54 Works

Data from: Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae)

Charles W. Linkem, Vladimir N. Minin & Adam D. Leaché
The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies...

Data from: A submersible, off-axis holographic microscope for detection of microbial motility and morphology in aqueous and icy environments

Christian A. Lindensmith, Stephanie Rider, Manuel Bedrossian, J. Kent Wallace, Eugene Serabyn, Gordon M. Showalter, Jody W. Deming & Jay L. Nadeau
Sea ice is an analog environment for several of astrobiology’s near-term targets: Mars, Europa, Enceladus, and perhaps other Jovian or Saturnian moons. Microorganisms, both eukaryotic and prokaryotic, remain active within brine channels inside the ice, making it unnecessary to penetrate through to liquid water below in order to detect life. We have developed a submersible digital holographic microscope (DHM) that is capable of resolving individual bacterial cells, and demonstrated its utility for immediately imaging samples...

Data from: Are more diverse parts of the mammalian skull more labile?

Marta Linde-Medina, Julia C. Boughner, Sharlene E. Santana & Rui Diogo
Morphological variation is unevenly distributed within the mammalian skull; some of its parts have diversified more than others. It is commonly thought that this pattern of variation is mainly the result of the structural organization of the skull, as defined by the pattern and magnitude of trait covariation. Patterns of trait covariation can facilitate morphological diversification if they are aligned in the direction of selection, or these patterns can constrain diversification if oriented in a...

Data from: Precipitation alters interactions in a grassland ecological community

Nicolas Deguines, Justin S. Brashares & Laura R. Prugh
Climate change is transforming precipitation regimes world-wide. Changes in precipitation regimes are known to have powerful effects on plant productivity, but the consequences of these shifts for the dynamics of ecological communities are poorly understood. This knowledge gap hinders our ability to anticipate and mitigate the impacts of climate change on biodiversity. Precipitation may affect fauna through direct effects on physiology, behaviour or demography, through plant-mediated indirect effects, or by modifying interactions among species. In...

Data from: Tracing the dynamics of gene transcripts after organismal death

Alexander E. Pozhitkov, Rafik Neme, Tomislav Domazet-Lošo, Brian G. Leroux, Shivani Soni, Diethard Tautz & Peter A. Noble
In life, genetic and epigenetic networks precisely coordinate the expression of genes—but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became...

Data from: A new Late Cretaceous iguanomorph from North America and the origin of New World Pleurodonta (Squamata, Iguania)

David G. DeMar, Jack L. Conrad, Jason J. Head, David J. Varricchio & Gregory P. Wilson
Iguanomorpha (stem + crown Iguania) is a diverse squamate clade with members that predominate many modern American lizard ecosystems. However, the temporal and palaeobiogeographic origins of its constituent crown clades (e.g. Pleurodonta (basilisks, iguanas, and their relatives)) are poorly constrained, mainly due to a meagre Mesozoic-age fossil record. Here, we report on two nearly complete skeletons from the Late Cretaceous (Campanian) of North America that represent a new and relatively large-bodied and possibly herbivorous iguanomorph...

Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

James Starrett, Shahan Derkarabetian, Marshal Hedin, , John E. McCormack, Brant C. Faircloth & Robert W. Bryson
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic...

Data from: Use of glacial fronts by narwhals (Monodon monoceros) in West Greenland

Kristin L. Laidre, Twila Moon, Donna D.W. Hauser, Richard McGovern, Mads Peter Heide-Joergensen, Rune Dietz, Benjamin Hudson, Donna D. W. Hauser & Ben Hudson
Glacial fronts are important summer habitat for narwhals (Monodon monoceros), however, no studies have quantified which glacial properties attract whales. We investigated the importance of glacial habitats using telemetry data from n=15 whales in September 1993-1994 and 2006-2007 in Melville Bay, West Greenland. For 41 marine-terminating glaciers, we estimated 1) narwhal presence/absence, 2) number of 24 h periods spent at glaciers, and 3) the fraction of narwhals that visited each glacier (at 5, 7, and...

