48 Works

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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...

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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...

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