55 Works

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...

Care-giver identity impacts offspring development and performance in an annually social bumble bee

Claudineia Costa, Kaleigh Fisher, Blanca Guillén, Naoki Yamanaka, Guy Bloch & S Hollis Woodard
Background: The developmental fates of offspring have the potential to be influenced by the identity of their care-givers and by the nature of the care that they receive. In animals that exhibit both parental and alloparental care, such as the annually eusocial insects, the influence of care-giver identity can be directly assessed to yield mechanistic and evolutionary insights into the origins and elaboration of brood care. Here, we performed a comparative investigation of maternal and...

Data from: On the rupture propagation of the 2019 M6.4 Searles Valley Earthquake, and the lack of immediate triggering of the M7.1 Ridgecrest Earthquake

Jordan Cortez, David Oglesby, Christodoulos Kyriakopoulos, Baoning Wu, Kuntal Chaudhuri, Abhijit Ghosh & Roby Douilly
The 2019 M6.4 Searles Valley, Southern California, earthquake nucleated on a buried right-lateral fault segment and propagated around a perpendicular fault intersection to a surface-outcropping left-lateral segment, but it did not propagate coseismically to the intersecting fault of the subsequent M7.1 Ridgecrest mainshock. We use the 3D finite element method to explore the physical reasons for this curious rupture path. Rather than model the details of the measured and inferred slip distribution, we use simple...

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...

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...

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)...

Impact of uncertainty in precipitation forcing datasets on the hydrologic budget of an integrated hydrologic model in mountainous terrain

Adam Schreiner-McGraw & Hoori Ajami
Precipitation is a key input variable in distributed surface water-groundwater models, and its spatial variability is expected to impact watershed hydrologic response via changes in subsurface flow dynamics. Gridded precipitation datasets based on gauge observations, however, are plagued by uncertainty, especially in mountainous terrain where gauge networks are sparse. To examine the mechanisms via which uncertainty in precipitation data propagates through a watershed, we perform a series of numerical experiments using an integrated surface water-groundwater...

A trait-based framework for predicting foodborne pathogen risk from wild birds

Olivia Smith, Elissa Olimpi, Nora Navarro-González, Kevin Cornell, Luke Frishkoff, Tobin Northfield, Timothy Bowles, Max Edworthy, Johnna Eilers, Zhen Fu, Karina Garcia, David Gonthier, Matthew Jones, Christina Kennedy, Christopher Latimer, Jeb Owen, Chika Sato, Joseph Taylor, Erin Wilson Rankin, William Snyder & Daniel Karp
Recent foodborne illness outbreaks have heightened pressures on growers to deter wildlife from farms, jeopardizing conservation efforts. However, it remains unclear which species, particularly birds, pose the greatest risk to food safety. Using >11,000 pathogen tests and 1,565 bird surveys covering 139 bird species from across the western U.S.A., we examined the importance of 11 traits in mediating wild bird risk to food safety. We tested whether traits associated with pathogen exposure (e.g., habitat associations,...

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...

VISSIM and real-world eco-approach and departure comparison

David Oswald, Nigel Williams, Peng Hao & Matthew Barth
In addition to providing safety and mobility benefits, Connected and Automated Vehicles (CAVs) have the potential to reduce fuel consumption and emissions. As new CAV applications are developed, it is valuable to estimate these potential environmental benefits, typically using vehicle activity data and emissions models. To date, most researchers in the U.S. have used the MOVES vehicle emissions model, developed and maintained by the U.S. Environmental Protection Agency (EPA). However, because MOVES uses a binning...

Enduring evolutionary embellishment of cloudinids

Tae-Yoon Park, Jikhan Jung, Mirinae Lee, Sangmin Lee, Yong Yi Zhen, Hong Hua, Lucas V. Warren & Nigel C. Hughes
The Ediacaran–Cambrian transition and the following Cambrian Explosion are among the most fundamental events in the evolutionary history of animals. Understanding these events is enhanced when phylogenetic linkages can be established among animal fossils across this interval and their trait evolution monitored. Doing this is challenging because the fossil record of animal lineages that span this transition is sparse, preserved morphologies generally simple, and lifestyles in the Ediacaran and Cambrian quite different. Here we identify...

