339 Works

Imaging the breakdown of ohmic transport in graphene

Alec Jenkins, Susanne Baumann, Haoxin Zhou, Simon Meynell, Daipeng Yang, Kenji Watanabe, Takashi Taniguchi, Andrew Lucas, Andrea Young & Ania Bleszynski Jayich
Ohm's law describes the proportionality of current density and electric field. In solid-state conductors, Ohm's law emerges due to electron scattering processes that relax the electrical current. Here, we use nitrogen-vacancy center magnetometry to directly image the local breakdown of Ohm's law in a narrow constriction fabricated in a high mobility graphene monolayer. Ohmic flow is visible at room temperature as current concentration on the constriction edges, with flow profiles entirely determined by sample geometry....

Type III secretion system effector proteins are mechanically labile

Marc-Andre LeBlanc, Morgan Fink, Thomas Perkins & Marcelo Sousa
Multiple Gram-negative bacteria encode Type III secretion systems (T3SS) that allow them to inject effector proteins directly into host cells to facilitate colonization. To be secreted, effector proteins must be at least partially unfolded to pass through the narrow needle-like channel (diameter < 2 nm) of the T3SS. Fusion of effector proteins to tightly packed proteins—such as GFP, ubiquitin, or dihydrofolate reductase (DHFR)—impairs secretion and results in obstruction of the T3SS. Prior observation that unfolding...

Data from: Behaviourally mediated predation avoidance in penguin prey: in situ evidence from animal-borne camera loggers

Jonathan M. Handley, Andréa Thiebault, Andrew Stanworth, David Schutt & Pierre Pistorius
Predator dietary studies often assume that diet is reflective of the diversity and relative abundance of their prey. This interpretation ignores species-specific behavioural adaptations in prey that could influence prey capture. Here, we develop and describe a scalable biologging protocol, using animal-borne camera loggers, to elucidate the factors influencing prey capture by a seabird, the gentoo penguin (Pygoscelis papua). From the video evidence, we show, for the first time, that aggressive behavioural defence mechanisms by...

Data from: Selection on a genetic polymorphism counteracts ecological speciation in a stick insect

Aaron A. Comeault, Samuel M. Flaxman, Rüdiger Riesch, Emma Curran, Víctor Soria-Carrasco, Zachariah Gompert, Timothy E. Farkas, Moritz Muschick, Thomas L. Parchman, Tanja Schwander, Jon Slate & Patrik Nosil
The interplay between selection and aspects of the genetic architecture of traits (such as linkage, dominance, and epistasis) can either drive or constrain speciation. Despite accumulating evidence that speciation can progress to “intermediate” stages—with populations evolving only partial reproductive isolation—studies describing selective mechanisms that impose constraints on speciation are more rare than those describing drivers. The stick insect Timema cristinae provides an example of a system in which partial reproductive isolation has evolved between populations...

Data from: Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives.

Gregory J. Baute, Nolan C. Kane, Christopher J. Grassa, Zhao Lai & Loren H. Rieseberg
• The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower, a globally important oilseed. • To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes,...

Data from: Acute maneb exposure significantly alters both glycolysis and mitochondrial function in neuroblastoma cells

Colin C. Anderson, Stefanos Aivazidis, Crystal L. Kuzyk, Abhilasha Jain & James R. Roede
The pesticides paraquat (PQ) and maneb (MB) have been described as environmental risk factors for Parkinson’s disease (PD), with mechanisms associated with mitochondrial dysfunction and reactive oxygen species generation. A combined exposure of PQ and MB in murine models and neuroblastoma cells has been utilized to further advance understanding of the PD phenotype. MB acts as a redox modulator through alkylation of protein thiols and has been previously characterized to inhibit complex III of the...

Data from: Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry

Elizabeth S.C. Scordato, Matthew R. Wilkins, Georgy Semenov, Alexander S. Rubtsov, Nolan C. Kane, Rebecca J. Safran & Elizabeth S. C. Scordato
Hybrid zones are geographic regions where isolating barriers between divergent populations are challenged by admixture. Identifying factors that facilitate or inhibit hybridization in sympatry can illuminate the processes that maintain those reproductive barriers. We analyzed patterns of hybridization and phenotypic variation across two newly-discovered hybrid zones between three subspecies of barn swallow (Hirundo rustica). These subspecies differ in ventral coloration and wing length, traits that are targets of sexual and natural selection, respectively, and are...

Data from: Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback

Jesse N. Weber, Gideon S. Bradburd, Yoel E. Stuart, William E. Stutz & Daniel I. Bolnick
Genetic divergence between populations is shaped by a combination of drift, migration, and selection, yielding patterns of isolation-by-distance (IBD) and isolation-by-environment (IBE). Unfortunately, IBD and IBE may be confounded when comparing divergence across habitat boundaries. For instance, parapatric lake and stream threespine stickleback (Gasterosteus aculeatus) may have diverged due to selection against migrants (IBE), or mere spatial separation (IBD). To quantitatively partition the strength of IBE and IBD, we used recently-developed population genetic software (BEDASSLE)...