Data from: Forty years of seagrass population stability and resilience in an urbanizing estuary

Andrew Olaf Shelton, Tessa B. Francis, Blake E. Feist, Gregory D. Williams, Adam Lindquist, Phillip S. Levin & Philip S. Levin
Coasts and estuaries contain among the most productive and ecologically important habitats in the world and face intense pressure from current and projected human activities, including coastal development. Seagrasses are a key habitat feature in many estuaries perceived to be in widespread decline owing to human actions. We use spatio-temporal models and a 41-year time series from 100s of km of shoreline which includes over 160 000 observations from Puget Sound, Washington, USA, to examine...

Data from: Multiple natural enemies cause distance-dependent mortality at the seed-to-seedling transition

Evan C. Fricke, Joshua J. Tewksbury & Haldre S. Rogers
Specialised natural enemies maintain forest diversity by reducing tree survival in a density- or distance-dependent manner. Fungal pathogens, insects and mammals are the enemy types most commonly hypothesised to cause this phenomenon. Still, their relative importance remains largely unknown, as robust manipulative experiments have generally targeted a single enemy type and life history stage. Here, we use fungicide, insecticide and physical exclosure treatments to isolate the impacts of each enemy type on two life history...

Data from: Phylogeny and new taxonomy of the Booted Eagles (Accipitriformes: Aquilinae)

Heather R. L. Lerner, Les Christidis, Anita Gamauf, Carole Griffiths, Elisabeth Haring, Christopher J. Huddleston, Sonia Kabra, Annett Kocum, Meade Krosby, Kirsti Kvaloy, David Mindell, Pamela Rasmussen, Nils Rov, Rachel Wadleigh, Michael Wink & Jan Ove Gjershaug
We present a phylogeny of all booted eagles (38 extant and one extinct species) based on analysis of published sequences from seven loci. We find molecular support for five major clades within the booted eagles: Nisaetus (10 species), Spizaetus (4 species), Clanga (3 species), Hieraaetus (6 species) and Aquila (11 species), requiring generic changes for 14 taxa. Additionally, we recommend that the Long-crested Eagle (Lophaetus occipitalis) and the Black Eagle (Ictinaetus malaiensis) remain in their...

Data from: Go big or go fish: morphological specializations in carnivorous bats

Sharlene E. Santana & Elena Cheung
Specialized carnivory is relatively uncommon across mammals, and bats constitute one of the few groups in which this diet has evolved multiple times. While size and morphological adaptations for carnivory have been identified in other taxa, it is unclear what phenotypic traits characterize the relatively recent evolution of carnivory in bats. To address this gap, we apply geometric morphometric and phylogenetic comparative analyses to elucidate which characters are associated with ecological divergence of carnivorous bats...

Data from: Genetic signatures of ecological diversity along an urbanization gradient

Ryan P. Kelly, James L. O'Donnell, Natalie C. Lowell, Andrew O. Shelton, Jameal F. Samhouri, Shannon M. Hennessey, Blake E. Feist & Gregory D. Williams
Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore...

Data from: Spatial and temporal dynamics and value of nature-based recreation, estimated via social media

Laura J. Sonter, Keri B. Watson, Spencer A. Wood & Taylor H. Ricketts
Conserved lands provide multiple ecosystem services, including opportunities for nature-based recreation. Managing this service requires understanding the landscape attributes underpinning its provision, and how changes in land management affect its contribution to human wellbeing over time. However, evidence from both spatially explicit and temporally dynamic analyses is scarce, often due to data limitations. In this study, we investigated nature-based recreation within conserved lands in Vermont, USA. We used geotagged photographs uploaded to the photo-sharing website...

