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University of South Florida

2017

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Articles 121 - 138 of 138

Full-Text Articles in Life Sciences

Recommendations On The Use Of Ecosystem Modeling For Informing Ecosystem-Based Fisheries Management And Restoration Outcomes In The Gulf Of Mexico, Arnaud Grüss, Kenneth A. Rose, James Simons, Cameron H. Ainsworth, Elizabeth A. Babcock, David D. Chagaris, Kim De Mutsert, John Froeschke, Peter Himchak, Isaac C. Kaplan, Halie O’Farrell, Manuel J. Zetina Rejon Jan 2017

Recommendations On The Use Of Ecosystem Modeling For Informing Ecosystem-Based Fisheries Management And Restoration Outcomes In The Gulf Of Mexico, Arnaud Grüss, Kenneth A. Rose, James Simons, Cameron H. Ainsworth, Elizabeth A. Babcock, David D. Chagaris, Kim De Mutsert, John Froeschke, Peter Himchak, Isaac C. Kaplan, Halie O’Farrell, Manuel J. Zetina Rejon

Marine Science Faculty Publications

Ecosystem-based fisheries management (EBFM) and ecosystem restoration are gaining momentum worldwide, including in U.S. waters of the Gulf of Mexico (GOM). Ecosystem models are valuable tools for informing EBFM and restoration activities. In this paper, we provide guidance and a roadmap for ecosystem modeling in the GOM region, with an emphasis on model development and use of model products to inform EBFM and the increasing investments in restoration. We propose eight “best practices” for ecosystem modeling efforts, including (1) identification of priority management questions, (2) scenarios as simulation experiments, (3) calibration and validation needs, (4) sensitivity and uncertainty analyses, (5) …

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Ictv Virus Taxonomy Profile: Circoviridae, Mya Breitbart, Eric Delwart, Karyna Rosario, Joaquim Segales, Arvind Varsani Jan 2017

Ictv Virus Taxonomy Profile: Circoviridae, Mya Breitbart, Eric Delwart, Karyna Rosario, Joaquim Segales, Arvind Varsani

Marine Science Faculty Publications

The family Circoviridae comprises viruses with small, circular, single-stranded DNA (ssDNA) genomes, including the smallest known animal viruses. Members of this family are classified into two genera, Circovirus and Cyclovirus, which are distinguished by the position of the origin of replication relative to the coding regions and the length of the intergenic regions. Within each genus, the species demarcation threshold is 80 % genome-wide nucleotide sequence identity. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Circoviridae, which is available at www.ictv.global/report/circoviridae.

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Diverse And Highly Recombinant Anelloviruses Associated With Weddell Seals In Antarctica, Elizabeth Fahsbender, Jennifer M. Burns, Stacy Kim, Simona Kraberger, Greg Frankfurter, Mya Breitbart Jan 2017

Diverse And Highly Recombinant Anelloviruses Associated With Weddell Seals In Antarctica, Elizabeth Fahsbender, Jennifer M. Burns, Stacy Kim, Simona Kraberger, Greg Frankfurter, Mya Breitbart

Marine Science Faculty Publications

The viruses circulating among Antarctic wildlife remain largely unknown. In an effort to identify viruses associated withWeddell seals (Leptonychotes weddellii) inhabiting the Ross Sea, vaginal and nasal swabs, and faecal samples were collectedbetween November 2014 and February 2015. In addition, a Weddell seal kidney and South Polar skua (Stercorariusmaccormicki) faeces were opportunistically sampled. Using high throughput sequencing, we identified and recovered 152anellovirus genomes that share 63–70% genome-wide identities with other pinniped anelloviruses. Genome-wide pairwisecomparisons coupled with phylogenetic analysis revealed two novel anellovirus species, tentatively named torque tenoLeptonychotes weddellii virus (TTLwV) -1 and -2. TTLwV-1 (n¼133, genomes encompassing 40 genotypes) is …

