72 Works

Dorsal Periaqueductal gray ensembles represent approach and avoidance states

Fernando Reis, Johannes Lee, Sandra Maesta-Pereira, Peter Schuette, Meghmik Chakerian, Jinhan Liu, Mimi La-Vu, Brooke Tobias, Newton Canteras, Jonathan Kao & Avishek Adhikari
Animals must balance needs to approach threats for risk-assessment and to avoid danger. The dorsal periaqueductal gray (dPAG) controls defensive behaviors, but it is unknown how it represents states associated with threat approach and avoidance. We identified a dPAG threat-avoidance ensemble in mice (Mus musculus) that showed higher activity far from threats such as the open arms of the elevated plus maze and a live predator. These cells were also more active during threat-avoidance behaviors...

Single cell transcriptomic analyses reveal the impact of bHLH factors on human retinal organoid development

Xian-Jie Yang, Xiangmei Zhang, Igor Mandric, Kevin Nguyen, Thao Nguyen, Matteo Pellegrini, James Grove & Steven Barnes
The developing retina expresses multiple bHLH transcription factors. Their precise functions and interactions in uncommitted retinal progenitors remain to be fully elucidated. Here, we investigate the roles of bHLH factors ATOH7 and Neurog2 in human ES cell-derived retinal organoids. Single-cell transcriptome analyses identify three states of proliferating retinal progenitors: pre-neurogenic, neurogenic, and cell cycle-exiting progenitors. Each shows different expression profile of bHLH factors. The cell cycle-exiting progenitors feed into a postmitotic heterozygous neuroblast pool that...

Delayed adaptive radiation among New Zealand stream fishes: joint estimation of divergence time and trait evolution in a newly delineated island species flock

Christine Thacker, James Shelley, William McCraney, Peter Unmack & Matthew McGee
Adaptive radiations are generally thought to occur soon after a lineage invades a region offering high levels of ecological opportunity. However, few adaptive radiations beyond a handful of exceptional examples are known, so a comprehensive understanding of their dynamics is still lacking. Here, we present a novel case of an island species flock of freshwater fishes with a radically different tempo of adaptive history than that found in many popular evolutionary model systems. Using a...

Evaluating Promising Practices in Undergraduate STEM Lecture Courses

Mark Warschauer, Lynn Reimer, Kameryn Denaro, Gabe Orona, Katerina Schenke, Tutrang Nguyen, Amanda Niili, Di Xu, Sabrina Solanki & Tate Tamara
Observations were collected to examine instructional practices in large undergraduate lecture courses at UCI, particularly in STEM (science, technology, engineering, and mathematics). The study began in 2012 with the intention of documenting the relative presence or absence of practices that potentially promote more active and engaged learning (e.g., enhanced faculty-student interaction, enhanced peer interaction, greater attention to problem-solving strategies, more opportunities for personalized learning, opportunities to receive and communicate information across diverse channels and modalities,...

Tuned inhibition in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior: S4 data, evidence for tuned inhibition in macaque superior colliculus

Megan Peters, Brian Maniscalco, Brian Odegaard, Piercesare Grimaldi, Seong Hah Cho, Michele Basso & Hakwan Lau
This dataset contains online spike-sorted single-unit recordings from one Rhesus macaque who performed a dot-motion discrimination task while neural data was recorded with a 16-channel v-probe from superior colliculus neurons. Full methods for data collection, including description of the stimuli and task, surgical details, ethics statement, funding information, and other relevant details, are available in the above-referenced manuscript, section S4 Text.

The width and value of residential streets

Adam Millard-Ball
This dataset provides street-level information on width and the land value of street rights-of-way for 20 of the largest counties in the United States. Land values are expressed in 2019 prices. It uses OpenStreetMap and tax parcel data as inputs to a GIS-based process. Substantively, residential street rights-of-way in the urbanized portion of these counties average 55 ft wide, far greater than the functional minimum of 16 ft required for access. The land value of...

Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome

Jesse Garcia & Kirk Lohmueller
While there has been extensive work on patterns of linkage disequilibrium (LD) for neutral loci, the extent to which negative selection impacts LD is less clear. Forces like Hill-Robertson interference and negative epistasis are expected to lead to deleterious mutations being found on distinct haplotypes. However, the extent to which these forces depend on the selection and dominance coefficients of deleterious mutations and shape genome-wide patterns of LD in natural populations with complex demographic histories...