Data from: Disparities in influenza mortality and transmission related to sociodemographic factors within Chicago in the pandemic of 1918

Kyra H. Grantz, Madhura S. Rane, Henrik Salje, Gregory E. Glass, Stephen E. Schachterle & Derek A. T. Cummings
Social factors have been shown to create differential burden of influenza across different geographic areas. We explored the relationship between potential aggregate-level social determinants and mortality during the 1918 influenza pandemic in Chicago using a historical dataset of 7,971 influenza and pneumonia deaths. Census tract-level social factors, including rates of illiteracy, homeownership, population, and unemployment, were assessed as predictors of pandemic mortality in Chicago. Poisson models fit with generalized estimating equations (GEEs) were used to...

Data from: Quantifying thermal extremes and biological variation to predict evolutionary responses to changing climate

Joel G. Kingsolver & Lauren B. Buckley
Central ideas from thermal biology, including thermal performance curves and tolerances, have been widely used to evaluate how changes in environmental means and variances generate changes in fitness, selection and microevolution in response to climate change. We summarize the opportunities and challenges for extending this approach to understanding the consequences of extreme climatic events. Using statistical tools from extreme value theory, we show how distributions of thermal extremes vary with latitude, time scale and climate...

Data from: Neonatal activation of the xenobiotic-sensors PXR and CAR results in acute and persistent down-regulation of PPARα-signaling in mouse liver

Cindy Yanfei Li, Sunny Lihua Cheng, Theo K. Bammler & Julia Yue Cui
Safety concerns have emerged regarding the potential long-lasting effects due to developmental exposure to xenobiotics. The pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are critical xenobiotic-sensing nuclear receptors that are highly expressed in liver. The goal of this study was to test our hypothesis that neonatal exposure to PXR- or CAR-activators not only acutely but also persistently regulates the expression of drug-processing genes (DPGs). A single dose of the PXR-ligand PCN (75 mg/kg),...

Data from: A cross-continental comparison of plant and beetle responses to retention of forest patches during timber harvest

Susan C. Baker, Charles B. Halpern, Timothy J. Wardlaw, Christel Kern, Graham J. Edgar, Russell J. Thomson, Richard E. Bigley, Jerry F. Franklin, Kamal J.K. Gandhi, Lena Gustafsson, Samuel Johnson, Brian J. Palik, Thomas A. Spies, E. Ashley Steel, Jan Weslien, Joachim Strengbom & Kamal J. K. Gandhi
Timber harvest can adversely affect forest biota. Recent research and application suggest that retention of mature forest elements (‘retention forestry’), including unharvested patches (or ‘aggregates’) within larger harvested units, can benefit biodiversity compared to clearcutting. However, it is unclear whether these benefits can be generalized among the diverse taxa and biomes in which retention forestry is practiced. Lack of comparability in methods for sampling and analysing responses to timber harvest and edge creation presents a...

Data from: Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation

Ramray Bhat, Mahul Chakraborty, Tilmann Glimm, Thomas A. Stewart & Stuart A. Newman
Background: A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied patterns of nodules, bars and plates, while tetrapod limbs exhibit tandem arrays of few, proximodistally increasing numbers of elements. We applied a comparative genomic and protein evolution approach to understand the origin of...

Data from: Physiological plasticity and local adaptation to elevated pCO2 in calcareous algae: an ontogenetic and geographic approach

Jacqueline L. Padilla-Gamiño, Juan D. Gaitán-Espitia, Morgan W. Kelly & Gretchen E. Hofmann
To project how ocean acidification will impact biological communities in the future, it is critical to understand the potential for local adaptation and the physiological plasticity of marine organisms throughout their entire life cycle, as some stages may be more vulnerable than others. Coralline algae are ecosystem engineers that play significant functional roles in oceans worldwide, and are considered vulnerable to ocean acidification. Using different stages of coralline algae, we tested the hypothesis that populations...