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An Ice Sheet Model Validation Framework For The Greenland Ice Sheet, Stephen F. Price, Matthew J. Hoffman, Jennifer A. Bonin, Ian M. Howat, Thomas Neumann, Jack Saba, Irina Tezaur, Jeffrey Guerber, Don P. Chambers, Katherine J. Evans, Joseph H. Kennedy, Jan Lenaerts, William H. Lipscomb, Mauro Perego, Andrew G. Salinger, Raymond S. Tuminaro, Michiel R. Van Den Broeke, Sophie M. Nowicki Jan 2017

An Ice Sheet Model Validation Framework For The Greenland Ice Sheet, Stephen F. Price, Matthew J. Hoffman, Jennifer A. Bonin, Ian M. Howat, Thomas Neumann, Jack Saba, Irina Tezaur, Jeffrey Guerber, Don P. Chambers, Katherine J. Evans, Joseph H. Kennedy, Jan Lenaerts, William H. Lipscomb, Mauro Perego, Andrew G. Salinger, Raymond S. Tuminaro, Michiel R. Van Den Broeke, Sophie M. Nowicki

Marine Science Faculty Publications

We propose a new ice sheet model validation framework – the Cryospheric Model Comparison Tool (CmCt) – that takes advantage of ice sheet altimetry and gravimetry observations collected over the past several decades and is applied here to modeling of the Greenland ice sheet. We use realistic simulations performed with the Community Ice Sheet Model (CISM) along with two idealized, non-dynamic models to demonstrate the framework and its use. Dynamic simulations with CISM are forced from 1991 to 2013, using combinations of reanalysis-based surface mass balance and observations of outlet glacier flux change. We propose and demonstrate qualitative and quantitative …

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Monitoring Biodiversity Change Through Effective Global Coordination, Laetitia M. Navarro, Néstor Fernández, Carlos Guerra, Rob Guralnick, W Daniel Kissling, Maria Cecilia Londoño, Frank Muller-Karger, Eren Turak, Patricia Balvanera, Mark J. Costello, Aurelie Delavaud, Gy El Serafy, Simon Ferrier, Ilse Geijzendorffer, Gary N. Geller, Walter Jetz, Eun-Shik Kim, Hyejin Kim, Corinne S. Martin, Melodie A. Mcgeoch, Tuyeni H. Mwampamba, Jeanne L. Nel, Emily Nicholson, Nathalie Pettorelli, Michael E. Schaepman, Andrew Skidmore, Isabel Sousa Pinto, Sheila Vergara, Petteri Vihervaara, Haigen Xu, Tetsukazu Yahara, Mike Gill, Henrique M. Pereira Jan 2017

Monitoring Biodiversity Change Through Effective Global Coordination, Laetitia M. Navarro, Néstor Fernández, Carlos Guerra, Rob Guralnick, W Daniel Kissling, Maria Cecilia Londoño, Frank Muller-Karger, Eren Turak, Patricia Balvanera, Mark J. Costello, Aurelie Delavaud, Gy El Serafy, Simon Ferrier, Ilse Geijzendorffer, Gary N. Geller, Walter Jetz, Eun-Shik Kim, Hyejin Kim, Corinne S. Martin, Melodie A. Mcgeoch, Tuyeni H. Mwampamba, Jeanne L. Nel, Emily Nicholson, Nathalie Pettorelli, Michael E. Schaepman, Andrew Skidmore, Isabel Sousa Pinto, Sheila Vergara, Petteri Vihervaara, Haigen Xu, Tetsukazu Yahara, Mike Gill, Henrique M. Pereira

Marine Science Faculty Publications

The ability to monitor changes in biodiversity, and their societal impact, is critical to conserving species and managing ecosystems. While emerging technologies increase the breadth and reach of data acquisition, monitoring efforts are still spatially and temporally fragmented, and taxonomically biased. Appropriate long-term information remains therefore limited. The Group on Earth Observations Biodiversity Observation Network (GEO BON) aims to provide a general framework for biodiversity monitoring to support decision-makers. Here, we discuss the coordinated observing system adopted by GEO BON, and review challenges and advances in its implementation, focusing on two interconnected core components — the Essential Biodiversity Variables as …

