130 Works

Phylogeny of the Norwegian flora

Ida M. Mienna, James D. M. Speed, Mika Bendiksby, Andrew H. Thornhill, Brent D. Mishler & Michael D. Martin
Abstract: Aim: In this study, we explored spatial patterns of phylogenetic diversity and endemism in the flora of Norway and tested hypothesized post-glacial environmental drivers of phylogenetic diversity, including temperature, precipitation, edaphic factors, and time since glacial retreat. Location: Norway. Taxon: Vascular plants (Trachaeophyta). Methods: We produced a multi-locus Maximum Likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with...

Harvestmen locomotion kinematics

Ignacio Escalante, Marc Badger & Damian Elias
Dataset is the experimental test of changes in biomechanics of Neotropical harvestmen after leg loss. Data includes locomotor performance, as well as postural and stride kinematic variables. Please see the associated manuscript for more details and information (Escalante, I., Badger, M.A. & Elias, D.O. Rapid recovery of locomotor performance after leg loss in harvestmen. Sci Rep 10, 13747 (2020). https://doi.org/10.1038/s41598-020-70557-2).

In transition: avian biogeographic responses to a century of climate change across desert biomes

Kelly Iknayan & Steven Beissinger
Transition zones between biomes, also known as ecotones, are areas of pronounced ecological change. They are primarily maintained by abiotic factors and disturbance regimes that could hinder or promote species range shifts in response to climate change. We evaluated how climate change has affected metacommunity dynamics in two adjacent biomes and across their ecotone by resurveying 106 sites that were originally surveyed for avian diversity in the early 20th century by Joseph Grinnell and colleagues....

Exploring whole-genome duplicate gene retention with complex genetic interaction analysis

Elena Kuzmin, Benjamin VanderSluis, Alex N. Nguyen Ba, Wen Wang, Elizabeth N. Koch, Matej Usaj, Anton Khmelinskii, Mojca Mattiazzi Usaj, Jolanda Van Leeuwen, Oren Kraus, Amy Tresenrider, Michael Pryszlak, Ming-Che Hu, Brenda Varriano, Michael Costanzo, Michael Knop, Alan Moses, Chad L. Myers, Brenda J. Andrews & Charles Boone
Whole-genome duplication has played a central role in genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated and factors that influence the retention of persisting duplicates remain poorly understood. Here, we describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping digenic interactions for a deletion mutant of each paralog and trigenic interactions for the double mutant provides insight into their roles and...

Data from: Low temperatures impact species distributions of jumping spiders across a desert elevational cline

Erin E. Brandt, Kevin T. Roberts, Caroline M. Williams & Damian O. Elias
Temperature is known to influence many aspects of organisms and is frequently linked to geographical species distributions. Despite the importance of a broad understanding of an animal’s thermal biology, few studies in- corporate more than one metric of thermal biology. Here we examined an elevational assemblage of Habronattus jumping spiders to measure different aspects of their thermal biology including thermal limits (CTmin , CTmax), thermal preference, V̇CO2 as proxy for metabolic rate, locomotor behavior and...

Data from: The utility of information flow in formulating discharge forecast models: a case study from an arid snow-dominated catchment

Dino Bellugi, Chris Tennant, Larsen Laurel, Edom Moges, Liang Zhang & Hongxu Ma
These data accompany the manuscript “The utility of information flow in formulating discharge forecast models: a case study from an arid snow-dominated catchment”, in review at WRR. They were compiled from Boise State’s University’s Dry Creek Experimental Watershed (DCEW) web site, and consist of measurements of climatic data and discharge at various stations in the watershed from 1 January 2001 through 19 July 2017. The data quality-controlled, gap-filled, and aggregated at scales varying from 1...