Raw data from: Dysregulation of host-control causes interspecific conflict over host investment into symbiotic organs

Kenjiro Quides, Fathi Salaheldine, Ruchi Jariwala & Joel Sachs
Microbial mutualists provide substantial benefits to hosts that feed back to enhance fitness of the associated microbes. In many systems, beneficial microbes colonize symbiotic organs, specialized host structures that house symbionts and mediate resources exchanged between parties. Mutualisms are characterized by net benefits exchanged among members of different species, however inequalities in the magnitude of these exchanges could result in evolutionary conflict, destabilizing the mutualism. We investigated joint fitness effects of root nodule formation, the...

The Ant Who Cried Wolf? Short-Term Repeated Exposure to Alarm Pheromone Reduces Behavioral Response in Argentine Ants

Brian Whyte, Jessica J. Maccaro & Neil D. Tsutsui
In this study we test whether Argentine ants (Linepithema humile) progressively reduce their response to a salient stimulus (alarm pheromone) with increased exposure over time. First, we used a two-chamber olfactometer to demonstrate three focal behaviors of Argentine ants that indicate an alarmed state in response to conspecific alarm pheromone and pure synthetic iridomyrmecin (a dominant component of L. humile alarm pheromone). We then measured how these behaviors changed after repeated exposure to conspecific alarm...

Data from: Ultraconserved elements reconstruct the evolution of the Chagas disease-vectoring kissing bugs (Reduviidae: Triatominae)

Troy J. Kieran, Eric R. L. Gordon, Alejandro Zaldivar-Riveron, Carlos N. Ibarra-Cerdena, Travis C. Glenn & Christiane Weirauch
With about 150 species, Triatominae, the kissing bugs, are the largest radiation of hematophagous species within the Hemiptera. Kissing bugs are the sole vectors of the causative agent of Chagas disease, a tropical neglected disease that affects millions, mostly in Central and South America. Surprisingly, given the medical importance of this group, the evolutionary origin of Triatominae from predatory assassin bug ancestors is still under debate and phylogenetic relationships among and within the five tribes...

Evolution of specialization in a plant-microbial mutualism is explained by the oscillation theory of speciation

Lorena Torres Martínez, Stehanie Porter, Camille Wendlandt, Jessica Purcell, Gabriel S Ortiz-Barbosa, Jacob Rothschild, Mathew Lampe, Farmasin Warisha, Tram Le, Alexandra J Weisberg, Jeff Chang & Joel L Sachs
This is a compilation of the different sets of data that were gathered and analyzed to understand the evolution of plant-microbial mutualisms in a genus of native legumes in California (Acmispon) described in the paper: "Torres-Martínez L, Porter SS, Wendlandt CE, Purcell J, Ortiz-Barbosa GS, Rothschild J, Lampe M, Warisha F, Le T, Weisberg AJ, Chang JH, Sachs JL. Evolution of specialization in a plant-microbial mutualism is explained by the oscillation theory of speciation. Evolution....

An organizing feature of bumble bee life history: worker emergence promotes queen reproduction and survival in young nests

Erica Sarro, Penglin Sun, Kerry Mauck, Damaris Rodriguez-Arellano, Naoki Yamanaka & Sarah Woodard
Bumble bee queens initiate nests solitarily and transition to living socially once they successfully rear their first cohort of offspring. Bumble bees are disproportionately important for early season pollination, and many populations are experiencing dramatic declines. In this system, the onset of the social stage is critical for nest survival, yet the mechanisms that facilitate this transition remain understudied. Further, the majority of conservation efforts targets the social stage of the bumble bee life cycle...

