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

Carl Boettiger, Marc Mangel, Stephan Munch, C. Boettiger & S. 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: 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: 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 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: 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: Condition dependence of male and female genital structures in the seed beetle Callosobruchus maculatus (Coleoptera: Bruchidae)

Luis Cayetano, Russell Bonduriansky, R. Bonduriansky & L. Cayetano
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, P. P. Sharma & L. A. Esposito
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: 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: 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 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: 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: Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate

Jeremy Chase Crawford, Christine M. Drea, J. C. Crawford & C. 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: Female preference for multi-modal courtship: multiple signals are important for male mating success in peacock spiders

Madeline B. Girard, Damian O. Elias & Michael M. Kasumovic
A long-standing goal for biologists has been to understand how female preferences operate in systems where males have evolved numerous sexually-selected traits. Jumping spiders of the Maratus genus are exceptionally sexually dimorphic in appearance and signaling behavior. Presumably, strong sexual selection by females has played an important role in the evolution of complex signals displayed by males of this group, however, this has not yet been demonstrated. In fact, despite apparent widespread examples of sexual...

Data from: Sharpening coarse-to-fine stereo vision by perceptual learning: asymmetric transfer across the spatial frequency spectrum

Roger W. Li, Truyet T. Tran, Ashley P. Craven, Tsz-Wing Leung, Sandy W. Chat & Dennis M. Levi
Neurons in the early visual cortex are finely tuned to different low-level visual features, forming a multi-channel system analysing the visual image formed on the retina in a parallel manner. However, little is known about the potential ‘cross-talk’ among these channels. Here, we systematically investigated whether stereoacuity, over a large range of target spatial frequencies, can be enhanced by perceptual learning. Using narrow-band visual stimuli, we found that practice with coarse (low spatial frequency) targets...

Data from: When field experiments yield unexpected results: lessons learned from measuring selection in White Sands lizards

Kayla M. Hardwick, Luke J. Harmon, Scott D. Hardwick & Erica Bree Rosenblum
Determining the adaptive significance of phenotypic traits is key for understanding evolution and diversification in natural populations. However, evolutionary biologists have an incomplete understanding of how specific traits affect fitness in most populations. The White Sands system provides an opportunity to study the adaptive significance of traits in an experimental context. Blanched color evolved recently in three species of lizards inhabiting the gypsum dunes of White Sands and is likely an adaptation to avoid predation....

Data from: Habitat restoration promotes pollinator persistence and colonization in intensively managed agriculture

Leithen K. M'Gonigle, Lauren C. Ponisio, Kerry Cutler & Claire Kremen
Widespread evidence of pollinator declines has led to policies supporting habitat restoration including in agricultural landscapes. Yet, little is yet known about the effectiveness of these restoration techniques for promoting stable populations and communities of pollinators, especially in intensively managed agricultural landscapes. Introducing floral resources, such as flowering hedgerows, to enhance intensively cultivated agricultural landscapes is known to increase the abundances of native insect pollinators in and around restored areas. Whether this is a result...

Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Carl J. Rothfels, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, , Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude DePamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer, C. Neal Stewart, Gane K-S. Wong … & Claude De Pamphilis
Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the...

Data from: Historical biogeography resolves the origins of endemic Arabian toad lineages (Anura: Bufonidae): evidence for ancient vicariance and dispersal events with the Horn of Africa and South Asia

Daniel M. Portik & Theodore J. Papenfuss
Background: The Arabian Peninsula is home to a unique fauna that has assembled and evolved throughout the course of major geophysical events, including the separation of the Arabian Plate from Africa and subsequent collision with Eurasia. Opportunities for faunal exchanges with particular continents occurred in temporally distinct periods, and the presence of African, Western Eurasian, and South Asian derived taxa on the Arabian Peninsula signifies the complexity of these historical biogeographic events. The six true...

Data from: Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks

Jeffrey M. Good, Dan Vanderpool, Sara Maria Keeble, Ke Bi & Sara Keeble
The idea that species boundaries can be semipermeable to gene flow is now widely accepted but the evolutionary importance of introgressive hybridization remains unclear. Here we examine the genomic contribution of gene flow between two hybridizing chipmunk species, Tamias ruficaudus and Tamias amoenus. Previous studies have shown that ancient hybridization has resulted in complete fixation of introgressed T. ruficaudus mitochondrial DNA (mtDNA) in some populations of T. amoenus, but the extent of nuclear introgression is...

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