45 Works

Data from: Subordinate plants mitigate drought effects on soil ecosystem processes by stimulating fungi

Pierre Mariotte, Bjorn J. M. Robroek, Vincent E. J. Jassey & Alexandre Buttler
The subordinate insurance hypothesis suggests that highly diverse communities contain greater numbers of subordinate species than less diverse communities. It has previously been reported that subordinate species can improve grassland productivity during drought, but the underlying mechanisms remain undetermined. Using a combination of subordinate species removal and summer drought, we show that soil processes play a critical role in community resistance to drought. Interestingly, subordinate species drive soil microbial community structure and largely mitigate the...

Data from: Avoiding tipping points in fisheries management through Gaussian process dynamic programming

Carl Boettiger, Marc Mangel & Stephan Munch
Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some...

Data from: Reconstructing the migratory behavior and long-term survivorship of juvenile Chinook salmon under contrasting hydrologic regimes

Anna M. Sturrock, J. D. Wikert, Timothy Heyne, Carl Mesick, Alan E. Hubbard, Travis M. Hinkelman, Peter K. Weber, George E. Whitman, Justin J. Glessner & Rachel C. Johnson
The loss of genetic and life history diversity has been documented across many taxonomic groups, and is considered a leading cause of increased extinction risk. Juvenile salmon leave their natal rivers at different sizes, ages and times of the year, and it is thought that this life history variation contributes to their population sustainability, and is thus central to many recovery efforts. However, in order to preserve and restore diversity in life history traits, it...

Data from: Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies

Bárbara Huber, Annabel Whibley, Yann Le Poul, Nicolas Navarro, Arnaud Martin, Simon Baxter, Abhijeet Shah, Benoît Gilles, Thierry Wirth, W. Owen McMillan & Mathieu Joron
Understanding the genetic architecture of adaptive traits has been at the centre of modern evolutionary biology since Fisher; however, evaluating how the genetic architecture of ecologically important traits influences their diversification has been hampered by the scarcity of empirical data. Now, high-throughput genomics facilitates the detailed exploration of variation in the genome-to-phenotype map among closely related taxa. Here, we investigate the evolution of wing pattern diversity in Heliconius, a clade of neotropical butterflies that have...

Data from: Shifting thresholds: rapid evolution of migratory life histories in steelhead/rainbow trout, Oncorhynchus mykiss

Corey C. Phillis, Jonathan W. Moore, Mathieu Buoro, Sean A. Hayes, John Carlos Garza & Devon E. Pearse
Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or declines in productivity and possibly extinction. Adaptation of conditional strategies following a change in the selection regime requires evolution of either the environmentally influenced cue (e.g., size-at-age) or the state (e.g., size threshold) at which an individual switches between alternative tactics. Using a population of steelhead (Oncorhynchus mykiss) introduced above a barrier...

Data from: An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the arboreal salamander (Aneides lugubris)

Sean Bryant Reilly, Ammon Corl & David B. Wake
Background: Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus data to reconstruct the evolutionary history of A. lugubris and to discover the geographic location of major genetic breaks within the species. We also used species distribution modeling...

Data from: A convex formulation for magnetic particle imaging x-space reconstruction

Justin J. Konkle, Patrick W. Goodwill, Daniel W. Hensley, Ryan D. Orendorff, Michael Lustig & Steven M. Conolly
Magnetic Particle Imaging (MPI) is an emerging imaging modality with exceptional promise for clinical applications in rapid angiography, cell therapy tracking, cancer imaging, and inflammation imaging. Recent publications have demonstrated quantitative mpi across rat sized fields of view with x-space reconstruction methods. Critical to any medical imaging technology is the reliability and accuracy of image reconstruction. Because the average value of the mpi signal is lost during direct-feedthrough signal filtering, mpi reconstruction algorithms must recover...

Data from: Phytochrome diversity in green plants and the origin of canonical plant phytochromes

Fay-Wei Li, Michael Melkonian, Carl J. Rothfels, Juan Carlos Villarreal, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer & Sarah Mathews
Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is...