Data from: Pollinators and plant nurseries: how irrigation and pesticide treatment of native ornamental plants impact solitary bees

Jacob Cecala & Erin Wilson Rankin
A key conservation goal in agroecosystems is to understand how management practices may affect beneficial species, such as pollinators. Currently, broad gaps exist in our knowledge as to how horticultural management practices, such as irrigation level, might influence bee reproduction, particularly for solitary bees. Despite the extensive use of ornamental plants by bees, especially little is known about how irrigation level may interact with insecticides, like water-soluble neonicotinoids, to influence floral rewards and bee reproduction....

Data for: Phylogeography of an endemic California silkmoth genus suggests the importance of an unheralded central California province in generating regional endemic biodiversity

Camiel Doorenweerd, Daniel Rubinoff, Steven McElfresh & Jocelyn Millar
The California Floristic province is a biodiversity hotspot. Understanding the phylogeographic patterns that exist in this diverse region is essential to understanding its evolution and for guiding conservation efforts. Calosaturnia is a charismatic silkmoth genus endemic to large portions of the region with three described species, C. mendocino, C. walterorum, and C. albofasciata. We sampled all three species from across their ranges, sequenced 1463 bp of mitochondrial COI and 1941 bp of nuclear DNA from...

Data for: Successful management of invasive rats across a fragmented landscape

Erin Rankin, Sarah Barney, Devin Leopold, Kainana Francisco, David Flaspohler, Tad Fukami, Christian Giardina, Daniel Gruner, Jessie Knowlton & William Pitt
This dataset is from the manuscript "Successful management of invasive rats across a fragmented landscape" and provides the details on snap trap and tracking card data in a broadscale rat removal effort 2011-2015 in the Upper Waiakea Forest Reserve on the Island of Hawai‘i. It describes the successful trapping efforts as well as long term tracking data, which allow us to describe patterns of habitat use of non-native vertebrate species in these naturally fragmented forests...

Comparative analysis of Dipodomys species indicates that kangaroo rat hindlimb anatomy is adapted for rapid evasive leaping

Grace Freymiller
Body size is a key factor that influences antipredator behavior. For animals that rely on jumping to escape from predators, there is a theoretical trade-off between jump distance and acceleration as body size changes at both the inter- and intraspecific levels. Assuming geometric similarity, acceleration will decrease with increasing body size due to a smaller increase in muscle cross-sectional area than body mass. Smaller animals will likely have a similar jump distance as larger animals...

No disruption of rhizobial symbiosis during early stages of cowpea domestication

Gabriel Ortiz Barbosa, Lorena Torres-Martínez, Angela Manci, Sierra Neal, Tarek Soubra, Fizzah Khairi, Jerry Trinh, Paola Cardenas & Joel Sachs
Modern agriculture intensely selects aboveground plant structures, while often neglecting belowground features, and evolutionary tradeoffs between these traits are predicted to disrupt host control over microbiota. Moreover, drift, inbreeding, and relaxed selection for symbiosis in crops might degrade plant mechanisms that support beneficial microbes. We studied the impact of domestication on the nitrogen fixing symbiosis between cowpea and root-nodulating Bradyrhizobium. We combined genome-wide analyses with a greenhouse inoculation study to investigate genomic diversity, heritability, and...

Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers

Kai He, Michael Berenbrink, Kevin Campbell, Triston Eastman, Hannah Czolacz, Shuhao Li, Akio Shinohara, Shin-Ichiro Kawada & Mark Springer
Identifying the phylogenomic underpinnings of specialized phenotypes that fueled evolutionary transitions into new adaptive zones is central to evolutionary biology. The order Eulipotyphla (e.g., moles, shrews, and hedgehogs) is ideally suited to address this question as semi-fossorial, fossorial, and semi-aquatic forms have repeatedly arisen from terrestrial forbearers. However, our understanding of the ecomorphological pathways leading to these diverse lifestyles has been confounded by a fragmentary fossil record and potential morphological convergence. The net surface charge...

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...

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...

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
  • Sun Yat-sen University
  • Stanford University
  • The Nature Conservancy