530 Works

Of woodlice and men: A Bayesian account of cognition, life and consciousness. An interview with Karl Friston.

Karl Friston, Martin Fortier & Daniel Friedman
Prof. Karl J. Friston is a scientist who has made fundamental contributions to areas such as functional brain imaging, statistical techniques for dynamical systems, and the Free Energy Principle (FEP). Here, various topics are formally and informally explored. First there are personal, scientific, and mathematical accounts related to the (origins of the) FEP, and how the FEP diverges from the Predictive coding and Bayesian brain hypotheses. Next, there is a discussion of how the FEP...

Data from: Detailed food web networks of three Greater Antillean coral reef systems: the Cayman Islands, Cuba, and Jamaica

Peter D. Roopnarine & Rachel Hertog
Food webs represent one of the most complex aspects of community biotic interactions. Complex food webs are represented as networks of interspecific interactions, where nodes represent species or groups of species, and links are predator-prey interactions. This paper presents reconstructions of coral reef food webs in three Greater Antillean regions of the Caribbean: the Cayman Islands, Cuba, and Jamaica. Though not taxonomically comprehensive, each food web nevertheless comprises producers and consumers, single-celled and multicellular organisms,...

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...

Data from: Altered physical and social conditions produce rapidly reversible mating systems in water striders

Andrew Sih, Pierre-Olivier Montiglio, Tina W. Wey & Sean Fogarty
Mating systems can vary within-species but the environmental drivers and behavioral mechanisms underlying this variation are seldom investigated experimentally. We experimentally assessed how individual behavioral plasticity in response to changes in pool and group size resulted in fundamental shifts in mating systems in water striders. We observed the same animals in larger and smaller pools, mimicking variation in pool size in natural streams, and observed a rapid, reversible change in the entire mating system. In...

Data from: Geosmithia associated with bark beetles and woodborers in the western USA: taxonomic diversity and vector specificity

Miroslav Kolařík, Steven J. Seybold, Ned Tisserat, Wilhelm De Beer, David M. Rizzo, Jiri Hulcr & Martin Kostovčík
Fungi in the genus Geosmithia (Ascomycota: Hypocreales) are frequent associates of bark beetles and woodborers that colonize hardwood and coniferous trees. One species, Geosmithia morbida, is an economically damaging invasive species. The authors surveyed the Geosmithia species of California and Colorado, USA, to (i) provide baseline data on taxonomy of Geosmithia and beetle vector specificity across the western USA; (ii) investigate the subcortical beetle fauna for alternative vectors of the invasive G. morbida; and (iii)...

Data from: A test of the invasive pathogen hypothesis of bumble bee decline in North America

Sydney A. Cameron, Haw C. Lim, Jeffrey D. Lozier, Michelle Audrey Duennes & Robbin Thorp
Emergent fungal diseases are critical factors in global biodiversity declines. The fungal pathogen Nosema bombi was recently found to be widespread in declining species of North American bumble bees (Bombus), with circumstantial evidence suggesting an exotic introduction from Europe. This interpretation has been hampered by a lack of knowledge of global genetic variation, geographic origin, and changing prevalence patterns of N. bombi in declining North American populations. Thus, the temporal and spatial emergence of N....

Data from: Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life-cycle in field-grown rice

Joseph A. Edwards, Christian Santos-Medellín, Zachary S. Liechty, Bao Nguyen, Eugene Lurie, Shane Eason, Gregory Phillips, Venkatesan Sundaresan & Christian M. Santos-Medellín
Bacterial communities associated with roots impact the health and nutrition of the host plant. The dynamics of these microbial assemblies over the plant life cycle is however, not well understood. Here, we use dense temporal sampling of 1588 samples from root spatial compartments to characterize the bacterial and archaeal components of the root-associated microbiota of field grown rice (Oryza sativa) over the course of three consecutive growing seasons, as well as two sites in diverse...

Data from: Fatal attraction: vegetation responses to nutrient inputs attract herbivores to infectious anthrax carcass sites

Wendy C. Turner, Kyrre L. Kausrud, Yathin S. Krishnappa, Joris P. G. M. Cromsigt, Holly H. Ganz, Isaac Mapaure, Claudine C. Cloete, Zepee Havarua, Martina Küsters, Wayne M. Getz, Nils Chr. Stenseth, K. L. Kausrud, Y. S. Krishnappa, W. C. Turner, J. P. G. M. Cromsigt, H. H. Ganz, W. M. Getz, C. C. Cloete, Z. Havarua & I. Mapaure
Parasites can shape the foraging behaviour of their hosts through cues indicating risk of infection. When cues for risk co-occur with desired traits such as forage quality, individuals face a trade-off between nutrient acquisition and parasite exposure. We evaluated how this trade-off may influence disease transmission in a 3-year experimental study of anthrax in a guild of mammalian herbivores in Etosha National Park, Namibia. At plains zebra (Equus quagga) carcass sites we assessed (i) carcass...

