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: 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: 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: Fluctuating, warm temperatures decrease the effect of a key floral repressor on flowering time in Arabidopsis thaliana

Liana T. Burghardt, Daniel E. Runcie, Amity M. Wilczek, Martha D. Cooper, Judith L. Roe, Stephen M. Welch & Johanna Schmitt
The genetic basis of growth and development is often studied in constant laboratory environments; however, the environmental conditions that organisms experience in nature are often much more dynamic. We examined how daily temperature fluctuations, average temperature, day length and vernalization influence the flowering time of 59 genotypes of Arabidopsis thaliana with allelic perturbations known to affect flowering time. For a subset of genotypes, we also assessed treatment effects on morphology and growth. We identified 17...

Data from: Severity of mitral valve degeneration is associated with chromosome 15 loci in Whippet dogs

Joshua A. Stern, Weihow Hsue, Kun-Ho Song, Eric S. Ontiveros, Virginia Luis Fuentes & Rebecca L. Stepien
Mitral valve degeneration (MVD) is the most common form of heart disease in dogs, frequently leading to left-sided congestive heart failure and cardiac mortality. Although breed-specific disease characteristics and overrepresentation point towards a genetic origin for MVD, a causative mutation and complete molecular pathogenesis are unknown. Whippet dogs are overrepresented in incidence of MVD, suggesting an inherited component in this breed. Expressivity of this condition is variable with some dogs showing evidence of more severe...

Data from: Linking transcriptional responses to organismal tolerance reveals mechanisms of thermal sensitivity in a mesothermal endangered fish

Lisa M. Komoroske, Richard E. Connon, Kenneth M. Jeffries, Nann A. Fangue & Ken M. Jeffries
Forecasting species' responses to climate change requires understanding the underlying mechanisms governing environmental stress tolerance, including acclimation capacity and acute stress responses. Current knowledge of these physiological processes in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. Yet many species of conservation concern exhibit tolerance windows and acclimation capacities in between these extremes. We linked transcriptome profiles to organismal tolerance in a mesothermal endangered fish, the delta smelt (Hypomesus transpacificus), to quantify...

Data from: Origin of tensile strength of a woven sample cut in bias directions

Ning Pan, Radko Kovar, Mehdi Kamali Dolatabadi, Ping Wang, Diantang Zhang, Ying Sun & Li Chen
Textile fabrics are highly anisotropic, so that their mechanical properties including strengths are a function of direction. An extreme case is when a woven fabric sample is cut in such a way where the bias angle and hence the tension loading direction is around 45° relative to the principal directions. Then, once loaded, no yarn in the sample is held at both ends, so the yarns have to build up their internal tension entirely via...

Data from: Prey state alters trait-mediated indirect interactions in rocky tide pools

Sarah A. Gravem & Steven G. Morgan
Several studies on trait-mediated indirect interactions (TMIIs) have shown that predators can initiate trophic cascades by altering prey behaviour. Although it is well recognized that individual prey state alters antipredator and foraging behaviour, few studies explore whether this state-dependent prey behaviour can alter the strength of the ensuing tritrophic cascade. Here, we link state-dependent individual behaviour to community processes by experimentally testing whether hunger level and body size of prey altered antipredator behaviour and thus...

Data from: Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation

Thomas J. Near, Alex Dornburg, Richard C. Harrington, Claudio Oliveira, Theodore W. Pietsch, Christine E. Thacker, Takashi P. Satoh, Eri Katayama, Peter C. Wainwright, Joseph T. Eastman & Jeremy M. Beaulieu
Background: Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited as the sister lineage of notothenioids remains unidentified. The phylogenetic placement of notothenioids among major lineages of perciform fishes, which include sculpins, rockfishes, sticklebacks, eelpouts, scorpionfishes, perches, groupers and soapfishes, remains unresolved. We investigate...

Data from: Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

Christopher Herbert Martin, Joseph S. Cutler, John P. Friel, Cyrille T. Dening, Graham Coop & Peter C. Wainwright
One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here we use comprehensive sampling from all four sympatric crater lake cichlid radiations in...

Data from: When the going gets tough: behavioral type dependent space use in the sleepy lizard changes as the season dries

Orr Spiegel, Stephan T. Leu, Andy Sih, Stephanie S. Godfrey, C. Michael Bull & Andrew Sih
Understanding space use remains a major challenge for animal ecology, with implications for species interactions, disease spread, and conservation. Behavioural type (BT) may shape the space use of individuals within animal populations. Bolder or more aggressive individuals tend to be more exploratory and disperse further. Yet, to date we have limited knowledge on how space use other than dispersal depends on BT. To address this question we studied BT-dependent space-use patterns of sleepy lizards (Tiliqua...

Data from: Plant diversity and endemism in the California Floristic Province

Dylan O. Burge, James H. Thorne, Susan P. Harrison, Bart C. O'Brien, Jon P. Rebman, James R. Shevock, Edward R. Alverson, Linda K. Hardison, José Delgadillo-Rodríguez, Steven A. Junak, Thomas A. Oberbauer, Hugo Riemann, Sula E. Vanderplank & Teri Barry
The California Floristic Province (CFP) is an area of high biodiversity and endemism corresponding roughly to the portion of western North America having a Mediterranean-type climate. High levels of diversity and endemism in the CFP are attributed to the unique geo-climatic setting of the region. In recent years, much has been learned about the origins of plant diversity in western North America. This work, however, has been hindered by a focus on political rather than...

Data from: Mitochondrial capture enriches mito-DNA 100 folds enabling PCR-free mitogenomics biodiversity analysis

Shanlin Liu, Xin Wang, Lin Xie, Meihua Tan, Zhenyu Li, Xu Su, Hao Zhang, Bernhard Misof, Karl M. Kjer, Min Tang, Oliver Niehuis, Hui Jiang & Xin Zhou
Biodiversity analyses based on Next Generation Sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of such a method is the lack of appropriate mitochondrial DNA enrichment ways. Because mitochondrial genomes (mitogenomes) make up only a small proportion of total DNA, PCR-free methods will inevitably result in...

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