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: A new phylogenetic method for identifying exceptional phenotypic diversification

Liam J. Revell, D. Luke Mahler, Pedro R. Peres-Neto & Benjamin D. Redelings
Currently available phylogenetic methods for studying the rate of evolution in a continuously valued character assume that the rate is constant throughout the tree or that it changes along specific branches according to an a priori hypothesis of rate variation provided by the user. Herein, we describe a new method for studying evolutionary rate variation in continuously valued characters given an estimate of the phylogenetic history of the species in our study. According to this...

Data from: Environmental variability and acoustic signals: A multilevel approach in songbirds

Iliana Medina & Clinton D. Francis
Among songbirds, growing evidence suggests that acoustic adaptation of song traits occurs in response to habitat features. Despite extensive study, most research supporting acoustic adaptation has only considered acoustic traits averaged for species or populations, overlooking intraindividual variation of song traits, which may facilitate effective communication in heterogeneous and variable environments. Fewer studies have explicitly incorporated sexual selection, which, if strong, may favour variation across environments. Here, we evaluate the prevalence of acoustic adaptation among...

Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales

Kate L. Hertweck
The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a non-model system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from eleven exemplar...

Data from: Shades of red: bird-pollinated flowers target the specific colour discrimination abilities of avian vision

Mani Shrestha, Adrian G. Dyer, Skye Boyd-Gerny, Bob B. M. Wong & Martin Burd
Colour signals are a major cue in putative pollination syndromes. There is evidence that the reflectance spectra of many flowers target the distinctive visual discrimination abilities of hymenopteran insects, but far less is known about bird-pollinated flowers. Birds are hypothesized to exert different selective pressures on floral colour compared with hymenopterans because of differences in their visual systems. We measured the floral reflectance spectra of 206 Australian angiosperm species whose floral visitors are known from...

Data from: Unraveling the determinants of insular body size shifts

Craig R. McClain, Paul A. P. Durst, Alison G. Boyer & Clinton D. Francis
The island rule, a pattern of size shifts on islands, is an oft-cited but little understood phenomenon of evolutionary biology. Here we explore the evolutionary mechanisms behind the rule in 184 mammal species, testing climatic, ecological, and phylogenetic hypotheses in a robust quantitative framework. Our findings confirm the importance of species’ ecological traits in determining both the strength and the direction of body size changes on islands. Although the island rule pattern appears relatively weak...

Data from: Influence of introgression and geological processes on phylogenetic relationships of western North American mountain suckers (Pantosteus, Catostomidae)

Peter J. Unmack, Thomas E. Dowling, Nina J. Laitinen, Carol L. Secor, Richard L. Mayden, Dennis K. Shiozawa & Gerald R. Smith
Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western...

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...

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...

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