42 Works

Data from: Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

Ron I. Eytan, Benjamin R. Evans, Alex Dornburg, Alan R. Lemmon, Emily Moriarty Lemmon, Peter C. Wainwright & Thomas J. Near
Background: The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes...

Data from: Nutrient distribution and absorption in the colonial hydroid Podocoryna carnea is sequentially diffusive and directional

Leo W. Buss, Christopher P. Anderson, Elena K. Perry, Evan D. Buss & Edward W. Bolton
The distribution and absorption of ingested protein was characterized within a colony of Podocoryna carnea when a single polyp was fed. Observations were conducted at multiple spatial and temporal scales at three different stages of colony ontogeny with an artificial food item containing Texas Red conjugated albumin. Food pellets were digested and all tracer absorbed by digestive cells within the first 2–3 hours post-feeding. The preponderance of the label was located in the fed polyp...

Data from: Rearing temperature influences adult response to changes in mating status

Erica L. Westerman, Antónia Monteiro & Erica Westerman
Rearing environment can have an impact on adult behavior, but it is less clear how rearing environment influences adult behavior plasticity. Here we explore the effect of rearing temperature on adult mating behavior plasticity in the butterfly Bicyclus anynana, a species that has evolved two seasonal forms in response to seasonal changes in temperature. These seasonal forms differ in both morphology and behavior. Females are the choosy sex in cohorts reared at warm temperatures (WS...

Data from: Cascading ecological effects of landscape moderated arthropod diversity

Jeffrey R. Smith & Oswald J. Schmitz
Understanding the mechanisms regulating the diversity and distribution of arthropods is essential to understanding food web interactions and ecosystem functioning. Local arthropod diversity is known to be linked to features of surrounding landscapes, including the area of human-developed land. Yet, how such landscape moderation of diversity affects processes within local sites remains understudied. We report on a study that 1) measured the impacts of human development surrounding old-field habitats of arthropods on arthropod food web...

Data from: Generalized selection to overcome innate immunity selects for host breadth in an RNA virus

Brian R. Wasik, Andrés R. Muñoz-Rojas, Kenichi W. Okamoto, Kathryn Miller-Jensen & Paul E. Turner
Virus-host co-evolution has selected for generalized host defense against viruses, exemplified by interferon production/signaling and other innate immune function in eukaryotes such as humans. Although cell-surface binding primarily limits virus infection success, generalized adaptation to counteract innate immunity across disparate hosts may contribute to RNA virus emergence potential. We examined this idea using vesicular stomatitis virus (VSV) populations prevoously evolved on strictly immune deficient (HeLa) cells, strictly immune competent (MDCK) cells, or on alternating deficient/competent...

Data from: A new barcheek darter species from Buck Creek (Cumberland River System), Kentucky (Percidae: Etheostomatinae: Catonotus: Oopareia)

Thomas J. Near & Matthew R. Thomas
Etheostoma nebra, the Buck Darter, is described as a new species endemic to the Buck Creek system of the Cumberland River drainage in Kentucky, USA. The earliest collection records of Etheostoma nebra date to 1955 and were considered a population of Etheostoma virgatum. Etheostoma nebra is delimited through morphological comparisons with Etheostoma virgatum and phylogenetic analyses using DNA sequences from a mitochondrial gene and five nuclear genes. Etheostoma nebra is distinguished from Etheostoma virgatum by...

Data from: Near-global freshwater-specific environmental variables for biodiversity analyses in 1km resolution

Sami Domisch, Giuseppe Amatulli & Walter Jetz
The lack of freshwater-specific environmental information at sufficiently fine spatial grain hampers broad-scale analyses in aquatic biology, biogeography, conservation, and ecology. Here we present a near-global, spatially continuous, and freshwater-specific set of environmental variables in a standardized 1 km grid. We delineate the sub-catchment for each grid cell along the HydroSHEDS river network and summarize the upstream climate, topography, land cover, surface geology and soil to each grid cell using various metrics (average, minimum, maximum,...