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Short Organic Carbon Turnover Time And Narrow 14C Age Spectra In Early Holocene Wetland Paleosols, Lael Vetter, Brad E. Rosenheim, Alvaro Fernandez, Torbjörn E. Törnqvist Jan 2017

Short Organic Carbon Turnover Time And Narrow 14C Age Spectra In Early Holocene Wetland Paleosols, Lael Vetter, Brad E. Rosenheim, Alvaro Fernandez, Torbjörn E. Törnqvist

Marine Science Faculty Publications

Paleosols contain information about the rates of soil organic carbon turnover when the soil was actively forming. However, this temporal information is often difficult to interpret without tight stratigraphic control on the age of the paleosol. Here we apply ramped pyrolysis/oxidation (Ramped PyrOx) 14C analyses to evaluate age spectra of transgressive early Holocene paleosols from the Mississippi Delta in southeastern Louisiana, USA. We find 14C age spectra from soil organic matter (SOM) in both paleosols and overlying basal peats that represent variability in age that is close to, or only slightly greater than, analytical uncertainty of 14C …

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Nearshore Sediment Thickness, Fire Island, New York, Stanley D. Locker, Jennifer L. Miselis, Noreen A. Buster, Cheryl J. Hapke, Heidi M. Wadman, Jesse E. Mcninch, Arnell S. Forde, Chelsea A. Stalk Jan 2017

Nearshore Sediment Thickness, Fire Island, New York, Stanley D. Locker, Jennifer L. Miselis, Noreen A. Buster, Cheryl J. Hapke, Heidi M. Wadman, Jesse E. Mcninch, Arnell S. Forde, Chelsea A. Stalk

Marine Science Faculty Publications

Investigations of coastal change at Fire Island, New York (N.Y.), sought to characterize sediment budgets and determine geologic framework controls on coastal processes. Nearshore sediment thickness is critical for assessing coastal system sediment availability, but it is largely unquantified due to the difficulty of conducting geological or geophysical surveys across the nearshore. This study used an amphibious vessel to acquire chirp subbottom profiles. These profiles were used to characterize nearshore geology and provide an assessment of nearshore sediment volume. Two resulting sediment-thickness maps are provided: total Holocene sediment thickness and the thickness of the active shoreface. The Holocene sediment section …

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Floating Algae Blooms In The East China Sea, Lin Qi, Chuanmin Hu, Mengqiu Wang, Shaoling Shang, Cara Wilson Jan 2017

Floating Algae Blooms In The East China Sea, Lin Qi, Chuanmin Hu, Mengqiu Wang, Shaoling Shang, Cara Wilson

Marine Science Faculty Publications

A floating algae bloom in the East China Sea was observed in Moderate Resolution Imaging Spectroradiometer (MODIS) imagery in May 2017. Using satellite imagery from MODIS, Visible Infrared Imaging Radiometer Suite, Geostationary Ocean Color Imager, and Ocean Land Imager, and combined with numerical particle tracing experiments and laboratory experiments, we examined the history of this bloom as well as similar blooms in previous years and attempted to trace the bloom source and identify the algae type. Results suggest that one bloom origin is offshore Zhejiang coast where algae slicks have appeared in satellite imagery almost every February–March since 2012. Following …

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Permafrost Organic Carbon Mobilization From The Watershed To The Colville River Delta: Evidence From 14C Ramped Pyrolysis And Lignin Biomarkers, Xiaowen Zhang, Thomas S. Bianchi, Xingqian Cui, Brad E. Rosenheim, Chien-Lu Ping, Andrea J. M. Hanna, Mikhail Kanevskiy, Kathryn M. Schreiner, Mead A. Allison Jan 2017

