31 Works

Data from: Vocal traits and diet explain avian sensitivities to anthropogenic noise

Clinton D. Francis
Global population growth has caused extensive human-induced environmental change, including a near-ubiquitous transformation of the acoustical environment due to the propagation of anthropogenic noise. Because the acoustical environment is a critical ecological dimension for countless species to obtain, interpret and respond to environmental cues, highly novel environmental acoustics have the potential to negatively impact organisms that use acoustics for a variety of functions, such as communication and predator/prey detection. Using a comparative approach with 308...

Data from: The energetics of life on the deep seafloor

Craig R. McClain, Andrew P. Allen, Derek P. Tittensor & Michael A. Rex
With frigid temperatures and virtually no in situ productivity, the deep oceans, Earth’s largest ecosystem, are especially energy-deprived systems. Our knowledge of the effects of this energy limitation on all levels of biological organization is very incomplete. Here we use the Metabolic Theory of Ecology to examine the relative roles of carbon flux and temperature in influencing metabolic rate, growth rate, lifespan, body size, abundance, biomass, and biodiversity for life on the deep seafloor. We...

Data from: Networks, trees, and treeshrews: assessing support and identifying conflict with multiple loci and a problematic root

Trina E. Roberts, Eric J. Sargis & Link E. Olson
Multiple unlinked genetic loci often provide a more comprehensive picture of evolutionary history than any single gene can, but analyzing multigene data presents particular challenges. Differing rates and patterns of nucleotide substitution, combined with the limited information available in any data set, can make it difficult to specify a model of evolution. In addition, conflict among loci can be the result of real differences in evolutionary process or of stochastic variance and errors in reconstruction....

Data from: Noise pollution alters ecological services: enhanced pollination and disrupted seed dispersal

Clinton D. Francis, Nathan J. Kleist, Catherine P. Ortega & Alexander Cruz
Noise pollution is a novel, widespread environmental force that has recently been shown to alter the behavior and distribution of birds and other vertebrates, yet whether noise has cumulative, community-level consequences by changing critical ecological services is unknown. Herein, we examined the effects of noise pollution on pollination and seed dispersal and seedling establishment within a study system that isolated the effects of noise from confounding stimuli common to human-altered landscapes. Using observations, vegetation surveys...

Data from: Increased energy promotes size-based niche availability in marine mollusks

Craig R. McClain, Taylor Gullet, Justine Jackson-Ricketts & Peter J. Unmack
Variation in chemical energy, i.e., food, availability is posited to cause variation in body size. However, examinations of the relationship are rare and primarily limited to amniotes and zooplankton. Moreover, the relationship between body size and chemical energy may be impacted by phylogenetic history, clade specific ecology, and heterogeneity of chemical energy in space and time. Considerable work remains to both document patterns in body size over gradients in food availability and understanding the processes...

Data from: Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach

Douglas E. Soltis, Mark E. Mort, Maribeth Latvis, Evgeny V. Mavrodiev, Brian C. O'Meara, Pamela S. Soltis, J. Gordon Burleigh & Rafael Rubio De Casas
Premise of the study: We sought novel evolutionary insights for the highly diverse Saxifragales by constructing a large phylogenetic tree encompassing 36.8% of the species-level biodiversity. Methods: We built a phylogenetic tree for 909 species of Saxifragales and used this hypothesis to examine character evolution for: annual or perennial habit, woody or herbaceous habit, ovary position, petal number, carpel number, and stamen: petal ratio. We employed likelihood approaches to investigate the effect of habit and...

Data from: Early bursts of body size and shape evolution are rare in comparative data

Luke J. Harmon, Jonathan B. Losos, T. Jonathan Davies, Rosemary G. Gillespie, John L. Gittleman, W. Bryan Jennings, Kenneth H. Kozak, Mark A. McPeek, Franck Moreno-Roark, Thomas J. Near, Andy Purvis, Robert E. Ricklefs, Dolph Schluter, , Ole Seehausen, Brian L. Sidlauskas, Omar Torres-Carvajal, Jason T. Weir & Arne Ø. Mooers
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed...

Data from: How much of the world is woody?