Data from: Diversification of R2R3-MYB transcription factors in the tomato family Solanaceae

Daniel J. Gates, Susan R. Strickler, Lukas A. Mueller, Bradley J. S. C. Olson & Stacey D. Smith
MYB transcription factors play an important role in regulating key plant developmental processes involving defense, cell shape, pigmentation, and root formation. Within this gene family, sequences containing an R2R3 MYB domain are the most abundant type and exhibit a wide diversity of functions. In this study, we identify 559 R2R3 MYB genes using whole genome data from four species of Solanaceae and reconstruct their evolutionary relationships. We compare the Solanaceae R2R3 MYBs to the well-characterized...

Data from: Animals alter precipitation legacies: trophic and ecosystem engineering effects on plant community temporal dynamics

Joshua B. Grinath, Nicolas Deguines, John W. Chesnut, Laura R. Prugh, Justin S. Brashares & Katharine N. Suding
1. Multi-year precipitation ‘legacies’ can have stronger effects on plant community composition than rainfall in the current growing season, but variation in the magnitude of these effects is not fully understood. Direct interactions between plants and animals, such as herbivory, and indirect interactions, such as ecosystem engineering (via changes in the physical environment), may influence precipitation legacies by altering mechanisms of lagged effects. However, the role of direct and indirect plant-animal interactions in determining the...

Data from: Genetic hitchhiking and the dynamic buildup of genomic divergence during speciation with gene flow

Samuel Melvin Flaxman, Jeffrey L. Feder & Patrik Nosil
A major issue in evolutionary biology is explaining patterns of differentiation observed in population genomic data, as divergence can be due to both direct selection on a locus and genetic hitchhiking. “Divergence hitchhiking” (DH) theory postulates that divergent selection on a locus reduces gene flow at physically linked sites, facilitating the formation of localized clusters of tightly linked, diverged loci. “Genome hitchhiking” (GH) theory emphasizes genome-wide effects of divergent selection. Past theoretical investigations of DH...

Data from: Plumage genes and little else distinguish the genomes of hybridizing warblers

David P. L. Toews, Scott A. Taylor, Rachel Vallender, Alan Brelsford, Bronwyn G. Butcher, Philipp W. Messer & Irby J. Lovette
When related taxa hybridize extensively, their genomes may become increasingly homogenized over time. This mixing via hybridization creates conservation challenges when it reduces genetic or phenotypic diversity and when it endangers previously distinct species via genetic swamping [ 1 ]. However, hybridization also facilitates admixture mapping of traits that distinguish each species and the associated genes that maintain distinctiveness despite ongoing gene flow [ 2 ]. We address these dual aspects of hybridization in the...

Data from: Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity

Jordan G. Kueneman, Douglas C. Woodhams, Reid Harris, Holly M. Archer, Rob Knight & Valerie J. McKenzie
Host-associated microbiomes perform many beneficial functions including resisting pathogens and training the immune system. Here, we show that amphibians developing in captivity lose substantial skin bacterial diversity, primarily due to reduced ongoing input from environmental sources. We combined studies of wild and captive amphibians with a database of over 1 000 strains that allows us to examine antifungal function of the skin microbiome. We tracked skin bacterial communities of 62 endangered boreal toads, Anaxyrus boreas,...

Data from: Fire-regime complacency and sensitivity to centennial- through millennial-scale climate change in Rocky Mountain subalpine forests, Colorado, U.S.A.

Philip E. Higuera, Christy E. Briles & Cathy Whitlock
1. Key uncertainties in anticipating future fire regimes are their sensitivity to climate change, and the degree to which climate will impact fire regimes directly, through increasing the probability of fire, versus indirectly, through changes in vegetation and landscape flammability. 2. We studied the sensitivity of subalpine forest fire regimes (i.e., fire frequency, fire severity) to previously documented climate variability over the past 6000 years, utilizing pollen and macroscopic charcoal from high-resolution lake-sediment records in...

Data from: Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout

Jessica L. Metcalf, Sierra L. Love Stowell, Christopher M. Kennedy, Kevin B. Rogers, Daniel McDonald, Kyle Keepers, Janet Epp, Alan Cooper, Jeremy J. Austin & Andrew P. Martin
Many species are threatened with extinction and efforts are underway worldwide to restore imperiled species to their native ranges. Restoration requires knowledge of species’ historic diversity and distribution, which may not be available. For some species, many populations were extirpated and humans moved individuals beyond their native range before native diversity and distribution were documented. Moreover, traditional taxonomic assessments often failed to accurately capture phylogenetic diversity. We illustrate a general approach for estimating regional native...

Data from: Phylogenetic uncertainty revisited: implications for ecological analyses

Thiago Fernando Rangel, Robert K. Colwell, Gary R. Graves, Karolina Fučíková, Carsten Rahbek & José Alexandre F. Diniz-Filho
Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify...

Data from: Evaluating shell variation across different populations of a freshwater snail

Daniela Vergara, Jesualdo A. Fuentes, Kayla S. Stoy & Curtis M. Lively
The freshwater snail Potamopyrgus antipodarum has become a model system for studying invasion ecology, host–parasite coevolution, the maintenance of sexual reproduction and ecotoxicology. One understudied aspect of this snail is the variation in morphology within and among populations, which could provide insights into ecological differences across its native range. In this study of 17 New Zealand lake populations of P. antipodarum we used linear measurements and geometric morphometrics to compare several aspects of shell size...

