54 Works

Data from: Indexed PCR primers induce template-specific bias in large-scale DNA sequencing studies

James L. O'Donnell, Ryan P. Kelly, Jesse A. Port, Natalie C. Lowell & James L. O’Donnell
Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at all levels, from genetic variation and expression to ecological community assemblage. However, the number of reads produced per sequencing run far exceeds the number required per sample for many applications, compelling researchers to sequence multiple samples per run in order to maximize efficiency. For studies that include a PCR step, this can be accomplished using primers that include an index sequence...

Data from: Estimation of a killer whale (Orcinus orca) population’s diet using sequencing analysis of DNA from feces

Michael J. Ford, Jennifer Hempelmann, M. Bradley Hanson, Katherine L. Ayres, Robin W. Baird, Candice K. Emmons, Jessica I. Lundin, Gregory S. Schorr, Samuel K. Wasser & Linda K. Park
Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their...

Data from: Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc

Hila Levy, Gemma V. Clucas, Alex D. Rogers, Adam D. Leaché, Kate L. Ciborowski, Michael J. Polito, Heather J. Lynch, Michael J. Dunn & Tom Hart
Climate change, fisheries pressure on penguin prey, and direct human disturbance of wildlife have all been implicated in causing large shifts in the abundance and distribution of penguins in the Southern Ocean. Without mark-recapture studies, understanding how colonies form and, by extension, how ranges shift is challenging. Genetic studies, particularly focused on newly established colonies, provide a snapshot of colonisation and can reveal the extent to which shifts in abundance and occupancy result from changes...

Data from: Intrinsic and extrinsic drivers of source-sink dynamics

Julie A. Heinrichs, Joshua L. Lawler & Nathan H. Schumaker
Many factors affect the presence and exchange of individuals among subpopulations and influence not only the emergence, but the strength of ensuing source–sink dynamics within metapopulations. Yet their relative contributions remain largely unexplored. To help identify the characteristics of empirical systems that are likely to exhibit strong versus weak source–sink dynamics and inform their differential management, we compared the relative roles of influential factors in strengthening source–sink dynamics. In a series of controlled experiments within...

Data from: Modelling tooth–prey interactions in sharks: the importance of dynamic testing

Katherine A. Corn, Stacy C. Farina, Jeffrey Brash & Adam P. Summers
The shape of shark teeth varies among species, but traditional testing protocols have revealed no predictive relationship between shark tooth morphology and performance. We developed a dynamic testing device to quantify cutting performance of teeth. We mimicked head-shaking behaviour in feeding large sharks by attaching teeth to the blade of a reciprocating power saw fixed in a custom-built frame. We tested three tooth types at biologically relevant speeds and found differences in tooth cutting ability...

Data from: Always chew your food: freshwater stingrays use mastication to process tough insect prey

Matthew A. Kolmann, Kenneth C. Welch, Adam P. Summers & Nathan R. Lovejoy
Chewing, characterized by shearing jaw motions and high-crowned molar teeth, is considered an evolutionary innovation that spurred dietary diversification and evolutionary radiation of mammals. Complex prey-processing behaviours have been thought to be lacking in fishes and other vertebrates, despite the fact that many of these animals feed on tough prey, like insects or even grasses. We investigated prey capture and processing in the insect-feeding freshwater stingray Potamotrygon motoro using high-speed videography. We find that Potamotrygon...

Data from: The comparative hydrodynamics of rapid rotation by predatory appendages

Mathew J. McHenry, Philip S. L. Anderson, Sam Van Wassenbergh, David Matthews, Adam Summers & S. N. Patek
Countless aquatic animals rotate appendages through the water, yet fluid forces are typically modeled with translational motion. To elucidate the hydrodynamics of rotation, we analyzed the raptorial appendages of mantis shrimp (Stomatopoda) using a combination of flume experiments, mathematical modeling and phylogenetic comparative analyses. We found that computationally efficient blade-element models offered an accurate first-order approximation of drag, when compared with a more elaborate computational fluid-dynamic model. Taking advantage of this efficiency, we compared the...

Data from: A public database of memory and naive B-cell receptor sequences

William S. DeWitt, Paul Lindau, Thomas M. Snyder, Anna M. Sherwood, Marissa Vignali, Christopher S. Carlson, Philip D. Greenberg, Natalie Duerkopp, Ryan O. Emerson & Harlan S. Robins
The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of...

Data from: Hidden histories of gene flow in highland birds revealed with genomic markers

Eugenia Zarza, Brant C. Faircloth, Whitney L. E. Tsai, , John Klicka, John E. McCormack, Whitney L.E. Tsai & Robert W. Bryson
Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial...

Data from: Relative importance of abiotic, biotic, and disturbance drivers of plant community structure in the sagebrush steppe

Rachel M. Mitchell, Jonathan D. Bakker, John B. Vincent & G. Matt Davies
Abiotic conditions, biotic factors, and disturbances can act as filters that control community structure and composition. Understanding the relative importance of these drivers would allow us to understand and predict the causes and consequences of changes in community structure. We used long-term data (1989-2002) from the sagebrush steppe in Washington state, USA, to ask three questions: 1) What are the key drivers of community-level metrics of community structure? 2) Do community-level metrics and functional groups...

Data from: Tooth occlusal morphology in the durophagous marine reptiles, Placodontia (Reptilia: Sauropterygia)

Stephanie B. Crofts, James M. Neenan, Torsten M. Scheyer & Adam P. Summers
Placodontia were a group of marine reptiles that lived in shallow nearshore environments during the Triassic. Based on tooth morphology it has been inferred that they were durophagous, but tooth morphology differs among species: placodontoid placodonts have teeth described as hemispherical, and the teeth of more highly nested taxa within the cyamodontoid placodonts have been described as flat. In contrast, the sister taxon to the placodonts, Palatodonta bleekeri, like many other marine reptiles, has tall...