Long-term evidence shows crop-rotation diversification increases agricultural resilience to adverse growing conditions in North America

Timothy Bowles, Maria Mooshammer, Yvonne Socolar, Franciso Calderón, Michel Cavigelli, Steve Culman, William Dean, Axel Garcia Y Garcia, Amélie Gaudin, W Scott Harkom, Michael Lehman, Shannon Osborne, G Philip Robertson, Jonathan Salerno, Marty Schmer, Jeffrey Strock, A Stuart Grandy & Craig Drury
A grand challenge facing humanity is how to produce food for a growing population in the face of a changing climate and environmental degradation. Though empirical evidence remains sparse, management strategies that increase environmental sustainability, like increasing agroecosystem diversity through crop rotations, may also increase resilience to weather extremes without sacrificing yields. We used multilevel regression analyses of long-term crop yield datasets across a continental precipitation gradient to assess how temporal crop diversification affects maize...

Environmental correlates of fine-scale juvenile steelhead trout (Oncorhynchus mykiss) habitat use and movement patterns in an intermittent estuary during drought

Stephanie Carlson & Eric Huber
We used acoustic telemetry and environmental monitoring to elucidate preferred microhabitats of juvenile steelhead trout (Oncorhynchus mykiss) in a Central California intermittent estuary (IE) during historic drought. We collected over half a million fish locations in the Pescadero IE (San Mateo County, CA) across 15 weeks during an extended sandbar-closed period which permitted quantification of fine scale habitat use and movement patterns. Tagged juvenile steelhead expressed strong site fidelity, especially at night when core habitat...

Locomotor endurance and oxygen consumption of harvestmen

Ignacio Escalante, Veronica Ellis & Damian O. Elias
Animal movements are highly constrained by morphology and energetics. In addition, predictable bodily damage can constrain locomotion even further. For example, for animals moving on land, losing legs may impose additional costs. We tested if losing legs affects the distance travelled over time (endurance) and the metabolic costs of locomotion (oxygen consumption) in Nelima paessleri harvestmen. These arachnids voluntary releases legs (i.e., autotomy) in response to predation attempts. We used flow-through respirometry as animals moved...

Data from: Aridity drives coordinated trait shifts but not decreased trait variance across the geographic range of eight Australian trees

Leander Anderegg, Xingwen Loy, Ian Markham, Christina Elmer, Mark Hovenden, Janneke HilleRisLambers & Margaret Mayfield
Large intraspecific functional trait variation strongly impacts many aspects of communities and ecosystems, and is the medium upon which evolution works. Yet intraspecific trait variation is inconsistent and hard to predict across traits, species, and locations. We measured within-species variation in leaf mass per area (LMA), leaf dry matter content (LDMC), branch wood density (WD), and allocation to stem area vs. leaf area in branches (branch Huber value, HV) across the aridity range of seven...

Data from: A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

Joel Nitta, Atsushi Ebihara & Alan Smith
Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176...

Data from: Predators can influence the host-parasite dynamics of their prey via non-consumptive effects

Nicolette Zukowski, Devin Kirk, Kiran Wadhawan, Dylan Shea, Denon Start & Martin Krkosek
Ecological communities are partly structured by indirect interactions, where one species can indirectly affect another by altering its interactions with a third species. In the absence of direct predation, non-consumptive effects of predators on prey have important implications for subsequent community interactions. To better understand these interactions, we used a Daphnia-parasite-predator cue system to evaluate if predation risk affects Daphnia responses to a parasite. We investigated the effects of predator cues on two aspects of...

Data from: Disentangling selection on genetically correlated polygenic traits using whole-genome genealogies

Aaron Stern
We present a full-likelihood method to estimate and quantify polygenic adaptation from contemporary DNA sequence data. The method combines population genetic DNA sequence data and GWAS summary statistics from up to thousands of nucleotide sites in a joint likelihood function to estimate the strength of transient directional selection acting on a polygenic trait. Through population genetic simulations of polygenic trait architectures and GWAS, we show that the method substantially improves power over current methods. We...