UF pre-treatment of seawater RO feedwater - performance data

Yoram Cohen, Yang Zhou, Bilal Khan & Han Gu
The datasets represent ultrafiltration (UF) operation, for pre-treatment of seawater RO feedwater, over a total period of 422 days. The operational data for UF filtration and backwash were obtained in a field study at Port Hueneme (CA) over a wide range of water quality conditions and coagulant dose. The data were utilized to develop a machine learning model for UF membrane resistance and backwash efficiency.

Body size and environment influence both intraspecific and interspecific variation in daily torpor use across hummingbirds

Austin Spence & Morgan Tingley
1. Torpor, or a regulated drop in body temperature and metabolic rate, allows animals to inhabit energetically costly environments, but among torpor-using species, we have a poor understanding of how plasticity in torpor use relates to the experienced environment. 2. To better understand the ecology of daily torpor, we completed the largest study to date on the intraspecific variation of daily torpor use in hummingbirds by exposing 149 individuals of two hummingbird species to ambient...

Habitat structure mediates vulnerability to climate change through its effects on thermoregulatory behavior

Lauren Neel, Michael Logan, Daniel Nicholson, Christina Miller, Albert Chung, Inbar Maayan, Zach Degon, Madeline DuBois, John David Curlis, Q Taylor, Kaitlin Keegan, Owen McMillan, Jonathan Losos & Christian Cox
Tropical ectotherms are thought to be especially vulnerable to climate change because they are thermal specialists, having evolved in aseasonal thermal environments. However, even within the tropics, habitat structure can influence opportunities for behavioral thermoregulation. Open (and edge) habitats likely promote more effective thermoregulation due to the high spatial heterogeneity of the thermal landscape, while forests are thermally homogenous and may constrain opportunities for behavioral buffering of environmental temperatures. Nevertheless, the ways in which behavior...

PacBio sequencing output increased through uniform and directional 5-fold concatenation

Celia Blanco, Nisha Kanwar, Irene A. Chen & Burckhard Seelig
Advances in sequencing technology have allowed researchers to sequence DNA with greater ease and at decreasing costs. Main developments have focused on either sequencing many short sequences or fewer large sequences. Methods for sequencing mid-sized sequences of 600-5,000 bp are currently less efficient. For example, the PacBio Sequel I system yields ~100,000-300,000 reads with an accuracy per base pair of 90-99%. We sought to sequence several DNA populations of ~870 bp in length with a...

Host energetics explain variation in parasite productivity across hosts and ecosystems

Rita Grunberg & David Anderson
Parasites are thought to play a role in ecosystem energetics, in part because some ecosystems harbor a substantial amount of parasite biomass. Nevertheless, the extent to which parasite biomass accurately reflects the flow of energy from hosts to parasites, and the linkages between their energetics, remain unclear. Here, we estimate parasite community energetics at the host and ecosystem-level and test predictions for parasite energetics using the metabolic theory of ecology. Across 27 host species, parasite...

Urban junco flight initiation distances correlate with approach velocities of anthropogenic sounds

Peter Nonacs, Hayley Stansell, Kara Lukas & Pamela Yeh
Urban-dwelling birds face novel visual cues and soundscapes. To thrive in these challenging environments, individuals must correctly identify and calibrate threats posed by humans and their activities. We showed that Dark-Eyed Juncos (Junco hyemalis) residing in an urban habitat responded differently to the sounds that approaching people and objects make. A person approached juncos simultaneously playing the sounds of object types that normally move at different relative velocities: faster (bicycles), intermediate (skateboards and scooters), or...

Functional biogeography of Neotropical moist forests: trait-climate relationships and assembly patterns of tree communities

Bruno Pinho, Marcelo Tabarelli, Cajo Ter Braak, S. J. Wright, Victor Arroyo-Rodriguez, Maíra Benchimol, Bettina Engelbrecht, Simon Pierce, Peter Hietz, Bráulio Santos, Carlos Peres, Sandra Müller, Ian Wright, Frans Bongers, Madelon Lohbeck, Ülo Niinemets, Martijn Slot, Steven Jansen, Davi Jamelli, Renato Augusto Ferreira De Lima, Nathan Swenson, Richard Condit, Jos Barlow, Ferry Slik, Manuel Hernández-Ruedas … & Felipe Melo
Aim: Here we examine the functional profile of regional tree species pools across the latitudinal distribution of Neotropical moist forests, and test trait-climate relationships among local communities. We expected opportunistic strategies (acquisitive traits, small seeds) to be overrepresented in species pools further from the equator due to long-term instability, but also in terms of abundance in local communities in currently wetter, warmer and more seasonal climates. Location: Neotropics. Time period: Recent. Major taxa studied: Trees....

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...

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...

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...

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...

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...

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...

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...

Registration Year

  • 2021

Resource Types

  • Dataset


  • 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