48 Works

Data from: Why close relatives make bad neighbors: phylogenetic conservatism in niche preferences and dispersal disproves Darwin’s Naturalization Hypothesis in the thistle tribe

Daniel S. Park & Daniel Potter
The number of exotic plant species that have been introduced into the United States far exceeds that of other groups of organisms, and many of these have become invasive. As in many regions of the globe, invasive members of the thistle tribe, Cardueae, are highly problematic in the California Floristic Province, an established biodiversity hotspot. While Darwin's naturalization hypothesis posits that plant invaders closely related to native species would be at a disadvantage, evidence has...

Data from: Seasonal cycles, phylogenetic assembly, and functional diversity of orchid bee communities

Santiago R. Ramírez, Carlos Hernández, Andres Link & Margarita M. López-Uribe
Neotropical rainforests sustain some of the most diverse terrestrial communities on Earth. Euglossine (or orchid) bees are a diverse lineage of insect pollinators distributed throughout the American tropics, where they provide pollination services to a staggering diversity of flowering plant taxa. Elucidating the seasonal patterns of phylogenetic assembly and functional trait diversity of bee communities can shed new light into the mechanisms that govern the assembly of bee pollinator communities and the potential effects of...

Data from: Forest disturbance accelerates thermophilization of understory plant communities

Jens T. Stevens, Hugh D. Safford, Susan Harrison & Andrew M. Latimer
1. Climate change is likely to shift plant communities towards species from warmer regions, a process termed “thermophilization.” In forests, canopy disturbances such as fire may hasten this process by increasing temperature and moisture stress in the understory, yet little is known about the mechanisms that might drive such shifts, or the consequences of these processes for plant diversity. 2. We sampled understory vegetation across a gradient of disturbance severity from a large-scale natural experiment...

Data from: Impact of nutrition and salinity changes on biological performances of green and white sturgeon

Pedro G. Vaz, Ermias Kebreab, Silas S.O. Hung, James G. Fadel, Seunghyung Lee, Nann A. Fangue & Silas S. O. Hung
Green and white sturgeon are species of high conservational and economic interest, particularly in the San Francisco Bay Delta (SFBD) for which significant climate change-derived alterations in salinity and nutritional patterns are forecasted. Although there is paucity of information, it is critical to test the network of biological responses underlying the capacity of animals to tolerate current environmental changes. Through nutrition and salinity challenges, climate change will likely have more physiological effect on young sturgeon...

Data from: Molecular evidence for hybridization in Colias (Lepidoptera: Pieridae): are Colias hybrids really hybrids?

Heather E. Dwyer, Marie Jasieniuk, Miki Okada & Arthur M. Shapiro
Gene flow and hybridization among species dramatically affect our understanding of the species as a biological unit, species relationships, and species adaptations. In North American Colias eurytheme and Colias eriphyle, there has been historical debate over the extent of hybridization occurring and the identity of phenotypically intermediate individuals as genetic hybrids. This study assesses the population structure of these two species to measure the extent of hybridization and the genetic identity of phenotypic intermediates as...

Data from: Flowering time of butterfly nectar food plants is more sensitive to temperature than the timing of butterfly adult flight

Heather M. Kharouba & Mark Vellend
1. Variation among species in their phenological responses to temperature change suggests that shifts in the relative timing of key life cycle events between interacting species are likely to occur under climate warming. However, it remains difficult to predict the prevalence and magnitude of these shifts given that there have been few comparisons of phenological sensitivities to temperature across interacting species. 2. Here, we used a broad-scale approach utilizing collection records to compare the temperature...

Data from: Macroevolutionary assembly of ant/plant symbioses: Pseudomyrmex ants and their ant-housing plants in the Neotropics

Guillaume Chomicki, Philip S. Ward & Susanne S. Renner
Symbioses include some of the clearest cases of coevolution, but their origin, loss, or reassembly with different partners can rarely be inferred. Here we use ant/plant symbioses involving three plant clades to investigate the evolution of symbioses. We generated phylogenies for the big-eyed arboreal ants (Pseudomyrmecinae), including 72% of their 286 species, as well as for five of their plant host groups, in each case sampling >61% of the species. We show that the ant-housing...

Data from: Differences in rheotactic responses contribute to divergent habitat use between parapatric lake and stream threespine stickleback

Yuexin Jiang, Louisa Torrance, Catherine L. Peichel & Daniel I. Bolnick
Migration among populations is widely thought to undermine adaptive divergence, assuming gene flow arises from random movement of individuals. If individuals instead differ in dispersal behavior, phenotype-dependent dispersal can reduce the effective rate of gene flow or even facilitae divergence. For example, parapatric populations of lake and stream stickleback tend to actively avoid dispersing into the adjoining habitat.. However, the behavioral basis of this non-random dispersal was previously unknown. Here we show that lake and...

