

Hematoma expansion shift analysis to assess acute intracerebral hemorrhage treatments

Vignan Yogendrakumar, Tim Ramsay, Bijoy Menon, Adnan Qureshi, Jeffrey Saver & Dar Dowlatshahi
Objective: Hematoma expansion (HE) is commonly analyzed as a dichotomous outcome in intracerebral hemorrhage (ICH) trials. In this proof-of-concept study, we propose a “HE shift” analysis model as a method to improve the evaluation of candidate ICH therapies. Methods: Using data from the Antihypertensive Treatment of Acute Cerebral Hemorrhage II (ATACH-2) trial, we performed HE shift analysis in response to intensive blood pressure lowering by generating polychotomous strata based on a) previously established HE definitions,...

Fastq files related to publication: At Palmyra Atoll, the fish‐community environmental DNA signal changes across habitats but not with tides

Kevin D. Lafferty, Ana E. Garcia‐Vedrenne, John P. McLaughlin, Jasmine N. Childress, Marisa F. Morse & Christopher L. Jerde
At Palmyra Atoll, the environmental DNA (eDNA) signal on tidal sand flats was associated with fish biomass density and captured 98%–100% of the expected species diversity there. Although eDNA spilled over across habitats, species associated with reef habitat contributed more eDNA to reef sites than to sand-flat sites, and species associated with sand-flat habitat contributed more eDNA to sand-flat sites than to reef sites. Tides did not disrupt the sand-flat habitat signal. At least 25...

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

Zachary Gold
DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a...

Data from: Limited refugia and high velocity range-shifts predicted for bat communities in drought-risk areas of the Northern Hemisphere

Rachel Blakey, Mattia Piccioli Cappelli, Daniel Taylor, Jon Flanders, Trish Badeen, Sally Butts, Winifred Frick & Hugo Rebelo
Species occupying semi-arid and dry regions around the globe face an uncertain future due to increases in the frequency and severity of droughts. In this study we modelled the potential effect of climate change on bat communities within two high-drought risk regions of the world and assessed the magnitude and direction of the predicted shifts in climatic suitability, locating climate change refugia and identifying species at greatest risk of population declines. To do this, we...

Data for: Dorsal premammillary projection to periaqueductal gray controls escape vigor from innate and conditioned threats

Peter Schuette, Weisheng Wang, Mimi La-Vu, Brooke Tobias, Marta Ceko, Philip Kragel, Fernando Reis, Shiyu Ji, Megha Sehgal, Sandra Maesta-Pereira, Meghmik Chakerian, Alcino Silva, Newton Canteras, Tor Wager, Jonathan Kao & Avishek Adhikari
Escape from threats has paramount importance for survival. However, it is unknown if a single circuit controls escape from innate and conditioned threats. The hypothalamic dorsal premammillary nucleus (PMd) may control escape, as it is strongly activated by escape-inducing threats and projects to the region most implicated in escape, the dorsolateral periaqueductal gray (dlPAG). We show that in mice cholecystokinin (cck)-expressing PMd cells are activated during escape, but not other defensive behaviors. PMd-cck ensemble activity...

Health care-related economic burden of polycystic ovary syndrome in the United States: Pregnancy-related and long-term health consequences - supplemental data

Carrie Riestenberg
Context: Polycystic ovary syndrome (PCOS) is the most common endocrine disorder of reproductive-aged women, affecting approximately 5-20% of women of reproductive age. A previous estimate noted that the economic burden of PCOS approximates $3.7 billion annually in 2020 USD when considering only the costs of the initial diagnosis and of reproductive endocrine morbidities, not considering the costs of pregnancy-related and long-term morbidities. Objective: To estimate the excess prevalence and economic burden of pregnancy-related and long-term...

Leveraging genomics to understand threats to migratory birds

Brenda Larison, Alec R. Lindsay, Christen Bossu, Michael D. Sorenson, Joseph D. Kaplan, David C. Evers, James Paruk, Jeffrey M. DaCosta, Thomas B. Smith & Kristen Ruegg
Understanding of how risk factors affect populations across their annual cycle is a major challenge for conserving migratory birds. For example, disease outbreaks may happen on the breeding grounds, the wintering grounds, or during migration, and are expected to accelerate under climate change. The ability to identify the geographic origins of individuals impacted, especially outside of breeding areas, might make it possible to predict demographic trends and inform conservation decision making. However, such an effort...

Ancient introgression between distantly related white oaks (Quercus sect Quercus) shows evidence of climate-associated asymmetric gene exchange

Scott O'Donnell
Ancient introgression can be an important source of genetic variation that shapes the evolution and diversification of many taxa. Here, we estimate the timing, direction and extent of gene flow between two distantly related oak species in the same section (Quercus sect. Quercus). We estimated these demographic events using genotyping by sequencing data (GBS), which generated 25,702 single nucleotide polymorphisms (SNPs) for 24 individuals of California scrub oak (Quercus berberidifolia) and 23 individuals of Engelmann...

Local canopy disturbance as an explanation for long-term increases in liana abundance

Stefan Schnitzer, David DeFilippis, Marco Visser, Sergio Estrada-Villegas, Rigoberto Rivera-Camaña, Boris Bernal, Salomé Peréz, Abelino Valdéz, Seberino Aguilar, James Dalling, Eben Broadbent, Angelica Almeyda Zambrano, Stephen Hubbell & Maria Garcia-Leon
Canopy disturbance explains liana abundance and distribution within tropical forests and thus may also explain the widespread pattern of increasing liana abundance; however, this hypothesis remains untested. We used a 10-year study (2007 – 2017) of 117,100 rooted lianas in an old-growth Panamanian forest to test whether local canopy disturbance explains increasing liana abundance. We found that liana density increased 29.2% and basal area 12.5%. The vast majority of these increases were associated with clonal...

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
  • US Forest Service
  • National Park Service
  • Columbia University