Data from: Zooming in on mechanistic predator-prey ecology: integrating camera traps with experimental methods to reveal the drivers of ecological interactions

Justine Smith, Justin Suraci, Jennifer Hunter, Kaitlyn Gaynor, Carson Keller, Meredith Palmer, Justine Atkins, Irene Castañeda, Michael Cherry, Patrick Garvey, Sarah Huebner, Dana Morin, Lisa Teckentrup, Martijn Weterings & Lydia Beaudrot
1. Camera trap technology has galvanized the study of predator-prey ecology in wild animal communities by expanding the scale and diversity of predator-prey interactions that can be analyzed. While observational data from systematic camera arrays have informed inferences on the spatiotemporal outcomes of predator-prey interactions, the capacity for observational studies to identify mechanistic drivers of species interactions is limited. 2. Experimental study designs that utilize camera traps uniquely allow for testing hypothesized mechanisms that drive...

Data from : Vacant yet invasible niches in forest community assembly

Pierre Gauzere, Xavier Morin, Cyrille Violle, Ivanna Caspeta, Courtenay Ray & Benjamin Blonder
It is controversial whether communities are saturated with species, or have vacant niches. The prevalence of vacant niches and the processes likely to promote their existence are poorly known. We used a process‐based forest gap‐model to simulate plant community dynamics in 11 sites along a climatic gradient across central Europe. We then used hypervolume analyses to study the existence of vacant niches (seen as empty volumes in the trait space of local species pools and...

Settlement-era public land survey data: Six Rivers National Forest

Clarke Knight, Charles Cogbill, Matthew Potts, James Wanket & John Battles
Historical baselines of forest conditions provide reference states to assess how forests have changed through time. In California, the Public Land Survey System (PLSS) provides tree inventory data between 1872-1884 at 93.2 km2 (36mi2) resolution. Although these data provide a spatially extensive record of settlement-era forest conditions, reconstructions using PLSS data have been limited and controversial in western landscapes. Recent improvements in the application of plotless density estimators (PDE) have made reconstructions more accurate and...

Data from: Mean annual temperature influences local fine root proliferation in tropical montane wet forest

Suzanne Pierre, Timothy J. Fahey, Creighton Litton, Christian Giardina & Jed Sparks
Mean annual temperature (MAT) is an influential climate factor affecting the bioavailability of growth-limiting nutrients nitrogen (N) and phosphorus (P). In tropical montane wet forests, warmer MAT drives higher N bioavailability, while patterns of P availability are inconsistent across MAT. Two important nutrient acquisition strategies, fine root proliferation into bulk soil and root association with arbuscular mycorrhizal fungi, are dependent on C availability to the plant via primary production. The case study presented here tests...

Methyl halide fluxes from rapeseed (Brassica napus) over its life cycle

Yi Jiao, Jerrold Jerrold Acdan, Rong Xu, Malte Deventer, Wanying Zhang & Robert Rhew
Rapeseed (Brassica napus) was quantified as one of the important terrestrial natural emitters of methyl bromide (CH3Br) to the atmosphere. In this study, we planted rapeseed (B. napus "Empire") in the field (Oxford Tract, UC Berkeley) and measured weekly methyl halide fluxes (CH3Cl, CH3Br and CH3I) using static-chamber measurements. The meteorological and physiological data, including air tempearture, plant height, leaf area, flowering number, biomass were also recorded over the life cycle of rapeseed.

Data from: Indirect genetic control of migration in a salmonid fish

Suzanne Kelson, Stephanie Carlson & Michael Miller
The paper titled "Indirect genetic control of migration in a salmonid fish" examines the genetic architecture of migration in a partially migratory salmonid fish, Oncorhynchus mykiss. We assess the shared genetic basis between early life growth and migration, and find a shared allelic basis on the Omy05 region of the genome. We then test if early life growth differs among resident/migratory genotype juvenile fish in streams in the South Fork Eel River watershed, in Northern...

Data from: Idiosyncratic perception: a link between acuity, perceived position and apparent size

Zixuan Wang, Yuki Murai & David Whitney
Perceiving the positions of objects is a prerequisite for most other visual and visuomotor functions, but human perception of object position varies from one individual to the next. The source of these individual differences in perceived position and their perceptual consequences are unknown. Here, we tested whether idiosyncratic biases in the underlying representation of visual space propagate across different levels of visual processing. In Experiment 1, using a position matching task, we found stable, observer-specific...