Data from: Understanding the dominant controls on litter decomposition

Mark A. Bradford, Bjorn Berg, Daniel S. Maynard, William R. Wieder & Stephen A. Wood
Litter decomposition is a biogeochemical process fundamental to element cycling within ecosystems, influencing plant productivity, species composition and carbon storage. Climate has long been considered the primary broad-scale control on litter decomposition rates, yet recent work suggests that plant litter traits may predominate. Both decomposition paradigms, however, rely on inferences from cross-biome litter decomposition studies that analyse site-level means. We re-analyse data from a classical cross-biome study to demonstrate that previous research may falsely inflate...

Data from: The selective myosin II inhibitor blebbistatin reversibly eliminates gastrovascular flow and stolon tip pulsations in the colonial hydroid Podocoryna carnea

Noah Connally, Christopher P. Anderson, Jules E. Bolton, Edward W. Bolton & Leo W. Buss
Blebbistatin reversibly disrupted both stolon tip pulsations and gastrovascular flow in the colonial hydroid Podocoryna carnea. Epithelial longitudinal muscles of polyps were unaffected by blebbistatin, as polyps contracted when challenged with a pulse of KCl. Latrunculin B, which sequesters G actin preventing F actin assembly, caused stolons to retract, exposing focal adhesions where the tip epithelial cells adhere to the substratum. These results are consistent with earlier suggestions that non-muscle myosin II provides the motive...

Data from: Plant-soil feedbacks shift from negative to positive with decreasing light in forest understory species

Lauren M. Smith & Heather L. Reynolds
Net pairwise plant–soil feedbacks (PSF) may be an important factor structuring plant communities, yet the influence of abiotic context on PSF is not yet understood. Abiotic factors such as light availability can alter plant–soil interactions, potentially resulting in strong context dependence of PSF. Here, we present an experiment in which we measured whole-soil net pairwise feedbacks amongst six common forest understory species across a gradient of light availability. Light treatments were imposed throughout both phases...

Data from: Bonobos and chimpanzees exhibit human-like framing effects

Christopher Krupenye, Alexandra G. Rosati & Brian Hare
Humans exhibit framing effects when making choices, appraising decisions involving losses differently from those involving gains. To directly test for the evolutionary origin of this bias, we examined decision-making in humans' closest living relatives: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). We presented the largest sample of non-humans to date (n = 40) with a simple task requiring minimal experience. Apes made choices between a ‘framed’ option that provided preferred food, and an alternative option...

Data from: Genetic structure in village dogs reveals a Central Asian domestication origin

Laura M. Shannon, Ryan H. Boyko, Marta Castelhano, Elizabeth Corey, Jessica J. Hayward, Corin McLean, Michelle E. White, Mounir Abi Said, Baddley A. Anita, Nono Bondjengo Ikombe, Jorge Calero, Ana Galov, Marius Hedimbi, Bulu Imam, Rajashree Khalap, Douglas Lally, Andrew Masta, Kyle C. Oliveira, Lucía Pérez, Julia Randall, Nguyen Minh Tam, Francisco J. Trujillo-Cornejo, Carlos Valeriano, Nathan B. Sutter, Rory J. Todhunter … & Adam R. Boyko
Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we...

Data from: Climate change impacts on bumblebees converge across continents

Jeremy T. Kerr, Alana Pindar, Paul Galpern, Laurence Packer, Stuart M. Roberts, Pierre Rasmont, Oliver Schweiger, Sheila R. Colla, Leif L. Richardson, David L. Wagner, Lawrence F. Gall, Derek S. Sikes & Alberto Pantoja
For many species, geographical ranges are expanding toward the poles in response to climate change, while remaining stable along range edges nearest the equator. Using long-term observations across Europe and North America over 110 years, we tested for climate change–related range shifts in bumblebee species across the full extents of their latitudinal and thermal limits and movements along elevation gradients. We found cross-continentally consistent trends in failures to track warming through time at species’ northern...