Data from: GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems

Ruben Rellán-Álvarez, Guillaume Lobet, Heike Lindner, Pierre-Luc Pradier, Jose Sebastian, Muh-Ching Yee, Yu Geng, Charlotte Trontin, Therese LaRue, Amanda Schrager-Lavelle, Cara H. Haney, Rita Nieu, Julin Maloof, John P. Vogel & José R. Dinneny
Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that...

Data from: Pathology and epidemiology of ceruminous gland tumors among endangered Santa Catalina Island foxes (Urocyon littoralis catalinae) in the Channel Islands, USA

T. Winston Vickers, Deana L. Clifford, David K. Garcelon, Julie L. King, Calvin L. Duncan, Patricia M. Gaffney & Walter M. Boyce
In this study, we examined the prevalence, pathology, and epidemiology of tumors in free-ranging island foxes occurring on three islands in the California Channel Islands, USA. We found a remarkably high prevalence of ceruminous gland tumors in endangered foxes (Urocyon littoralis catalinae) occurring on Santa Catalina Island (SCA) - 48.9% of the dead foxes examined from 2001-2008 had tumors in their ears, and tumors were found in 52.2% of randomly-selected mature (≥ 4 years) foxes...

Data from: Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family.

Stephen Pearce, Alison K. Huttly, Ian M. Prosser, Yi-Dan Li, Simon P. Vaughan, Barbora Gallova, Archana Patil, Jane A. Coghill, Jorge Dubcovsky, Peter Hedden & Andrew L. Phillips
Background: The gibberellin (GA) pathway plays a central role in the regulation of plant development, with the 2-oxoglutarate-dependent dioxygenases (2-ODDs: GA20ox, GA3ox, GA2ox) that catalyse the later steps in the biosynthetic pathway of particularly importance in regulating bioactive GA levels. Although GA has important impacts on crop yield and quality, our understanding of the regulation of GA biosynthesis during wheat and barley development remains limited. In this study we identified or assembled genes encoding the...

Data from: Contrasting patterns in species and functional-trait diversity of bees in an agricultural landscape

Jessica R. K. Forrest, Robbin W. Thorp, Claire Kremen & Neal M. Williams
Land-use change frequently reduces local species diversity. Species losses will often result in loss of trait diversity, with likely consequences for community functioning. However, the converse need not be generally true: management approaches that succeed in retaining species richness could nevertheless fail to maintain trait diversity. We evaluated this possibility using bee communities in a California agroecosystem. We examined among-site patterns in bee species diversity and functional-trait diversity in a landscape composed of a mosaic...

Data from: BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

Brad T. Townsley, Michael F. Covington, Yasunori Ichihashi, Kristina Zumstein & Neelima R. Sinha
Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing inherent properties of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing...

Data from: Genetic architecture, biochemical underpinnings, and ecological impact of floral UV patterning

Marcus Brock, Lauren Lucas, Nickolas A. Anderson, Matthew Rubin, R. J. Markelz, Michael Covington, Upendra Devisetty, Clint Chapple, Julin Maloof, Cynthia Weinig, Lauren K. Lucas, Marcus T. Brock, Matthew J. Rubin, R. J. Cody Markelz, Michael F. Covington, Upendra K. Devisetty & Julin N. Maloof
Floral attraction traits can significantly affect pollinator visitation patterns, but adaptive evolution of these traits may be constrained by correlations with other traits. In some cases, molecular pathways contributing to floral attraction are well-characterized, offering the opportunity to explore loci potentially underlying variation among individuals. Here, we quantify the range of variation in floral UV patterning (i.e., UV “bulls-eye” nectar guides) among crop and wild accessions of Brassica rapa. We then use experimental crosses to...

Data from: Initial disturbance intensity affects recovery rates and successional divergence on abandoned ski slopes

Jennifer W. Burt & Jeffrey J. Clary
The importance of site history (including initial disturbance intensity and propagule arrival) in determining successional trajectories is a key theoretical and applied line of research in ecology. Abandoned ski slopes provide an opportunity to study successional processes following differing initial disturbance intensities. Some ski slopes are graded with heavy equipment when constructed (‘graded’, severe initial disturbance), while others are simply cleared of tall woody vegetation (‘cleared’, lesser initial disturbance). In a blocked chronosequence study of...

Data from: Immune response and insulin signalling alter mosquito feeding behaviour to enhance malaria transmission potential

Jose E. Pietri, Lauren J. Cator, Courtney C. Murdock, Johanna R. Ohm, Edwin E. Lews, Andrew F. Read, Shirley Luckhart & Matthew B. Thomas
Malaria parasites alter mosquito feeding behaviour in a way that enhances parasite transmission. This is widely considered a prime example of manipulation of host behaviour to increase onward transmission, but transient immune challenge in the absence of parasites can induce the same behavioural phenotype. Here, we show that alterations in feeding behaviour depend on the timing and dose of immune challenge relative to blood ingestion and that these changes are functionally linked to changes in...

