Studies to understanding interspecies transmission of transmissible spongiform encephalopathies (TSEs, prion diseases) are challenging in that they typically rely upon lengthy and costly in vivo animal challenge studies. A number of in vitro assays have been developed to aid in measuring prion species barriers, thereby reducing animal use and providing quicker results than animal bioassays. Here, we present the protocol for a rapid in vitroprion conversion assay called the conversion efficiency ratio (CER) assay. In this assay cellular prion protein (PrPC) from an uninfected host brain is denatured at both pH 7.4 and 3.5 to produce two substrates. When the pH 7.4 substrate is incubated with TSE agent, the amount of PrPC that converts to a proteinase K (PK)-resistant state is modulated by the original host’s species barrier to the TSE agent. In contrast, PrPC in the pH 3.5 substrate is misfolded by any TSE agent. By comparing the amount of PK-resistant prion protein in the two substrates, an assessment of the host’s species barrier can be made. We show that the CER assay correctly predicts known prion species barriers of laboratory mice and, as an example, show some preliminary results suggesting that bobcats (Lynx rufus) may be susceptible to white-tailed deer (Odocoileus virginianus) chronic wasting disease agent.
","language":"English","publisher":"JoVE","doi":"10.3791/52522","usgsCitation":"Johnson, C.J., Carlson, C.M., Morawski, A.R., Manthei, A., and Cashman, N.R., 2015, Assessing transmissible spongiform encephalopathy species barriers with an in vitro prion protein conversion assay: Journal of Visualized Experiments, v. 97, e52522, https://doi.org/10.3791/52522.","productDescription":"e52522","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-060906","costCenters":[{"id":456,"text":"National Wildlife Health Center","active":true,"usgs":true}],"links":[{"id":472217,"rank":0,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"https://doi.org/10.3791/52522","text":"External Repository"},{"id":299759,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"97","publishingServiceCenter":{"id":6,"text":"Columbus PSC"},"noUsgsAuthors":false,"publicationDate":"2015-03-10","publicationStatus":"PW","scienceBaseUri":"55322ebbe4b0b22a158063d2","contributors":{"authors":[{"text":"Johnson, Christopher J. cjjohnson@usgs.gov","contributorId":3491,"corporation":false,"usgs":true,"family":"Johnson","given":"Christopher","email":"cjjohnson@usgs.gov","middleInitial":"J.","affiliations":[{"id":456,"text":"National Wildlife Health Center","active":true,"usgs":true}],"preferred":true,"id":545120,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Carlson, Christina M. 0000-0002-4950-8273 cmcarlson@usgs.gov","orcid":"https://orcid.org/0000-0002-4950-8273","contributorId":5968,"corporation":false,"usgs":true,"family":"Carlson","given":"Christina","email":"cmcarlson@usgs.gov","middleInitial":"M.","affiliations":[{"id":456,"text":"National Wildlife Health Center","active":true,"usgs":true}],"preferred":true,"id":545121,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Morawski, Aaron R.","contributorId":140311,"corporation":false,"usgs":false,"family":"Morawski","given":"Aaron","email":"","middleInitial":"R.","affiliations":[{"id":13450,"text":"NIH","active":true,"usgs":false}],"preferred":false,"id":545122,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Manthei, Alyson","contributorId":140312,"corporation":false,"usgs":false,"family":"Manthei","given":"Alyson","email":"","affiliations":[{"id":13451,"text":"Univ. of Wisconsin","active":true,"usgs":false}],"preferred":false,"id":545123,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Cashman, Neil R.","contributorId":140313,"corporation":false,"usgs":false,"family":"Cashman","given":"Neil","email":"","middleInitial":"R.","affiliations":[{"id":13452,"text":"Univ. British Columbia","active":true,"usgs":false}],"preferred":false,"id":545124,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70160544,"text":"70160544 - 2015 - Mercury in Pacific bluefin tuna (Thunnus orientalis):bioaccumulation and trans-Pacific Ocean migration","interactions":[],"lastModifiedDate":"2015-12-22T15:56:51","indexId":"70160544","displayToPublicDate":"2015-03-10T00:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1169,"text":"Canadian Journal of Fisheries and Aquatic Sciences","active":true,"publicationSubtype":{"id":10}},"title":"Mercury in Pacific bluefin tuna (Thunnus orientalis):bioaccumulation and trans-Pacific Ocean migration","docAbstract":"Pacific bluefin