45 Works

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: Genetics, morphology, advertisement calls, and historical records distinguish six new polyploid species of African clawed frog (Xenopus, Pipidae) from West and Central Africa

Ben J. Evans, Timothy F. Carter, Eli Greenbaum, Václav Gvoždík, Darcy B. Kelley, Patrick J. McLaughlin, Olivier S. G. Pauwels, Daniel M. Portik, Edward L. Stanley, Richard C. Tinsley, Martha L. Tobias & David C. Blackburn
African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of their polyploid species and the high number of independent polyploidization events that occurred during their diversification. Here we update current understanding of the evolutionary history of this group and describe six new species from west and central sub-Saharan Africa, including four tetraploids and two dodecaploids. We provide information on molecular variation, morphology, karyotypes, vocalizations, and estimated geographic ranges, which support the distinctiveness...

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: Detecting recent selective sweeps while controlling for mutation rate and background selection

Christian D. Huber, Michael DeGiorgio, Ines Hellmann & Rasmus Nielsen
A composite likelihood ratio test implemented in the program SweepFinder is a commonly used method for scanning a genome for recent selective sweeps. SweepFinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum (SFS) around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power...

Data from: Seasonal patterns of hormones, macroparasites, and microparasites in wild African ungulates: the interplay between stress, reproduction, and disease

Carrie A. Cizauskas, Wendy C. Turner, Neville I. Pitts, Wayne M. Getz & Neville Pitts
Sex hormones, reproductive status, and pathogen load all affect stress. Together with stress, these factors can modulate the immune system and affect disease incidence. Thus, it is important to concurrently measure these factors, along with their seasonal fluctuations, to better understand their complex interactions. Using steroid hormone metabolites from fecal samples, we examined seasonal correlations among zebra and springbok stress, reproduction, gastrointestinal (GI) parasite infections, and anthrax infection signatures in zebra and springbok in Etosha...

Data from: Charting the complete elastic properties of inorganic crystalline compounds

Maarten De Jong, Wei Chen, Thomas Angsten, Anubhav Jain, Randy Notestine, Anthony Gamst, Marcel Sluiter, Chaitanya Krishna Ande, Sybrand Van Der Zwaag, Jose J. Plata, Cormac Toher, Stefano Curtarolo, Gerbrand Ceder, Kristin A. Persson & Mark Asta
The elastic constant tensor of an inorganic compound provides a complete description of the response of the material to external stresses in the elastic limit. It thus provides fundamental insight into the nature of the bonding in the material, and it is known to correlate with many mechanical properties. Despite the importance of the elastic constant tensor, it has been measured for a very small fraction of all known inorganic compounds, a situation that limits...

Data from: Indirect effects of global change accumulate to alter plant diversity but not ecosystem function in alpine tundra

Emily Farrer, Isabel Ashton, Marko Spasojevic, Shiyang Fu, David Gonzalez, Katharine Suding, Emily C. Farrer, David J. X. Gonzalez, Katharine N. Suding & Marko J. Spasojevic
1. Environmental change can affect species directly by altering their physical environment and indirectly by altering the abundance of interacting species. A key challenge at the interface of community ecology and conservation biology is to predict how direct and indirect effects combine to influence response in a changing environment. In particular, little is known about how direct and indirect effects on biodiversity develop over time or their potential to influence ecosystem function. 2. We studied...

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: Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with genotyping-by-sequencing

Andrew M. Glazer, Emily E. Killingbeck, Therese Mitros, Daniel S. Rokhsar & Craig T. Miller
Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds...

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: Taxonomic and functional composition of arthropod assemblages across contrasting Amazonian forests

P. A. Greg Lamarre, Bruno Hérault, Paul V. A. Fine, Vincent Vedel, Roland Lupoli, Italo Mesones, Christopher Baraloto & Greg P. A. Lamarre
Arthropods represent most of global biodiversity, with the highest diversity found in tropical rainforests. Nevertheless, we have a very incomplete understanding of how tropical arthropod communities are assembled. We conducted a comprehensive mass-sampling of arthropod communities within three major habitat types of lowland Amazonian rainforest, including terra firme clay, white-sand, and seasonally-flooded forests in Peru and French Guiana. We examined how taxonomic and functional composition (at the family level) differed across these habitat types in...

Registration Year

  • 2015
    45

Resource Types

  • Dataset
    45

Affiliations

  • University of California, Berkeley
    45
  • Duke University
    6
  • University of Alberta
    3
  • University of California, Santa Cruz
    3
  • The Bronx Defenders
    2
  • Stanford University
    2
  • Centre for Australian National Biodiversity Research
    2
  • University of California System
    2
  • University of Cologne
    2
  • University of Wisconsin-Madison
    2