Data from: Ear mite removal in the Santa Catalina Island fox (Urocyon littoralis catalinae): controlling risk factors for cancer development

Megan E. Moriarty, T. Winston Vickers, Deana L. Clifford, David K. Garcelon, Patricia M. Gaffney, Kenneth W. Lee, Julie L. King, Calvin L. Duncan & Walter M. Boyce
Ear mites (Otodectes cynotis) and ear canal tumors are highly prevalent among federally endangered Island foxes (Urocyon littoralis catalinae) living on Santa Catalina Island off the coast of Southern California. Since studies began in the 1990s, nearly all foxes examined were found to be infected with ear mites, and ceruminous gland tumors (carcinomas and adenomas) were detected in approximately half of all foxes ≥ 4 years of age. We hypothesized that reduction of ear mite...

Data from: Shared genomic regions between derivatives of a large segregating population of maize identified using bulked segregant analysis sequencing and traditional linkage analysis

Nicholas J. Haase, Timothy Beissinger, Candice N. Hirsch, Brieanne Vaillancourt, Shweta Deshpande, Kerrie Barry, C. Robin Buell, Shawn M. Kaeppler & Natalia De Leon
Delayed transition from the vegetative stage to the reproductive stage of development and increased plant height have been shown to increase biomass productivity in grasses. The goal of this project was to detect quantitative trait loci using extremes from a large synthetic population, as well as a related recombinant inbred line mapping population for these two traits. Ten thousand individuals from a B73 × Mo17 noninbred population intermated for 14 generations (IBM Syn14) were grown...

Data from: Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulate field fitness

Rachel Kerwin, Julie Feusier, Jason Corwin, Matthew Rubin, Catherine Lin, Alise Muok, Brandon Larson, Baohua Li, Bindu Joseph, Marta Francisco, Daniel Copeland, Cynthia Weinig & Daniel J. Kliebenstein
Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific...

Data from: Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

Philip Lavretsky, Jeffrey M. DaCosta, Blanca E. Hernández-Baños, , Michael D. Sorenson, Jeffrey L. Peters & Andrew Engilis
Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172...

Data from: How predation shaped fish: the impact of fin spines on body form evolution across teleosts

Samantha A. Price, Sarah T. Friedman & Peter C. Wainwright
It is well known that predators can induce morphological changes in some fish: individuals exposed to predation cues increase body depth and the length of spines. We hypothesize that these structures may evolve synergistically, as together, these traits will further enlarge the body dimensions of the fish that gape-limited predators must overcome. We therefore expect that the orientation of the spines will predict which body dimension increases in the presence of predators. Using phylogenetic comparative...

Data from: Complex genome evolution in A. coluzzii associated with increased insecticide usage in Mali

Bradley J. Main, Yoosook Lee, Travis C. Collier, Laura C. Norris, Katherine Brisco, Abdrahamane Fofana, Anthoney J. Cornel, Gregory C. Lanzaro & Anthony J. Cornel
In certain cases, a species may have access to important genetic variation present in a related species via adaptive introgression. These novel alleles may interact with their new genetic background, resulting in unexpected phenotypes. In this study, we describe a selective sweep on standing variation on the X chromosome in the mosquito Anopheles coluzzii, a principal malaria vector in West Africa. This event may have been influenced by the recent adaptive introgression of the insecticide...

Data from: Molecular dynamic simulations reveal the structural determinants of fatty acid binding to oxy-myoglobin

Sree V. Chintapalli, Gaurav Bhardwaj, Reema Patel, Natasha Shah, Randen L. Patterson, Damian B. Van Rossum, Andriy Anishkin & Sean H. Adams
The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolites; however, the binding pocket and regulation of the interaction remains to be established. In this study, we employed a computational strategy to elucidate the structural determinants of fatty acids...

Data from: Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity.

Susanna Atwell, Jason Corwin, Nicole Soltis, Anushryia Subedy, Katherine Denby, Daniel J. Kliebenstein, Jason A. Corwin, Nicole E. Soltis & Katherine J. Denby
How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a...

Data from: Using multiple markers to elucidate the ancient, historical, and modern relationships among North American Arctic dog breeds

Sarah K. Brown, Christyann M. Darwent, Elizabeth J. Wictum & Benjamin N. Sacks
Throughout most of the Americas, post-colonial dogs largely erased the genetic signatures of pre-historical dogs. However, the North American Arctic harbors dogs that are potentially descended from pre-historical ancestors, as well as those affected by post-colonial translocations and admixtures. In particular, Inuit dogs from Canada and Greenland are thought to descend from dogs associated with Thule peoples, who relied on them for transportation ca. 1000 years ago. Whether Thule dogs reflected an earlier colonization by...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of California, Davis
  • University of California System
  • California Department of Fish and Wildlife
  • Oregon State University
  • University of Wyoming
  • University of California, San Diego
  • University of Minnesota
  • University of California, Berkeley
  • National Autonomous University of Mexico
  • University of Wisconsin-Madison