tuna (Thunnus orientalis) have the largest home range of any tuna species and are well known for the capacity to make transoceanic migrations. We report the measurement of mercury (Hg) concentrations in wild Pacific bluefin tuna (PBFT), the first reported with known size-of-fish and capture location. The results indicate juvenile PBFT that are recently arrived in the California Current from the western Pacific Ocean have significantly higher Hg concentrations in white muscle (0.51 ug/g wet mass, wm) than PBFT of longer California Current residency (0.41 ug/g wm). These new arrivals are also higher in Hg concentration than PBFT in farm pens (0.43 ug/g wm) that were captured on arrival in the California Current and raised in pens on locally derived feed. Analysis by direct Hg analyzer and attention to Hg by tissue type and location on the fish allowed precise comparisons of mercury among wild and captive fish populations. Analysis of migration and nearshore residency, determined through extensive archival tagging, bioaccumulation models, trophic investigations, and potential coastal sources of methylmercury, indicates Hg bioaccumulation is likely greater for PBFT juvenile habitats in the western Pacific Ocean (East China Sea, Yellow Sea) than in the eastern Pacific Ocean (California Current). Differential bioaccumulation may be a trophic effect or reflect methylmercury availability, with potential sources for coastal China (large hypoxic continental shelf receiving discharge of three large rivers, and island-arc volcanism) different from those for coastal Baja California (small continental shelf, no large rivers, spreading-center volcanism).
","language":"English","publisher":"NRC Research Press","usgsCitation":"Colman, J.A., Nogueira, J.I., Pancorbo, O.C., Batdorf, C.A., and Block, B.A., 2015, Mercury in Pacific bluefin tuna (Thunnus orientalis):bioaccumulation and trans-Pacific Ocean migration: Canadian Journal of Fisheries and Aquatic Sciences, v. 72, p. 1-9.","productDescription":"10 p.","startPage":"1","endPage":"9","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-060319","costCenters":[{"id":376,"text":"Massachusetts Water Science Center","active":true,"usgs":true}],"links":[{"id":312748,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":312737,"type":{"id":15,"text":"Index Page"},"url":"https://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2014-0476#.Vnmeik3oumu"}],"geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -122.607421875,\n 36.63316209558658\n ],\n [\n -129.8583984375,\n 35.99578538642032\n ],\n [\n -115.7080078125,\n 18.93746442964186\n ],\n [\n -110.21484375,\n 22.2280904167845\n ],\n [\n -122.607421875,\n 36.63316209558658\n ]\n ]\n ]\n }\n },\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -218.671875,\n 41.37680856570233\n ],\n [\n -127.96875,\n 26.902476886279807\n ],\n [\n -121.81640624999999,\n 26.58852714730864\n ],\n [\n -218.671875,\n 41.37680856570233\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"72","publishingServiceCenter":{"id":11,"text":"Pembroke PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"567a8245e4b0a04ef490fd11","contributors":{"authors":[{"text":"Colman, John A. 0000-0001-9327-0779 jacolman@usgs.gov","orcid":"https://orcid.org/0000-0001-9327-0779","contributorId":2098,"corporation":false,"usgs":true,"family":"Colman","given":"John","email":"jacolman@usgs.gov","middleInitial":"A.","affiliations":[{"id":466,"text":"New England Water Science Center","active":true,"usgs":true},{"id":376,"text":"Massachusetts Water Science Center","active":true,"usgs":true}],"preferred":true,"id":583096,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Nogueira, Jacob I.","contributorId":150812,"corporation":false,"usgs":false,"family":"Nogueira","given":"Jacob","email":"","middleInitial":"I.","affiliations":[{"id":18108,"text":"Tuna Research and Conservation Center, Stanford University, Hopkins Marine Station, Pacific Grove, California 93950, U.S.A","active":true,"usgs":false}],"preferred":false,"id":583097,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Pancorbo, Oscar C.","contributorId":150813,"corporation":false,"usgs":false,"family":"Pancorbo","given":"Oscar","email":"","middleInitial":"C.","affiliations":[{"id":18109,"text":"Massachusetts Department of Environmental Protection, 37 Shattuck Street, Lawrence, Massachusetts 01843, U.S.A.","active":true,"usgs":false}],"preferred":false,"id":583098,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Batdorf, Carol