Data from: Flowering time of butterfly nectar food plants is more sensitive to temperature than the timing of butterfly adult flight

Heather M. Kharouba & Mark Vellend
1. Variation among species in their phenological responses to temperature change suggests that shifts in the relative timing of key life cycle events between interacting species are likely to occur under climate warming. However, it remains difficult to predict the prevalence and magnitude of these shifts given that there have been few comparisons of phenological sensitivities to temperature across interacting species. 2. Here, we used a broad-scale approach utilizing collection records to compare the temperature...

Data from: Chaotic genetic patchiness without sweepstakes reproduction in the shore crab Hemigrapsus oregonensis

Brendan H. Cornwell, Jennifer L. Fisher, Steven G. Morgan, Joseph E. Neigel, BH Cornwell, JE Neigel, JL Fisher & SG Morgan
Fine-scale spatial and temporal variation in the genetic composition of benthic recruits, known as chaotic genetic patchiness, is often observed in marine and estuarine species with planktonic larvae. Several explanations have been proposed for chaotic genetic patchiness, including sweepstakes reproductive success, variability in larval source and natural selection. In a survey of the green shore crab Hemigrapsus oregonensis in Bodega Bay, California, allele frequencies at a mitochondrial single nucleotide polymorphism were found to differ significantly...

Data from: Top predators determine how biodiversity is partitioned across time and space

Benjamin G. Van Allen, Nick L. Rasmussen, Christopher J. Dibble, Patrick A. Clay, Volker H.W. Rudolf & Volker H. W. Rudolf
Natural ecosystems are shaped along two fundamental axes, space and time, but how biodiversity is partitioned along both axes is not well understood. Here, we show that the relationship between temporal and spatial biodiversity patterns can vary predictably according to habitat characteristics. By quantifying seasonal and annual changes in larval dragonfly communities across a natural predation gradient we demonstrate that variation in the identity of top predator species is associated with systematic differences in spatio-temporal...

Data from: A connection between colony biomass and death in Caribbean reef-building corals

Daniel J. Thornhill, Randi D. Rotjan, Brian D. Todd, Geoff C. Chilcoat, Roberto Iglesias-Prieto, Todd C. LaJeunesse, Dustin W. Kemp, Jennifer McCabe Reynolds, Gregory W. Schmidt, Thomas Shannon, Mark E. Warner & William K. Fitt
Increased sea-surface temperatures linked to warming climate threaten coral reef ecosystems globally. To better understand how corals and their endosymbiotic dinoflagellates (Symbiodinium spp.) respond to environmental change, tissue biomass and Symbiodinium density of seven coral species were measured on various reefs approximately every four months for up to thirteen years in the Upper Florida Keys, United States (1994–2007), eleven years in the Exuma Cays, Bahamas (1995–2006), and four years in Puerto Morelos, Mexico (2003–2007). For...

Data from: GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems

Ruben Rellán-Álvarez, Guillaume Lobet, Heike Lindner, Pierre-Luc Pradier, Jose Sebastian, Muh-Ching Yee, Yu Geng, Charlotte Trontin, Therese LaRue, Amanda Schrager-Lavelle, Cara H. Haney, Rita Nieu, Julin Maloof, John P. Vogel & José R. Dinneny
Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that...

Data from: Alongshore variation in barnacle populations is determined by surfzone hydrodynamics

Alan L. Shanks, Steven G. Morgan, Jamie MacMahan, Ad J.H.M. Reniers & Ad J. H. M. Reniers
Larvae in the coastal ocean are transported toward shore by a variety of mechanisms. Crossing the surf zone is the last step in a shoreward migration and surf zones may act as semipermeable barriers altering delivery of larvae to the shore. We related variation in the structure of intertidal barnacle populations to surfzone width (surfzone hydrodynamics proxy), wave height, alongshore wind stress (upwelling proxy), solar radiation, and latitude at 40 rocky intertidal sites from San...

Data from: Exceptional convergence on the macroevolutionary landscape in island lizard radiations

D. Luke Mahler, Travis Ingram, Liam J. Revell & Jonathan B. Losos
G. G. Simpson, one of the chief architects of evolutionary biology’s modern synthesis, proposed that diversification occurs on a macroevolutionary adaptive landscape, but landscape models are seldom used to study adaptive divergence in large radiations. We show that for Caribbean Anolis lizards, diversification on similar Simpsonian landscapes leads to striking convergence of entire faunas on four islands. Parallel radiations unfolding at large temporal scales shed light on the process of adaptive diversification, indicating that the...

