53 Works

Data for: Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone

Erin Molloy, John Gatesy & Mark Springer
A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and...

Raw data from: Experimental evolution can enhance benefits of rhizobia to novel legume hosts

Kenjiro Quides, Alexandra Weisberg, Jerry Trinh, Fathi Salaheldine, Paola Cardenas, Hsu-Han Lee, Ruchi Jariwala, Jeff Chang & Joel Sachs
Legumes preferentially associate with and reward beneficial rhizobia in root nodules, but the processes by which rhizobia evolve to provide benefits to novel hosts remain poorly understood. Using cycles of in planta and in vitro evolution, we experimentally simulated lifestyles where rhizobia repeatedly interact with novel plant genotypes with which they initially provide negligible benefits. Using a fullfactorial replicated design, we independently evolved two rhizobia strains in associations with each of two Lotus japonicus genotypes...

Traffic and accident data for AEB environmental impact research

Guoyuan Wu & Xishun Liao
As one of the key advances in vehicle safety, Automatic Emergency Braking (AEB) has been introduced in the U.S. and the number of vehicles equipped with this technology has increased significantly in recent years. Most of existing studies have evaluated this technology at the individual vehicle level or focused on its safety performance. In this study, we tried to quantify its effectiveness on the energy consumption and tailpipe emissions. Towards this end, we: 1) performed...

Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti)

Timothy O'Connor, Marissa Sandoval, Jiarui Wang, Jacob Hans, Risa Takenaka, & Noah Whiteman
Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are notably polymorphic in both color and karyotype, making them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across...

Mode of maternal provisioning in the fish genus Phalloceros: a variation on the theme of matrotrophy

Eugenia Zandona, Maja Kajin, Paulo Buckup, Jeferson Amaral, Igor Souto-Santos & David Reznick
The placenta is a complex organ that shows high morphological diversity. Among fish, the first vertebrates that have evolved a placenta, the family Poeciliidae exhibits very diverse modes of maternal provisioning even among congeneric species. Here, we investigated the embryonic growth curve across seven recently-described species of the highly diverse genus Phalloceros (Eigenmann, 1907). We also investigated possible intraspecific differences and whether other female characteristics affected embryo mass. We found that embryo mass decreased until...

Evolutionary impacts of introgressive hybridization in a rapidly evolving group of jumping spiders (F. Salticidae, Habronattus americanus group)

Tierney Bougie, Alan Brelsford & Marshal Hedin
Introgressive hybridization can be a powerful force impacting patterns of evolution at multiple taxonomic levels. We aimed to understand how introgression has affected speciation and diversification within a species complex of jumping spiders. The Habronattus americanus subgroup is a recently radiating group of jumping spiders, with species now in contact after hypothesized periods of isolation during glaciation cycles of the Pleistocene. Effects of introgression on genomes and morphology were investigated using phylogenomic and clustering methods...

Data from: Substantial intraspecific variation in energy budgets: biology or artefact?

Tomos Potter, David Reznick & Tim Coulson
Data on the growth and reproduction of Trinidadian guppies (Poecilia reticulata) from sixteen different populations, reared under experimental conditions of either high or low food availability. These data were used to fit dynamic energy budgets models for each of the populations. For twelve populations, there are three sets of observations per individual, recorded at each successive parturition event. For four of the populations, data were recorded at each parturition event over the full lifespan of...

Ediacara growing pains: Modular addition and development in Dickinsonia costata

Scott Evans, James G. Gehling, Douglas Erwin & Mary Droser
Constraining patterns of growth using directly observable and quantifiable characteristics can reveal a wealth of information regarding the biology of the Ediacara Biota – the oldest macroscopic, complex community forming organisms in the fossil record. However, these rely on individuals captured at an instant in time at various growth stages, and so different interpretations can be derived from the same material. Here we leverage newly discovered and well-preserved Dickinsonia costata Sprigg 1947 from South Australia,...

Fire emissions data before and after peatland restoration, Indonesia, 2004-2015

L. Kiely, D.V. Spracklen & C. Wiedinmyer
This dataset contains fire emissions from Equatorial Asia for the years 2004, 2006, 2009, 2012, 2014 and 2015. The data is based on the Fire Inventory from National Center for Atmospheric Research with the addition of emissions from Indonesian peat fires, which contribute substantially to fire emissions in the region. The files for each year contain daily information on the area burned and emissions of several species, including CO, CO2 and PM2.5. Data is given...