Data from: Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach

Jeannine Cavender-Bares, Antonio González-Rodríguez, Deren A. R. Eaton, Andrew A. L. Hipp, Anne Beulke & Paul S. Manos
The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil-calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron...

Data from: Cognitive capacities for cooking in chimpanzees

Felix Warneken & Alexandra G. Rosati
The transition to a cooked diet represents an important shift in human ecology and evolution. Cooking requires a set of sophisticated cognitive abilities, including causal reasoning, self-control and anticipatory planning. Do humans uniquely possess the cognitive capacities needed to cook food? We address whether one of humans' closest relatives, chimpanzees (Pan troglodytes), possess the domain-general cognitive skills needed to cook. Across nine studies, we show that chimpanzees: (i) prefer cooked foods; (ii) comprehend the transformation...

Data from: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

Allison Y. Hsiang, Daniel J. Field, Timothy H. Webster, Adam D. B. Behlke, Matthew B. Davis, Rachel A. Racicot & Jacques A. Gauthier
Background: The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive...

Data from: Life in the unthinking depths: energetic constraints on encephalization in marine fishes

Teresa L. Iglesias, Alex Dornburg, Matthew C. Brandley, Michael E. Alfaro & Dan L. Warren
Several hypotheses have been proposed to explain the limitation of brain size in vertebrates. Here we test three hypotheses of brain size evolution using marine teleost fishes: the direct metabolic constraints hypothesis, the expensive tissue hypothesis, and the temperature-dependent hypothesis. Our analyses indicate that there is a robust positive correlation between encephalization and basal metabolic rate that spans the full range of depths occupied by teleosts from the epipelagic (< 200m), mesopelagic (200-1000m), and bathypelagic...

Data from: Distributions of irritative zones are related to individual alterations of resting-state networks in focal epilepsy

Yinchen Song, Basavaraju G. Sanganahalli, Fahmeed Hyder, Wei-Chiang Lin & Jorge J. Riera
Alterations in the connectivity patterns of the fMRI-based resting-state networks (RSNs) have been reported in several types of epilepsies. Evidence pointed out these alterations might be associated with the genesis and propagation of interictal epileptiform discharges (IEDs). IEDs also evoke blood-oxygen-level dependent (BOLD) responses, which have been used to delineate irritative zones during preoperative work-up. Therefore, one may expect a relationship between the topology of the IED-evoked BOLD response network and the altered spatial patterns...

Data from: Rate of novel host invasion affects adaptability of evolving RNA virus lineages

Valerie J. Morley, Sandra Y. Mendiola & Paul E. Turner
Although differing rates of environmental turnover should be consequential for the dynamics of adaptive change, this idea has been rarely examined outside of theory. In particular, the importance of RNA viruses in disease emergence warrants experiments testing how differing rates of novel host invasion may impact the ability of viruses to adaptively shift onto a novel host. To test whether the rate of environmental turnover influences adaptation, we experimentally evolved 144 Sindbis virus lineages in...

Data from: Diffusion tensor imaging in patients with glioblastoma multiforme using the supertoroidal model

Choukri Mekkaoui, Philippe Metellus, William J. Kostis, Roberto Martuzzi, Fabricio R. Pereira, Jean-Paul Beregi, Timothy G. Reese, Todd R. Constable & Marcel P. Jackowski
Purpose: Diffusion Tensor Imaging (DTI) is a powerful imaging technique that has led to improvements in the diagnosis and prognosis of cerebral lesions and neurosurgical guidance for tumor resection. Traditional tensor modeling, however, has difficulties in differentiating tumor-infiltrated regions and peritumoral edema. Here, we describe the supertoroidal model, which incorporates an increase in surface genus and a continuum of toroidal shapes to improve upon the characterization of Glioblastoma multiforme (GBM). Materials and Methods: DTI brain...