Permafrost Organic Carbon Mobilization From The Watershed To The Colville River Delta: Evidence From 14C Ramped Pyrolysis And Lignin Biomarkers, Xiaowen Zhang, Thomas S. Bianchi, Xingqian Cui, Brad E. Rosenheim, Chien-Lu Ping, Andrea J. M. Hanna, Mikhail Kanevskiy, Kathryn M. Schreiner, Mead A. Allison

Marine Science Faculty Publications

The deposition of terrestrial-derived permafrost particulate organic carbon (POC) has been recorded in major Arctic river deltas. However, associated transport pathways of permafrost POC from the watershed to the coast have not been well constrained. Here we utilized a combination of ramped pyrolysis-oxidation radiocarbon analysis (RPO 14C) along with lignin biomarkers, to track the linkages between soils and river and delta sediments. Surface and deep soils showed distinct RPO thermographs which may be related to degradation and organo-mineral interaction. Soil material in the bed load of the river channel was mostly derived from deep old permafrost. Both surface and …

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Changing Measurements Or Changing Movements? Sampling Scale And Movement Model Identifiability Across Generations Of Biologging Technology, Leah R. Johnson, Philipp H. Boersch-Supan, Richard A. Phillips, Sadie J. Ryan Jan 2017

Changing Measurements Or Changing Movements? Sampling Scale And Movement Model Identifiability Across Generations Of Biologging Technology, Leah R. Johnson, Philipp H. Boersch-Supan, Richard A. Phillips, Sadie J. Ryan

Integrative Biology Faculty and Staff Publications

Animal movement patterns contribute to our understanding of variation in breeding success and survival of individuals, and the implications for population dynamics. Over time, sensor technology for measuring movement patterns has improved. Although older technologies may be rendered obsolete, the existing data are still valuable, especially if new and old data can be compared to test whether a behavior has changed over time. We used simulated data to assess the ability to quantify and correctly identify patterns of seabird flight lengths under observational regimes used in successive generations of wet/dry logging technology. Care must be taken when comparing data collected …

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Accuracy Of Climate-Based Forecasts Of Pathogen Spread, Annakate M. Schatz, Andrew M. Kramer, John M. Drake Jan 2017

Accuracy Of Climate-Based Forecasts Of Pathogen Spread, Annakate M. Schatz, Andrew M. Kramer, John M. Drake

Integrative Biology Faculty and Staff Publications

Species distribution models (SDMs) are a tool for predicting the eventual geographical range of an emerging pathogen. Most SDMs, however, rely on an assumption of equilibrium with the environment, which an emerging pathogen, by definition, has not reached. To determine if some SDM approaches work better than others for modelling the spread of emerging, non-equilibrium pathogens, we studied time-sensitive predictive performance of SDMs for Batrachochytrium dendrobatidis, a devastating infectious fungus of amphibians, using multiple methods trained on time-incremented subsets of the available data. We split our data into timeline-based training and testing sets, and evaluated models on each set …

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Major Advance Of South Georgia Glaciers During The Antarctic Cold Reversal Following Extensive Sub-Antarctic Glaciation, Alastair G. C. Graham, Gerhard Kuhn, Ove Meisel, Claus-Dieter Hillenbrand, Dominic A. Hodgson, Werner Ehrmann, Lukas Wacker, Paul Wintersteller, Santos Ferreira, Dos Santos Ferreira, Miriam Römer, Duanne White, Gerhard Bohrmann Jan 2017

Major Advance Of South Georgia Glaciers During The Antarctic Cold Reversal Following Extensive Sub-Antarctic Glaciation, Alastair G. C. Graham, Gerhard Kuhn, Ove Meisel, Claus-Dieter Hillenbrand, Dominic A. Hodgson, Werner Ehrmann, Lukas Wacker, Paul Wintersteller, Santos Ferreira, Dos Santos Ferreira, Miriam Römer, Duanne White, Gerhard Bohrmann