Complex landscapes stabilize farm bird communities and their expected ecosystem services

Olivia Smith, Christina M. Kennedy, Alejandra Echeverri, Daniel Karp, Christopher Latimer, Joseph Taylor, Erin Wilson-Rankin, Jeb Owen & William Snyder
1. Birds play many roles within agroecosystems including as consumers of crops and pests, carriers of pathogens, and beloved icons. Birds are also rapidly declining across North America, in part due to agricultural intensification. Thus, it is imperative to identify how to manage agroecosystems to best support birds for multi-functional outcomes (e.g., crop production and conservation). Both the average amounts of services/disservices provided and their temporal stability are important for effective farm planning. 2. Here,...

Anchored phylogenomics and a revised classification of the Planidial Larva Clade of Jewel Wasps (Hymenoptera: Chalcidoidea)

JUNXIA ZHANG, John Heraty, Christopher Darling, Robert Kresslein, Austin Baker, Javier Torréns, Jean-Yves Rasplus, Alan Lemmon & Emily Lemmon
Planidia are free-living, mobile first-instar larvae that are notable in their ability to transition on a single host between different larval stadia, and for completing their development on the host prepupa as ectoparasitoids, effectively acting as larval-pupal external koinobionts. Within Chalcidoidea, a mega-diverse superfamily of parasitoid wasps, taxa with a planidium form a monophyletic group, the Planidial-Larva-Clade (PLC), which has been comprised of three recognized groups: Eutrichosomatinae (Pteromalidae), Perilampidae (Chrysolampinae, Perilampinae, Philomidinae and the unplaced...

Data from: The effects of temperature on the kinematics of rattlesnake predatory strikes in both captive and field environments

Malachi Whitford, Grace Freymiller, Timothy Higham & Rulon Clark
The outcomes of predator-prey interactions between endotherms and ectotherms can be heavily influenced by environmental temperature, owing to the difference in how body temperature affects locomotor performance. However, as elastic energy storage mechanisms can allow ectotherms to maintain high levels of performance at cooler body temperatures, detailed analyses of kinematics are necessary to fully understand how changes in temperature might alter endotherm-ectotherm predator-prey interactions. Viperid snakes are widely distributed ectothermic mesopredators that interact with endotherms...

VCF data file and code for: CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone

Alexander Kirschel, Emmanuel Nwankwo, Daniel Pierce, Sifiso Lukhele, Alan Brelsford, Michaella Moysi, Bridget Ogolowa, Sophia Hayes & Ara Monadjem
It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. But evidence that CYP2J19 explains variation between red and yellow feather coloration in wild...

Wild bee functional diversity and plant associations in native and conventional plant nurseries

Jacob Cecala & Erin Wilson Rankin
An ongoing challenge in ecology is predicting how characteristics of communities correspond to habitat features. Examining variation in functional traits across species may reveal patterns not discernible from measures of mere abundance or richness. For beneficial insects like wild bees, functional trait-based approaches are often used to characterize communities in different agricultural habitats. However, no such approach has yet been applied in horticultural plant nurseries, which represent intensively managed artificial flowering plant assemblages. Certain nurseries...

Data from: Differential habitat use and recruitment facilitate coexistence in a community with intraguild predation

Joshua Goldberg, Doug Fraser, Bradley Lamphere & David Reznick
Theory predicts that species engaged in intraguild predation (IGP) can only coexist under limited conditions, yet IGP is common in nature. Habitat complexity can promote co-existence by reducing encounter rates, but little is known about the contribution of differential habitat use. We hypothesized that differential use of alternative habitats promotes coexistence of an IG predator and prey. We evaluated predictions of this hypothesis with an experimental introduction of an IG predator fish into four natural...

Data from: Petals and leaves: quantifying the use of nest building materials by the world’s most valuable solitary bee

Jacob Cecala & Erin Wilson Rankin
The alfalfa leafcutter bee (“ALCB”, Megachile rotundata) is a solitary, cavity-nesting bee native to Eurasia, managed as an agricultural pollinator of alfalfa and several other crops in North America since the 1940s (Pitts-Singer and Cane 2011). The most intensively managed and economically valuable solitary bee worldwide, it serves as a model organism for studying solitary bee biology (Pitts-Singer and Cane 2011). Understanding this species’ nesting behavior is critical to its propagation for commercial pollination services....

Data from: Time of day prioritizes the pool of translating mRNAs in response to heat stress

Dawn Nagel & Titouan Bonnot
The circadian clock helps organisms to anticipate and coordinate gene regulatory responses to changes in environmental stimuli. Under growth limiting temperatures, time of day modulates the accumulation of polyadenylated mRNAs. In response to heat stress, plants will conserve energy and selectively translate mRNAs. How the clock and/or time of day regulates polyadenylated mRNAs bound by ribosomes in response to heat stress is unknown. In-depth analysis of Arabidopsis thaliana translating mRNAs found that time of day...