Data from: Genetic stock composition of marine bycatch reveals disproportional impacts on depleted river herring genetic stocks

Daniel J. Hasselman, Eric C. Anderson, Emily E. Argo, N. David Bethoney, Stephen R. Gephard, David M. Post, Bradley P. Schondelmeier, Thomas F. Schultz, Theodore V. Willis & Eric P. Palkovacs
Bycatch of mid-trophic level anadromous fishes that connect marine and freshwater ecosystems is a growing conservation concern. Anadromous alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) are important components of coastal freshwater and marine food webs, but have experienced dramatic declines in the abundances of spawning adults. Freshwater-focused restoration efforts have yielded few consistent signs of recovery; raising concerns that bycatch in Northwest Atlantic commercial fisheries may be negating these conservation actions. Using data from...

Data from: Environmental fluctuations promote intraspecific diversity and population persistence via inflationary effects

Daniel J. Wieczynski & David A. Vasseur
The impact of temporal variation in the environment, specifically the amount of temporal autocorrelation, on population processes is of growing interest in ecology and evolutionary biology. It was recently discovered that temporal autocorrelation in the environment can significantly increase the abundance of populations that would otherwise have low, or even negative long-term growth rates (via so-called ‘inflationary effects’), provided that immigration from another source prevents extinction. Here we use a mathematical model to ask whether...

Data from: Multiple paternity in the Norway rat, Rattus norvegicus, from urban slums in Salvador, Brazil

Federico Costa, Jonathan L. Richardson, Kirstin Dion, Carol Mariani, Arsinoe C. Pertile, Mary K. Burak, James E. Childs, Albert I. Ko & Adalgisa Caccone
The Norway rat, Rattus norvegicus, is one of the most important pest species globally and the main reservoir of leptospires causing human leptospirosis in the urban slums of tropical regions. Rodent control is a frequent strategy in those settings to prevent the disease but rapid growth from residual populations and immigration limit the long-term effectiveness of interventions. To characterize the breeding ecology of R. norvegicus and provide needed information for the level of genetic mixing,...

Data from: Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation

Thomas J. Near, Alex Dornburg, Richard C. Harrington, Claudio Oliveira, Theodore W. Pietsch, Christine E. Thacker, Takashi P. Satoh, Eri Katayama, Peter C. Wainwright, Joseph T. Eastman & Jeremy M. Beaulieu
Background: Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited as the sister lineage of notothenioids remains unidentified. The phylogenetic placement of notothenioids among major lineages of perciform fishes, which include sculpins, rockfishes, sticklebacks, eelpouts, scorpionfishes, perches, groupers and soapfishes, remains unresolved. We investigate...

Data from: Whole genome sequencing shows sleeping sickness relapse is due to parasite regrowth and not reinfection

Joshua Richardson, Benjamin Evans, Patient P. Pyana, Nick Van Reet, Mark Sistrom, Philippe Buscher, Serap Aksoy, Aldalgisa Caccone, Joshua B. Richardson & Adalgisa Caccone
The trypanosome Trypanosoma brucei gambiense (Tbg) is a cause of human African trypanosomiasis (HAT) endemic to many parts of sub-Saharan Africa. The disease is almost invariably fatal if untreated and there is no vaccine, which makes monitoring and managing drug resistance highly relevant. A recent study of HAT cases from the Democratic Republic of the Congo reported a high incidence of relapses in patients treated with melarsoprol. Of the 19 Tbg strains isolated from patients...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Yale University
  • Duke University
  • Columbia University
  • National Autonomous University of Mexico
  • University of Tennessee at Knoxville
  • University of Connecticut
  • University of Sao Paulo
  • University of California, Santa Cruz
  • Harvard University
  • National Institute for Mathematical and Biological Synthesis