Data from: Seed origin and warming constrain lodgepole pine recruitment, slowing the pace of population range shifts

Erin Conlisk, Cristina Castanha, Matthew J. Germino, Thomas T. Veblen, Jeremy M. Smith, Andrew B. Moyes & Lara M. Kueppers
Understanding how climate warming will affect the demographic rates of different ecotypes is critical to predicting shifts in species distributions. Here we present results from a common garden, climate change experiment in which we measured seedling recruitment of lodgepole pine, a widespread North American conifer that is also planted globally. Seeds from a low-elevation provenance had greater recruitment to their third year (by 323%) than seeds from a high-elevation provenance across sites within and above...

Data from: Natural selection on MHC IIβ in parapatric lake and stream stickleback: balancing, divergent, both or neither?

William E. Stutz & Daniel I. Bolnick
Major histocompatibility (MHC) genes encode proteins that play a central role in vertebrates’ adaptive immunity to parasites. MHC loci are among the most polymorphic in vertebrates’ genomes, inspiring many studies to identify evolutionary processes driving MHC polymorphism within populations, and divergence between populations. Leading hypotheses include balancing selection favoring rare alleles within populations, and spatially divergent selection. These hypotheses do not always produce diagnosably distinct predictions, causing many studies of MHC to yield inconsistent or...

Data from: Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species)

Dawson M. White, Melissa B. Islam & Roberta J. Mason-Gamer
This investigation establishes the first sequence-based phylogenetic hypothesis of species relationships in the Coca family (Erythroxylaceae). We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O. E. Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. We show that Neotropical Erythroxylum are monophyletic within the Paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack...

Data from: Continental-scale patterns reveal potential for warming-induced shifts in cattle diet

Joseph M. Craine, Jay P. Angerer, Andrew Elmore & Noah Fierer
In North America, it has been shown that cattle in warmer, drier grasslands have lower quality diets than those cattle grazing cooler, wetter grasslands, which suggests warming will increase nutritional stress and reduce weight gain. Yet, little is known about how the plant species that comprise cattle diets change across these gradients and whether these shifts in dietary quality coincide with shifts in dietary composition, i.e. the relative abundance of different plant species consumed by...

Data from: Repeated fires reduce plant diversity in low-elevation Wyoming big sagebrush ecosystems (1984-2014)

Adam L. Mahood & Jennifer K. Balch
Sagebrush is one of the most imperiled ecosystems in Western North America, having lost about half of its original 62 million hectare extent. Annual grass invasions are known to be increasing wildfire occurrence and burned area, but the lasting effects (> five years post-fire) that the resulting reburns have on these plant communities are unclear. We created a fire history atlas from 31 years (1984 to 2014) of Landsat-derived fire data to sample along a...

Data from: A rich fossil record yields calibrated phylogeny for Acanthaceae (Lamiales) and evidence for marked biases in timing and directionality of intercontinental disjunctions

Erin A. Tripp & Lucinda A. McDade
More than a decade of phylogenetic research has yielded a well-sampled, strongly supported hypothesis of relationships within the large (> 4,000 species) plant family Acanthaceae. This hypothesis points to intriguing biogeographic patterns and asymmetries in sister clade diversity but, absent a time-calibrated estimate for this evolutionary history, these patterns have remained unexplored. Here, we reconstruct divergence times within Acanthaceae using fossils as calibration points, experimenting both with fossil selection and effects of invoking a maximum...

Data from: Spatially explicit models of divergence and genome hitchhiking

Samuel M. Flaxman, Jeffrey L. Feder & Patrik Nosil
Strong barriers to genetic exchange can exist at divergently selected loci, whereas alleles at neutral loci flow more readily between populations, thus impeding divergence and speciation in the face of gene flow. However, ‘divergence hitchhiking’ theory posits that divergent selection can generate large regions of differentiation around selected loci. ‘Genome hitchhiking’ theory suggests that selection can also cause reductions in average genome-wide rates of gene flow, resulting in widespread genomic divergence (rather than divergence only...

Data from: Microbial richness and composition independently drive soil multifunctionality

Manuel Delgado-Baquerizo, Pankaj Trivedi, Chanda Trivedi, David J. Eldridge, Peter B. Reich, Thomas C. Jeffries & Brajesh K. Singh
Soil microbes provide multiple ecosystem functions such as nutrient cycling, decomposition and climate regulation. However, we lack a quantitative understanding of the relative importance of microbial richness and composition in controlling multifunctionality. This knowledge gap limits our capacity to understand the influence of biotic attributes in the provision of services and functions on which humans depend. We used two independent approaches (i.e. experimental and observational), and applied statistical modeling to identify the role and relative...

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  • University of Colorado Boulder
  • Okayama University
  • Japan Aerospace Exploration Agency
  • Colorado State University
  • University of Washington
  • Chiba Institute of Technology
  • University of California, Berkeley
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  • University of British Columbia
  • Cornell University