Data from: Describing a developing hybrid zone between red wolves and coyotes in eastern North Carolina, USA

Justin H. Bohling, Justin Dellinger, Justin N. McVey, David T. Cobb, Christopher E. Moorman, Lisette P. Waits & Justin M. McVey
When hybridizing species come into contact, understanding the processes that regulate their interactions can help predict the future outcome of the system. This is especially relevant in conservation situations where human activities can influence hybridization dynamics. We investigated a developing hybrid zone between red wolves and coyotes in North Carolina, USA to elucidate patterns of hybridization in a system heavily managed for preservation of the red wolf genome. Using noninvasive genetic sampling of scat, we...

Data from: Geographic extent of introgression in Sebastes mentella and its effect on genetic population structure

Atal Saha, Torild Johansen, Rasmus Hedeholm, Einar E. Nielsen, Jon-Ivar Westgaard, Lorenz Hauser, Benjamin Planque, Steven X. Cadrin & Jesper Boje
Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2,562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the “shallow” and “deep” groups, beyond the...

Data from: Positive selection of the TRIM family regulatory region in primate genomes

Dan-Dan He, Yueer Lu, Rachel Gittelman, Yabin Jin, Fei Ling, Joshua Akey & Akey Joshua
Viral selection pressure has acted on restriction factors that play an important role in the innate immune system by inhibiting the replication of viruses during primate evolution. Tripartite motif-containing (TRIM) family members are some of these restriction factors. It is becoming increasingly clear that gene expression differences, rather than protein-coding regions changes, could play a vital role in the anti-retroviral immune mechanism. Increasingly, recent studies have created genome-scale catalogues of DNase I hypersensitive sites (DHSs),...

Eurasian pollen data from 21 kiloannum to the present

A. Binney. H., A. Lozhkin, P Anderson, A. Andreev, E. Bezrukova, T. Blyakharchuk, V. Jankovska, I. Khazhina, S. Krivonogov, K. Kremenetski, E. Novenko, N. Ryabogina, N. Solovieva & V. Zernitzkaya
This dataset contains fossil and modern pollen data collated during a workshop held in the UK in 2008 as part of the NERC (Quantifying and Understanding the Earth System) QUEST programme. The 96 sampling sites are located from 24°E (western Ukraine and Belarus) to easternmost Siberia, and lie north of latitude 40°N. The sample ages range from 21ka to present and are assigned to 1,000 year time slices. The dataset has been checked for consistent...

Data from: Genomic islands of divergence linked to ecotypic variation in sockeye salmon

Wesley A. Larson, Morten T. Limborg, Garrett J. McKinney, Daniel E. Schindler, Jim E. Seeb, Lisa W. Seeb & James E. Seeb
Regions of the genome displaying elevated differentiation (genomic islands of divergence) are thought to play an important role in local adaptation, especially in populations experiencing high gene flow. However, the characteristics of these islands as well as the functional significance of genes located within them remain largely unknown. Here, we used data from thousands of SNPs aligned to a linkage map to investigate genomic islands of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka)...

Data from: Characteristics and outcomes of women utilizing emergency medical services for third-trimester pregnancy-related complaints in India: a prospective observational study

Matthew C. Strehlow, Jennifer A. Newberry, Corey B. Bills, Hyeyoun Min, Ann E. Evensen, Lawrence Leeman, Elizabeth A. Pirrotta, G. V. Ramana Rao & S. V. Mahadevan
Objectives: Characterize the demographics, management, and outcomes of obstetric patients transported by emergency medical services (EMS). Design: Prospective observational study. Setting: Five Indian states utilizing a centralized EMS agency that transported 3.1 million pregnant women in 2014. Participants: This study enrolled a convenience sample of 1684 women in third trimester of pregnancy calling with a “pregnancy-related” complaint for free-of-charge ambulance transport. Calls were deemed “pregnancy-related” if categorized by EMS dispatchers as “pregnancy”, “childbirth”, “miscarriage”, or...

Data from: Bayesian estimation of the global biogeographical history of the Solanaceae

Julia Dupin, Nicholas J. Matzke, Tiina Särkinen, Sandra Knapp, Richard G. Olmstead, Lynn Bohs & Stacey D. Smith
Aim: The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution. Location:...

Shrub Consumption and Immediate Changes in Shrub Community and Spatial Patterns by Reintroduced Fire in Yosemite National Park, California, USA; Supplemental Information

James Lutz, T. J. Furniss, S. J. Germain, K. M. L. Becker, Erika Blomdahl, S. A. Jeronimo, C. Alina Cansler, J. A. Freund, M. E. Swanson & A. J. Larson
Fire behavior in the Yosemite Forest Dynamics Plot during the Rim Fire as captured by the USFS Fire Behavior Assessment Team and reported in Ewell, C., D.F. Smith, M. Hilden, S. Greene, D. Coultrap, K. Robinson, N. Vaillant, A. Reiner, T. Norman. 2015. 2013 Rim Fire Stanislaus National Forest and Yosemite National Park Fire Behavior Assessment Team Summary Report. Each video was started based on a thermocouple trigger when the fire reached it.

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: 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: 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: 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: 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: 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...

Registration Year

  • 2016
    54

Resource Types

  • Dataset
    54

Affiliations

  • University of Washington
    54
  • Stanford University
    4
  • Duke University
    3
  • Oregon State University
    3
  • Occidental College
    3
  • University of California, Santa Barbara
    3
  • University of Oxford
    3
  • Northwest Fisheries Science Center
    3
  • University of North Carolina
    2
  • Australian National University
    2