Data from: Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls

Allison J. Miller, Naim Matasci, Heidi Schwaninger, Mallikarjuna K. Aradhya, Bernard Prins, Gan-Yuan Zhong, Charles Simon, Edward S. Buckler & Sean Myles
Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and...

Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera

Michael G. Branstetter, John T. Longino, Philip S. Ward & Brant C. Faircloth
1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them. 2. We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The...

Data from: Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

Zhao Lai, Nolan C. Kane, Alex Kozik, Kathryn A. Hodgins, Katrina M. Dlugosch, Michael S. Barker, Marta Matvienko, Qian Yu, Kathryn G. Turner, Stephanie A. Pearl, Graeme D.M. Bell, Yi Zou, Chris Grassa, Alessia Guggisberg, Keith L. Adams, James V. Anderson, David P. Horvath, Richard V. Kesseli, John M. Burke, Richard W. Michelmore, Loren H. Rieseberg, Stephanie Anne Pearl & Graeme D. M. Bell
PREMISE OF THE STUDY: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we report on the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic...

Data from: Decoupled diversification dynamics of feeding morphology following a major functional innovation in marine butterflyfishes

Nicolai Konow, Samantha Price, Rickard Abom, David Bellwood, Peter Wainwright & Richard Abom
The diversity of fishes on coral reefs is influenced by the evolution of feeding innovations. For instance, the evolution of an intramandibular jaw joint has aided shifts to corallivory in Chaetodon butterflyfishes following their Miocene colonization of coral reefs. Today, over half of all Chaetodon species consume coral, easily the largest concentration of corallivores in any reef fish family. In contrast with Chaetodon, other chaetodontids, including the long-jawed bannerfishes, remain less intimately associated with coral...

Data from: Plastic transcriptomes stabilize immunity to pathogen diversity: the jasmonic acid and salicylic acid networks within the Arabidopsis/Botrytis pathosystem

Wei Zhang, Jason A. Corwin, Daniel Copeland, Julie Feusier, Robert Eshbaugh, Fang Chen, Susanna Atwell & Daniel J. Kliebenstein
To respond to pathogen attack, selection and associated evolution has led to the creation of plant immune system that are a highly effective and inducible defense system. Central to this system are the plant defense hormones jasmonic acid (JA) and salicylic acid (SA) and crosstalk between the two, which may play an important role in defense responses to specific pathogens or even genotypes. Here, we used the Arabidopsis-B. cinerea pathosystem to test how the host's...

Data from: Commonness, rarity and oligarchies of woody plants in the tropical dry forests of Mexico

John N. Williams, Irma Trejo & Mark W. Schwartz
We assessed woody plant communities in two widely separated forests in the tropical dry forest (TDF) biome of Mexico for evidence of similar patterns of species commonness and rarity. We used belt transects laid out along contour lines (i.e., constant elevation) and stratified across elevation gradients at sites in Jalisco and Oaxaca to sample woody plant species diversity, abundance, relative frequency and basal area. We assembled a combined species list and compared species found in...

Data from: Disentangling the effects of geographic and ecological isolation on genetic differentiation

Gideon S. Bradburd, Peter L. Ralph & Graham M. Coop
Populations can be genetically isolated by both geographic distance and by differences in their ecology or environment that decrease the rate of successful migration. Empirical studies often seek to investigate the relationship between genetic differentiation and some ecological variable(s) while accounting for geographic distance, but common approaches to this problem (such as the partial Mantel test) have a number of drawbacks. In this article, we present a Bayesian method that enables users to quantify the...

Data from: Three-dimensional morphological variability of recent rhynchonellide brachiopod crura

Holly A. Schreiber, Peter D. Roopnarine & Sandra J. Carlson
Crura, the calcareous support structures of the lophophore in rhynchonellide brachiopods, have historically been used to justify higher-level rhynchonellide classification and reveal major evolutionary lineages within rhynchonellides. Seventeen crural types have been described and categorized into four groups based on variation in overall structure and cross-sectional shape, but not evaluated in a quantitative or comprehensive manner. Heterochrony has been hypothesized to play a role in the evolutionary transitions among some types, but the structural, developmental,...

Soil Water Content at MMWD

Peter Hartsough
These data were collected using Decagon (Meter) GS1 sensors at two different depths, 30cm and 60cm. Data were collected hourly and these are mean values at the three different sites.

Heterotrophic N2-fixation contributes to nitrogen economy of a common wetland sedge, Schoenoplectus californicus

Eliska Rejmankova, Dagmara Sirova, Stephanie Castle, Jiri Barta & Heather Carpenter
These data sets document environmental characteristics of sampling locations of Schoenoplectus californicus, california bulrush, throughout its range in the Americas. In addition, the data on nif gene in rhizomes and roots of Schoenoplectus are provided.

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