Data from: Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors

Brian Helmuth, Francis Choi, Allison Matzelle, Jessica L. Torossian, Scott L. Morella, K. A. S. Mislan, Lauren Yamane, Denise Strickland, P. Lauren Szathmary, Sarah Gilman, Alyson Tockstein, Thomas J. Hilbish, Michael T. Burrows, Anne Marie Power, Elizabeth Gosling, Nova Mieszkowska, Christopher D. G. Harley, Michael Nishizaki, Emily Carrington, Bruce Menge, Laura Petes, Melissa M. Foley, Angela Johnson, Megan Poole, Mae M. Noble … & Gerardo Zardi
At a proximal level, the physiological impacts of global climate change on ectothermic organisms are manifest as changes in body temperatures. Especially for plants and animals exposed to direct solar radiation, body temperatures can be substantially different from air temperatures. We deployed biomimetic sensors that approximate the thermal characteristics of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers recorded temperatures at 10–30 min intervals nearly continuously at multiple intertidal elevations. Comparisons against direct measurements...

Data from: Chimpanzee females queue but males compete for social status

Steffen Foerster, Mathias Franz, Carson M. Murray, Ian C. Gilby, Joseph T. Feldblum, Kara K. Walker & Anne E. Pusey
Dominance hierarchies are widespread in animal social groups and often have measureable effects on individual health and reproductive success. Dominance ranks are not static individual attributes, however, but instead are influenced by two independent processes: 1) changes in hierarchy membership and 2) successful challenges of higher-ranking individuals. Understanding which of these processes dominates the dynamics of rank trajectories can provide insights into fitness benefits of within-sex competition. This question has yet to be examined systematically...

Data from: Biodiversity-ecosystem functioning relationships in long-term time series and palaeoecological records: deep sea as a test bed

Moriaki Yasuhara, Hideyuki Doi, Chih-Lin Wei, Roberto Danovaro & Sarah E. Myhre
The link between biodiversity and ecosystem functioning (BEF) over long temporal scales is poorly understood. Here, we investigate biological monitoring and palaeoecological records on decadal, centennial and millennial time scales from a BEF framework, by using deep-sea, soft-sediment environments as a test bed. Results generally show positive BEF relationships, in agreement with BEF studies based on present-day spatial analyses and short-term manipulative experiments. However, the deep-sea BEF relationship is much noisier across longer time scales...

Data from: Lifespan and reproductive cost explain interspecific variation in the optimal onset of reproduction

Emeline Mourocq, Pierre Bize, Sandra Bouwhuis, Russell Bradley, Anne Charmantier, Carlos De La Cruz, Szymon Marian Obniak, Richard H. M. Espie, Márton Herenyi, Hermann Hötker, Oliver Kruger, John Marzluff, Anders P. Møller, Shinichi Nakagawa, Richard A. Phillips, Andrew N. Radford, Alexandre Roulin, János Török, Juliana Valencia, Martijn Van De Pol, Ian G. Warkentin, Isabel S. Winney, Andrew G. Wood, Michael Griesser & Szymon M. Drobniak
Fitness can be profoundly influenced by the age at first reproduction (AFR), but to date the AFR-fitness relationship only has been investigated intraspecifically. Here we investigated the relationship between AFR and average lifetime reproductive success (LRS) across 34 bird species. We assessed differences in the deviation of the Optimal AFR (i.e., the species-specific AFR associated with the highest LRS) from the age at sexual maturity, considering potential effects of life-history as well as social and...

Data from: Global test of Eltonian niche conservatism of nonnative freshwater fish species between their native and introduced ranges

Lise Comte, Julien Cucherousset & Julian D. Olden
Despite growing evidence that biotic interactions limit the distribution of species and their potential redistribution under climate change, the recent surge of interest in niche conservatism has predominantly focused on the Grinellian (abiotic) niche, whereas few studies have attempted to quantify potential lability in the Eltonian (biotic or trophic) niche. Here, we test for conservatism in the Eltonian niche of 32 freshwater fish species between their introduced and native ranges from 435 populations across the...

Registration Year

  • 2016

Resource Types

  • Dataset


  • University of Washington
  • Stanford University
  • Duke University
  • Oregon State University
  • Occidental College
  • University of California, Santa Barbara
  • University of Oxford
  • Northwest Fisheries Science Center
  • University of North Carolina
  • Australian National University