X-Ray CT scans of barley panicles and their individual seeds from the Composite Cross II experiment

Erik Amézquita, Michelle Quigley, Tim Ophelders, Jacob Landis, Daniel Koenig, Elizabeth Munch & Daniel Chitwood
Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare, and analyze this information embedded in a robust and concise way, we turn to Topological Data Analysis (TDA), specifically the Euler Characteristic Transform. TDA measures shape comprehensively using mathematical representations based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to...

Modeling phenological reaction norms over an elevational gradient reveals contrasting strategies of Dusky Flycatchers and Mountain Chickadees in response to early season temperatures

John Rotenberry, Sharon Coe & Kathryn Purcell
We developed an approach to distinguish among three alternative strategies birds may employ relating the timing of egg-laying across elevations to annual variation in spring temperature (phenological reaction norms), which we applied to analyze breeding phenology of two species over an elevational gradient in the Sierra Nevada, California. In a “simple offset” strategy, birds at different elevations initiate breeding relative to environmental temperature in a consistent manner, in that breeding onset is triggered by a...

The evolution of size-dependent competitive interactions promotes species coexistence

Jaime Mauricio Anaya-Rojas, Ronald D Bassar, Tomos Potter, Allison Blanchette, Shay Callahan, Nick Framstead, David Reznick & Joseph Travis
1. Theory indicates that competing species coexist in a community when intraspecific competition is stronger than interspecific competition. When body size determines the outcome of competitive interactions between individuals, coexistence depends also on how resource use and the ability to compete for these resources change with body size. Testing coexistence theory in size-structured communities, therefore, requires disentangling the effects of size-dependent competitive abilities and niche shifts. 2. Here, we tested the hypothesis that the evolution...

High-speed terrestrial substrate transitions: how a fleeing cursorial day gecko copes with compliance changes that are experienced in nature

Emily Naylor, Emily Naylor & Timothy Higham
1. Animal movement is often largely determined by abiotic conditions of the environment, including substrate properties. While a large body of work has improved our understanding of how different substrate properties can impact locomotor performance and behavior, few of these studies have investigated this relationship during transitions within a single locomotor event. 2. In nature, terrestrial animals frequently encounter substrate transitions, or changes in substrate level, incline, texture, and/or compliance during a single bout of...

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)...

Data for: Advanced infections by cucurbit yellow stunting disorder virus encourage whitefly vector colonization while discouraging non-vector aphid competitors

Kerry Mauck, Quentin Chesnais & Penglin Sun
Plant viruses can change hosts in ways that increase vector contacts, virion acquisition, and subsequent vector dispersal to susceptible hosts. Based on this, researchers have proposed that virus-induced phenotypes are the product of adaptations to “manipulate” hosts in ways that increase transmission. Theoretical models of virus spread in crops support this proposition; “manipulative” viruses spread faster and to a greater extent. However, both empirical and theoretical studies on manipulation are disproportionately focused on a few...

What evolutionary processes maintain MHCIIβ diversity within and among populations of stickleback?

Foen Peng, Kimberly Ballare, S. Hollis Woodard, Stijn Haan & Daniel Bolnick
Major Histocompatibility Complex (MHC) genes encode for proteins that recognize foreign protein antigens to initiate T-cell mediated adaptive immune responses. They are often the most polymorphic genes in vertebrate genomes. How evolution maintains this diversity is still an unsettled issue. Three main hypotheses seek to explain the maintenance of MHC diversity by invoking pathogen-mediated selection: heterozygote advantage, frequency-dependent selection, and fluctuating selection across landscapes or through time. Here, we use a large-scale field parasite survey...

Data from: A geology and geodesy based model of dynamic earthquake rupture on the Rodgers Creek-Hayward-Calaveras fault system, California

Michael Barall, Ruth Harris, David Lockner, Diane Moore, Ponce David, Russell Graymer, Gareth Funning, Carolyn Morrow, Christodoulos Kyriakopoulos & Donna Eberhart-Phillips
The Hayward fault in California's San Francisco Bay area produces large earthquakes, with the last occurring in 1868. We examine how physics-based dynamic rupture modeling can be used to numerically simulate large earthquakes on not only the Hayward fault, but also its connected companions to the north and south, the Rodgers Creek and Calaveras faults. Equipped with a wealth of images of this fault system, including those of its 3D geology and 3D geometry, in...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of California, Riverside
  • University of California, Davis
  • University of Georgia
  • Oregon State University
  • University of California, Berkeley
  • Washington State University
  • National Research Institute for Agriculture, Food and Environment
  • Stanford University
  • The Nature Conservancy
  • University of Memphis