Marine Science Faculty Publications

The history of glaciations on Southern Hemisphere sub-polar islands is unclear. Debate surrounds the extent and timing of the last glacial advance and termination on sub-Antarctic South Georgia in particular. Here, using sea-floor geophysical data and marine sediment cores, we resolve the record of glaciation offshore of South Georgia through the transition from the Last Glacial Maximum to Holocene. We show a sea-bed landform imprint of a shelf-wide last glacial advance and progressive deglaciation. Renewed glacier resurgence in the fjords between c. 15,170 and 13,340 yr ago coincided with a period of cooler, wetter climate known as the Antarctic Cold …

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Limited Grounding-Line Advance Onto The West Antarctic Continental Shelf In The Easternmost Amundsen Sea Embayment During The Last Glacial Period, Johann P. Klages, Gerhard Kuhn, Claus-Dieter Hillenbrand, James A. Smith, Alastair G. C. Graham, Frank O. Nitsche, Thomas Frederichs, Patrycja E. Jernas, Karsten Gohl, Lukas Wacker Jan 2017

Limited Grounding-Line Advance Onto The West Antarctic Continental Shelf In The Easternmost Amundsen Sea Embayment During The Last Glacial Period, Johann P. Klages, Gerhard Kuhn, Claus-Dieter Hillenbrand, James A. Smith, Alastair G. C. Graham, Frank O. Nitsche, Thomas Frederichs, Patrycja E. Jernas, Karsten Gohl, Lukas Wacker

Marine Science Faculty Publications

Precise knowledge about the extent of the West Antarctic Ice Sheet (WAIS) at the Last Glacial Maximum (LGM; c. 26.5–19 cal. ka BP) is important in order to 1) improve paleo-ice sheet reconstructions, 2) provide a robust empirical framework for calibrating paleo-ice sheet models, and 3) locate potential shelf refugia for Antarctic benthos during the last glacial period. However, reliable reconstructions are still lacking for many WAIS sectors, particularly for key areas on the outer continental shelf, where the LGM-ice sheet is assumed to have terminated. In many areas of the outer continental shelf around Antarctica, direct geological data for …

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Persistent Spatial Structuring Of Coastal Ocean Acidification In The California Current System, F. Chan, J. A. Barth, C. A. Blanchette, R. H. Byrne, F. Chavez, O. Cheriton, R. A. Feely, G. Friederich, B. Gaylord, T. Gouhier, S. Hacker, T. Hill, G. Hofmann, M. A. Mcmanus, B. A. Menge, K. J. Nielsen, A. Russell, E. Sanford, J. Sevadjian, L. Washburn Jan 2017

Persistent Spatial Structuring Of Coastal Ocean Acidification In The California Current System, F. Chan, J. A. Barth, C. A. Blanchette, R. H. Byrne, F. Chavez, O. Cheriton, R. A. Feely, G. Friederich, B. Gaylord, T. Gouhier, S. Hacker, T. Hill, G. Hofmann, M. A. Mcmanus, B. A. Menge, K. J. Nielsen, A. Russell, E. Sanford, J. Sevadjian, L. Washburn

Marine Science Faculty Publications

The near-term progression of ocean acidification (OA) is projected to bring about sharp changes in the chemistry of coastal upwelling ecosystems. The distribution of OA exposure across these early-impact systems, however, is highly uncertain and limits our understanding of whether and how spatial management actions can be deployed to ameliorate future impacts. Through a novel coastal OA observing network, we have uncovered a remarkably persistent spatial mosaic in the penetration of acidified waters into ecologically-important nearshore habitats across 1,000 km of the California Current Large Marine Ecosystem. In the most severe exposure hotspots, suboptimal conditions for calcifying organisms encompassed up …

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Challenges In Methane Column Retrievals From Aviris-Ng Imagery Over Spectrally Cluttered Surfaces: A Sensitivity Analysis, Minwei Zhang, Ira Leifer, Chuanmin Hu Jan 2017

Challenges In Methane Column Retrievals From Aviris-Ng Imagery Over Spectrally Cluttered Surfaces: A Sensitivity Analysis, Minwei Zhang, Ira Leifer, Chuanmin Hu