The effectiveness of flower strips and hedgerows on pest control, pollination services and crop yield: a quantitative synthesis

Matthias Albrecht, David Kleijn, Neal Williams, Matthias Tschumi, Brett Blaauw, Riccardo Bommarco, Alistair Campbell, Matteo Dainese, Frank Drummond, Martin Entling, Dominik Ganser, Arjen De Groot, David Goulson, Heather Grab, Hannah Hamilton, Felix Herzog, Rufus Isaacs, Katja Jacot, Philippe Jeanneret, Mattias Jonsson, Eva Knop, Claire Kremen, Doug Landis, Greg Loeb, Lorenzo Marini … & Louis Sutter
Floral plantings are promoted to foster ecological intensification of agriculture through provisioning of ecosystem services. However, a comprehensive assessment of the effectiveness of different floral plantings, their characteristics and consequences for crop yield is lacking. Here we quantified the impacts of flower strips and hedgerows on pest control (18 studies) and pollination services (17 studies) in adjacent crops in North America, Europe and New Zealand. Flower strips, but not hedgerows, enhanced pest control services in...

Stan code from: Branching networks can have opposing influences on genetic variation in riverine metapopulations

Ming-Chih Chiu, Bin Li, Kei Nukazawa, Vincent Resh, Thaddeus Carvajal & Kozo Watanabe
Aim: Fractal networks, represented by branching complexity in rivers, are ubiquitous in nature. In rivers, the number of either distal (e.g., in headwater streams) or confluent (e.g., in mainstems) locations can be increased along with their branching complexity. Distal- or confluent-spatial locations can result in fewer or greater corridor linkages that can alter genetic divergence at the metapopulation scale. These mechanisms underlying the resulting genetic structuring remain poorly understood at the metapopulation scale, particularly in...

Protea repens whole transcriptome count data for control and drought treatment for 8 populations, climatic data for the 8 populations and phenotypic data collected, and data used for linear mixed models for climate gene expression/trait correlation testing

Melis Akman
Long term environmental variation often drives local adaptation and leads to trait differentiation across populations. Additionally, when traits change in an environment-dependent way through phenotypic plasticity, the genetic variation underlying plasticity will also be under selection. These processes could create a landscape of differentiation across populations in traits and their plasticity. Here, we performed a dry-down experiment under controlled conditions to measure responses in seedlings of a shrub species from the Cape Floristic Region, the...

Stochastic processes and ecological connectivity drive stream invertebrate community responses to short-term drought

Romain Sarremejane, Amélie Truchy, Brendan McKie, Heikki Mykrä, Richard Johnson, Ari Huusko, Ryan Sponseller & Timo Muotka
1. Community responses to and recovery from disturbances depend on local (e.g. presence of refuges) and regional (connectivity to recolonization sources) factors. Droughts are becoming more frequent in boreal regions, and are likely to constitute a severe disturbance for boreal stream communities where organisms largely lack adaptations to such hydrological extremes. 2. We conducted an experiment in 24 seminatural stream flumes to assess the effects of local and regional factors on the responses of benthic...

Data from: Critical slowing down associated with critical transition and risk of collapse in cryptocurrency

Chengyi Tu, Paolo D'Odorico & Samir Suweis
The year 2017 saw the rise and fall of the crypto-currency market, followed by high variability in the price of all crypto-currencies. In this work, we study the abrupt transition in crypto-currency residuals, which is associated with the critical transition (the phenomenon of critical slowing down) or the stochastic transition phenomena. We find that, regardless of the specific crypto-currency or rolling window size, the autocorrelation always fluctuates around a high value, while the standard deviation...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of California, Berkeley
  • University of California, Davis
  • Cornell University
  • University of Minnesota
  • University of Georgia
  • University of Washington
  • Stanford University
  • Duke University
  • Ehime University
  • University of Pennsylvania