Richard G. FitzJohn, Matt W. Pennell, Amy E. Zanne, Peter F. Stevens, David C. Tank, William K. Cornwell & Matthew W. Pennell
1.The question posed by the title of this paper is a basic one, and it is surprising that the answer is not known. Recently assembled trait datasets provide an opportunity to address this, but scaling these datasets to the global scale is challenging because of sampling bias. Although we currently know the growth form of tens of thousands of species, these data are not a random sample of global diversity; some clades are exhaustively characterised,...

Data from: Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies

Thomas Alexander Dececchi, James P. Balhoff, Hilmar Lapp & Paula M. Mabee
The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB; kb.phenoscape.org), to automatically...

Data from: Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution

Prashanti Manda, James P. Balhoff, Hilmar Lapp, Paula Mabee & Todd J. Vision
The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discovery of phenotypic variation among species. Because phenotypes in the KB are annotated using standard ontologies, evolutionary phenotypes can be compared with phenotypes from genetic perturbations in model organisms. To illustrate the power of this approach, we review...

Data from: Data reuse and the open data citation advantage

Heather A. Piwowar & Todd J. Vision
Background: Attribution to the original contributor upon reuse of published data is important both as a reward for data creators and to document the provenance of research findings. Previous studies have found that papers with publicly available datasets receive a higher number of citations than similar studies without available data. However, few previous analyses have had the statistical power to control for the many variables known to predict citation rate, which has led to uncertain...

Data from: The role of continental shelf width in determining freshwater phylogeographic patterns in southeastern Australian pygmy perches (Teleostei: Percichthyidae)

Peter J. Unmack, Michael P. Hammer, Mark Adams, Jerald B. Johnson & Thomas E. Dowling
Biogeographic patterns displayed by obligate freshwater organisms are intimately related to the nature and extent of connectivity between suitable habitats. Two of the more significant barriers to freshwater connections are seawater and major drainage divides. South-eastern Australia provides a contrast between these barriers as it has discrete areas that are likely influenced to a greater or lesser extent by each barrier type. We use continental shelf width as a proxy for the potential degree of...

Data from: Are shy individuals less behaviorally variable? Insights from a captive population of mouse lemurs

Jennifer L. Verdolin & John Harper
Increasingly, individual variation in personality has become a focus of behavioral research in animal systems. Boldness and shyness, often quantified as the tendency to explore novel situations, are seen as personality traits important to the fitness landscape of individuals. Here we tested for individual differences within and across contexts in behavioral responses of captive mouse lemurs (Microcebus murinus) to novel objects, novel foods, and handling. We report consistent differences in behavioral responses for objects and...

Data from: Marine-freshwater transitions are associated with the evolution of dietary diversification in terapontid grunters (Teleostei: Terapontidae)

Aaron M. Davis, Peter J. Unmack, Bradley J. Pusey, Richard G. Pearson & Jerry B. Johnson
The ecological opportunities associated with transitions across the marine-freshwater interface are regarded as an important catalyst of diversification in a range of aquatic taxa. Here, we examined the role of these major habitat transitions and trophic diversification in a radiation of Australasian fishes using a new molecular phylogeny incorporating 37 Terapontidae species. A combined mitochondrial and nuclear gene analysis yielded a well supported tree with most nodes resolved. Ancestral terapontids appear to have been euryhaline...

Data from: Convergent evolution of phenotypic integration and its alignment with morphological diversification in Carribean Anolis ecomorphs

Jason J. Kolbe, Liam J. Revell, Brian Szekely, & Jonathan B Losos
The adaptive landscape and the G-matrix are keys concepts for understanding how quantitative characters evolve during adaptive radiation. In particular, whether the adaptive landscape can drive convergence of phenotypic integration (i.e., the pattern of phenotypic variation and covariation summarized in the P-matrix) is not well studied. We estimated and compared P for 19 morphological traits in eight species of Caribbean Anolis lizards, finding that similarity in P among species was not correlated with phylogenetic distance....

Data from: The biogeography of introgression in the critically endangered African monkey Rungweceubs kipunji

Trina E. Roberts, Tim R. B. Davenport, Kyndall B. P. Hildebrandt, Trevor Jones, William T. Stanley, Eric J. Sargis & Link E. Olson
In the four years since its original description, the taxonomy of the kipunji (Rungwecebus kipunji), a geographically restricted and critically endangered African monkey, has been the subject of much debate, and recent research suggesting that the first voucher specimen of Rungwecebus has baboon mitochondrial DNA has intensified the controversy. We show that Rungwecebus from a second region of Tanzania has a distinct mitochondrial haplotype that is basal to a clade containing all Papio species and...