Data from: A database to enable discovery and design of piezoelectric materials

Maarten De Jong, Wei Chen, Henry Geerlings, Mark Asta & Kristin Persson
Piezoelectric materials are used in numerous applications requiring a coupling between electrical fields and mechanical strain. Despite the technological importance of this class of materials, for only a small fraction of all inorganic compounds which display compatible crystallographic symmetry, has piezoelectricity been characterized experimentally or computationally. In this work we employ first-principles calculations based on density functional perturbation theory to compute the piezoelectric tensors for nearly a thousand compounds, thereby increasing the available data for...

Data from: Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate

Jeremy Chase Crawford & Christine M. Drea
Olfactory cues play an integral, albeit underappreciated, role in mediating vertebrate social and reproductive behaviour. These cues fluctuate with the signaller's hormonal condition, coincident with and informative about relevant aspects of its reproductive state, such as pubertal onset, change in season and, in females, timing of ovulation. Although pregnancy dramatically alters a female's endocrine profiles, which can be further influenced by fetal sex, the relationship between gestation and olfactory cues is poorly understood. We therefore...

Data from: Eco-genomic analysis of the poleward range expansion of the wasp spider Argiope bruennichi shows rapid adaptation and genomic admixture

Henrik Krehenwinkel, Dennis Rödder & Diethard Tautz
Poleward range expansions are commonly attributed to global change, but could alternatively be driven by rapid evolutionary adaptation. A well-documented example of a range expansion during the past decades is provided by the European wasp spider Argiope bruennichi. Using ecological niche modeling, thermal tolerance experiments and a genome-wide analysis of gene expression divergence, we show that invasive populations have adapted to novel climatic conditions in the course of their expansion. Their climatic niche shift is...

Data from: Contemporary land change alters fish communities in a San Francisco Bay drainage, California, U.S.A.

Kristina Cervantes-Yoshida, Robert A. Leidy & Stephanie M. Carlson
Urbanization is one of the leading threats to freshwater biodiversity, and urban regions continue to expand globally. Here we examined the relationship between recent urbanization and shifts in stream fish communities. We sampled fishes at 32 sites in the Alameda Creek Watershed, near San Francisco, California, in 1993–1994 and again in 2009, and we quantified univariate and multivariate changes in fish communities between the sampling periods. Sampling sites were classified into those downstream of a...

Data from: A single microphone noise reduction algorithm based on the detection and reconstruction of spectro-temporal features

Tyler P. Lee & Frederic E. Theunissen
Animals throughout the animal kingdom excel at extracting individual sounds from competing background sounds, yet current state-of-the-art signal processing algorithms struggle to process speech in the presence of even modest background noise. Recent psychophysical experiments in humans and electrophysiological recordings in animal models suggest that the brain is adapted to process sounds within the restricted domain of spectro-temporal modulations found in natural sounds. Here, we describe a novel single microphone noise reduction algorithm called spectro-temporal...

Data from: Genetic isolation between two recently diverged populations of a symbiotic fungus

Sara Branco, Pierre Gladieux, Christopher E. Ellison, Alan Kuo, Kurt LaButii, Anna Lipzen, Igor V. Grigoriev, Hui-Ling Liao, Rytas Vilgalys, Kabir G. Peay, John W. Taylor, Thomas D. Bruns & Kurt LaButti
Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here, we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind-dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for Su. brevipes and resequenced...

Data from: Condition dependence of male and female genital structures in the seed beetle Callosobruchus maculatus (Coleoptera: Bruchidae)

Luis Cayetano & Russell Bonduriansky
Theory predicts that costly secondary sexual traits will evolve heightened condition dependence, and many studies have reported strong condition dependence of signal and weapon traits in a variety of species. However, although genital structures often play key roles in intersexual interactions and appear to be subject to sexual or sexually antagonistic selection, few studies have examined the condition dependence of genital structures, especially in both sexes simultaneously. We investigated the responses of male and female...

Data from: Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

Prashant P. Sharma, Rosa Fernández, Lauren A. Esposito, Edmundo González-Santillán, Lionel Monod, E. Gonzalez-Santillan & R. Fernandez
Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships...

Data from: Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta

Pierre Gladieux, Benjamin A. Wilson, Fanny Perraudeau, Liliam A. Montoya, David Kowbel, Christopher Hann-Soden, Monika Fischer, Iman Sylvain, David J. Jacobson & John W. Taylor
Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population...