Marine Science Faculty Publications

A comparison between efforts to detect methane anomalies by a simple band ratio approach from the Airborne Visual Infrared Imaging Spectrometer-Classic (AVIRIS-C) data for the Kern Front oil field, Central California, and the Coal Oil Point marine hydrocarbon seep field, offshore southern California, was conducted. The detection succeeded for the marine source and failed for the terrestrial source, despite these sources being of comparable strength. Scene differences were investigated in higher spectral and spatial resolution collected by the AVIRIS-C successor instrument, AVIRIS Next Generation (AVIRIS-NG), by a sensitivity study. Sensitivity to factors including water vapor, aerosol, planetary boundary layer (PBL) …

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Cloud And Sun-Glint Statistics Derived From Goes And Modis Observations Over The Intra-Americas Sea For Geo-Cape Mission Planning, Lian Feng, Chuanmin Hu, Brian B. Barnes, Antonio Mannino, Andrew K. Heidinger, Kathleen Strabala, Laura T. Iraci Jan 2017

Cloud And Sun-Glint Statistics Derived From Goes And Modis Observations Over The Intra-Americas Sea For Geo-Cape Mission Planning, Lian Feng, Chuanmin Hu, Brian B. Barnes, Antonio Mannino, Andrew K. Heidinger, Kathleen Strabala, Laura T. Iraci

Marine Science Faculty Publications

Knowledge of cloud cover, frequency, and duration is not only important to study cloud dynamics, but also critical in determining when and where to take ocean measurements from geostationary orbits such as the Geostationary Coastal and Air Pollution Events (GEO-CAPE) mission due to the challenges in achieving complete hemispheric coverage of coastal oceans, estuaries, and inland waters at hourly frequency. Using GOES hourly measurements at 4 km nadir resolution between 2006 and 2011, the number of cloud-free hourly observations per day (Ncf) for solar zenith angle θo < 80° was estimated for each 0.1° location of the Intra-Americas Sea. The number of Sun-glint-affected hourly observations per day (Nsg) was also calculated based on the …

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Predicting Sargassum Blooms In The Caribbean Sea From Modis Observations, Mengqiu Wang, Chuanmin Hu Jan 2017

Predicting Sargassum Blooms In The Caribbean Sea From Modis Observations, Mengqiu Wang, Chuanmin Hu

Marine Science Faculty Publications

Recurrent and significant Sargassum beaching events in the Caribbean Sea (CS) have caused serious environmental and economic problems, calling for a long-term prediction capacity of Sargassum blooms. Here we present predictions based on a hindcast of 2000–2016 observations from Moderate Resolution Imaging Spectroradiometer (MODIS), which showed Sargassum abundance in the CS and the Central West Atlantic (CWA), as well as connectivity between the two regions with time lags. This information was used to derive bloom and nonbloom probability matrices for each 1° square in the CS for the months of May–August, predicted from bloom conditions in a hotspot region in …

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Remote-Sensing Estimation Of Phytoplankton Size Classes From Goci Satellite Measurements In Bohai Sea And Yellow Sea, Deyong Sun, Yu Huan, Zhongfeng Qiu, Chuanmin Hu, Shengqiang Wang, Yijun He Jan 2017

Remote-Sensing Estimation Of Phytoplankton Size Classes From Goci Satellite Measurements In Bohai Sea And Yellow Sea, Deyong Sun, Yu Huan, Zhongfeng Qiu, Chuanmin Hu, Shengqiang Wang, Yijun He

Marine Science Faculty Publications

Phytoplankton size class (PSC), a measure of different phytoplankton functional and structural groups, is a key parameter to the understanding of many marine ecological and biogeochemical processes. In turbid waters where optical properties may be influenced by terrigenous discharge and nonphytoplankton water constituents, remote estimation of PSC is still a challenging task. Here based on measurements of phytoplankton diagnostic pigments, total chlorophyll a, and spectral reflectance in turbid waters of Bohai Sea and Yellow Sea during summer 2015, a customized model is developed and validated to estimate PSC in the two semienclosed seas. Five diagnostic pigments determined through high-performance …

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