Data from: Data archiving is a good investment

Heather A. Piwowar, Todd J. Vision & Michael C. Whitlock
Funding agencies are reluctant to support data archiving, even though large research funders such as the National Science Foundation (NSF) and the National Institutes of Health acknowledge its importance for scientific progress. Our quantitative estimates of data reuse indicate that ongoing financial investment in data-archiving infrastructure provides a high scientific return.

Data from: Flower colour and phylogeny along an altitudinal gradient in the Himalaya of Nepal

Mani Shrestha, Adrian Dyer, Prakash Bhattarai, Martin Burd & Adrian G. Dyer
1. Both the phylogenetic structure and trait composition of flowering plant communities may be expected to change with altitude. In particular, floral colours are thought to vary with altitude because Hymenoptera typically decline in importance as pollinators while Diptera and Lepidoptera become more important at higher elevations. Thus, ecological filtering among elevation zones and competitive processes among co-occurring species within zones could influence the floral chromatic cues present at low and high elevations. 2. We...

Data from: Ontogenetic development of intestinal length and relationships to diet in an Australasian fish family (Terapontidae)

Aaron M. Davis, Peter J. Unmack, Bradley J. Pusey, Richard G. Pearson & David L. Morgan
Background: One of the most widely accepted ecomorphological relationships in vertebrates is the negative correlation between intestinal length and proportion of animal prey in diet. While many fish groups exhibit this general pattern, other clades demonstrate minimal, and in some cases contrasting, associations between diet and intestinal length. Moreover, this relationship and its evolutionary derivation have received little attention from a phylogenetic perspective. This study documents the phylogenetic development of intestinal length variability, and resultant...

Data from: Folding wings like a cockroach: a review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania)

István Mikó, Robert S. Copeland, James P. Balhoff, Matthew J. Yoder & Andrew R. Deans
We revise two relatively rare ensign wasp genera, whose species are restricted to Sub-Saharan Africa: Afrevania and Trissevania. Afrevania longipetiolata sp. nov., Trissevania heatherae sp. nov., T. hugoi sp. nov., T. mrimaensis sp. nov. and T. slideri sp. nov. are described, males and females of T. anemotis and Afrevania leroyi are redescribed, and an identification key for Trissevaniini is provided. We argue that Trissevania mrimaensis sp. nov. and T. heatherae sp. nov. populations are vulnerable,...

Data from: Linked morphological changes during palate evolution in early tetrapods

Charles B. Kimmel, Brian Sidlauskas & Jennifer A. Clack
We examined the shapes and sizes of dermal bones of the palate of selected Palaeozoic tetrapods in order to identify the ancestral states of palatal bone morphologies in the earliest tetrapods, to learn how the composition of the palate varies within and among early tetrapod radiations, and recognize evolutionary correlations among the size and shapes of skeletal elements in this important group of animals. We find that whereas the palatal bones themselves and their arrangements...

Data from: Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf Galaxias (G. pusilla)

Peter J. Unmack, Justin C. Bagley, Mark Adams, Michael P. Hammer & Jerald B. Johnson
The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate...

Data from: The Teleost Anatomy Ontology: anatomical representation for the genomics age

Wasila M. Dahdul, John G. Lundberg, Peter E. Midford, James P. Balhoff, Hilmar Lapp, Todd J. Vision, Melissa A. Haendel, Monte Westerfield & Paula M. Mabee
The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis...

Data from: A unified anatomy ontology of the vertebrate skeletal system

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke, Matthew K. Vickaryous, Monte Westerfield & Paula M. Mabee
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate...

Stable resource polymorphism along the benthic littoral-pelagic axis in an invasive crayfish

Iris Lang, Charlotte Evangelista, Rebecca Marie Everts, Géraldine Loot & Julien Cucherousset
Although intraspecific variability is now widely recognized as affecting evolutionary and ecological processes, our knowledge on the importance of intraspecific variability within invasive species is still limited. This is despite the fact that quantifying the extent of within-population morphological divergences associated with the use of different trophic or spatial resources (i.e. resource polymorphism) can help to better predict their ecological impacts on recipient ecosystems. Here, we quantified the extent of resource polymorphism within populations of...

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