Data from: Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating

Fabien L. Condamine, Nathalie S. Nagalingum, Charles R. Marshall & Hélène Morlon
Background Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of plant evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of...

Data from: Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

Christopher E. Ellison & Doris Bachtrog
Transposable elements (TEs) allow rewiring of regulatory networks, and the recent amplification of the ISX element dispersed 77 functional but suboptimal binding sites for the dosage compensation complex to a newly formed X chromosome in Drosophila. Here we identify two linked refining mutations within ISX that interact epistatically to increase binding affinity to the dosage compensation complex. Selection has increased the frequency of this derived haplotype in the population, which is fixed at 30% of...

Data from: Orchid phylogenomics and multiple drivers of their extraordinary diversification

Thomas J. Givnish, Daniel Spalink, Mercedes Ames, Stephanie P. Lyon, Steven J. Hunter, Alejandro Zuluaga, William J. D. Iles, Mark A. Clements, Mary T. K. Arroyo, James Leebens-Mack, Lorena Endara, Ricardo Kriebel, Kurt M. Neubig, W. Mark Whitten, Norris H. Williams & Kenneth M. Cameron
Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144...

Data from: The origin and evolution of phototropins

Fay-Wei Li, Kathleen M. Pryer, Gane K.-S. Wong, Carl J. Rothfels, Michael Melkonian, Sarah Mathews, Juan C. Villarreal & Sean W. Graham
Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent...

Data from: Small-scale restoration in intensive agricultural landscapes supports more specialized and less mobile pollinator species

Claire Kremen & Leithen K. M'Gonigle
1. Agriculture now constitutes 40–50% of terrestrial land use globally. By enhancing habitat suitability and connectivity, restoration within agricultural landscapes could have a major influence on biodiversity conservation. However, habitat management within intensive agricultural landscapes may primarily boost abundances of common, highly mobile generalists, rather than vulnerable or endangered species. We studied pollinator community response to small-scale habitat restoration in the intensively farmed Central Valley of California to determine whether restoration could also promote more...

Data from: Quantifying physiological influences on otolith microchemistry

Anna M. Sturrock, Ewan Hunter, J. Andrew Milton, Edinburgh Ion Microprobe Facility, Rachel C. Johnson, Colin P. Waring & Clive N. Trueman
1. Trace element concentrations in fish earstones (“otoliths”) are widely used to discriminate spatially discrete populations or individuals of marine fish, based on a commonly held assumption that physiological influences on otolith composition are minor, and thus variations in otolith elemental chemistry primarily reflect changes in ambient water chemistry. 2. We carried out a long-term (1-yr) experiment, serially sampling seawater, blood plasma and otoliths of mature and immature European plaice (Pleuronectes platessa L.) to test...

Data from: Exon capture phylogenomics: efficacy across scales of divergence

Jason G. Bragg, Sally Potter, Ke Bi & Craig Moritz
The evolutionary histories of species are not measured directly, but estimated using genealogies inferred for particular loci. Individual loci can have discordant histories, but in general we expect to infer evolutionary histories more accurately as more of the genome is sampled. High Throughput Sequencing (HTS) is now providing opportunities to incorporate thousands of loci in ‘phylogenomic’ studies. Here, we used target enrichment to sequence c.3000 protein-coding exons in a group of Australian skink lizards (crown...

Data from: Fog as a source of nitrogen for redwood trees: evidence from fluxes and stable isotopes

Pamela H. Templer, Kathleen C. Weathers, Holly A. Ewing, Todd E. Dawson, Stefania Mambelli, Amanda M. Lindsey, Jeramy Webb, Vanessa K. Boukili & Mary K. Firestone
A defining feature of the redwood forest in coastal California is the presence of fog in the summer months, a time when there is typically little rainfall. Our goal was to determine the role of summer fog in canopy transformation of nitrogen, nitrogen uptake by trees and photosynthesis within a coastal redwood forest ecosystem. We measured horizontal and vertical inputs of nitrogen, the isotopic composition of nitrogen in a variety of atmospheric sources (summer fog,...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of California, Berkeley
  • Duke University
  • University of Alberta
  • University of California, Santa Cruz
  • The Bronx Defenders
  • Stanford University
  • Centre for Australian National Biodiversity Research
  • University of California System
  • University of Cologne
  • University of Wisconsin-Madison