A.","contributorId":150814,"corporation":false,"usgs":false,"family":"Batdorf","given":"Carol","email":"","middleInitial":"A.","affiliations":[{"id":18109,"text":"Massachusetts Department of Environmental Protection, 37 Shattuck Street, Lawrence, Massachusetts 01843, U.S.A.","active":true,"usgs":false}],"preferred":false,"id":583099,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Block, Barbara A.","contributorId":150815,"corporation":false,"usgs":false,"family":"Block","given":"Barbara","email":"","middleInitial":"A.","affiliations":[{"id":18108,"text":"Tuna Research and Conservation Center, Stanford University, Hopkins Marine Station, Pacific Grove, California 93950, U.S.A","active":true,"usgs":false}],"preferred":false,"id":583100,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70124468,"text":"fs20143076 - 2015 - Invasive Species Science Branch: research and management tools for controlling invasive species","interactions":[],"lastModifiedDate":"2015-03-09T12:42:18","indexId":"fs20143076","displayToPublicDate":"2015-03-09T12:30:00","publicationYear":"2015","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":313,"text":"Fact Sheet","code":"FS","onlineIssn":"2327-6932","printIssn":"2327-6916","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"2014-3076","title":"Invasive Species Science Branch: research and management tools for controlling invasive species","docAbstract":"Invasive, nonnative species of plants, animals, and disease organisms adversely affect the ecosystems they enter. Like “biological wildfires,” they can quickly spread and affect nearly all terrestrial and aquatic ecosystems. Invasive species have become one of the greatest environmental challenges of the 21st century in economic, environmental, and human health costs, with an estimated effect in the United States of more than $120 billion per year. Managers of the Department of the Interior and other public and private lands often rank invasive species as their top resource management problem. The Invasive Species Science Branch of the Fort Collins Science Center provides research and technical assistance relating to management concerns for invasive species, including understanding how these species are introduced, identifying areas vulnerable to invasion, forecasting invasions, and developing control methods. To disseminate this information, branch scientists are developing platforms to share invasive species information with DOI cooperators, other agency partners, and the public. From these and other data, branch scientists are constructing models to understand and predict invasive species distributions for more effective management. The branch also has extensive herpetological and population biology expertise that is applied to harmful reptile invaders such as the Brown Treesnake on Guam and Burmese Python in Florida.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/fs20143076","usgsCitation":"Reed, R., and Walters, K.D., 2015, Invasive Species Science Branch: research and management tools for controlling invasive species: U.S. Geological Survey Fact Sheet 2014-3076, 4 p., https://doi.org/10.3133/fs20143076.","productDescription":"4 p.","numberOfPages":"4","onlineOnly":"Y","additionalOnlineFiles":"N","ipdsId":"IP-056936","costCenters":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"links":[{"id":298376,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/fs20143076.jpg"},{"id":298374,"rank":1,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/fs/2014/3076/"},{"id":298375,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/fs/2014/3076/pdf/fs2014-3076.pdf","text":"Report","size":"5.8 MB","linkFileType":{"id":1,"text":"pdf"},"description":"Report"}],"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"54feb61ce4b02419550deb9d","contributors":{"authors":[{"text":"Reed, Robert N. reedr@usgs.gov","contributorId":1686,"corporation":false,"usgs":true,"family":"Reed","given":"Robert N.","email":"reedr@usgs.gov","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":false,"id":519444,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Walters, Katie D. waltersk@usgs.gov","contributorId":741,"corporation":false,"usgs":true,"family":"Walters","given":"Katie","email":"waltersk@usgs.gov","middleInitial":"D.","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":false,"id":519443,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70124469,"text":"fs20143073 - 2015 - Aquatics Systems Branch: transdisciplinary research to address water-related environmental problems","interactions":[],"lastModifiedDate":"2015-03-09T11:48:49","indexId":"fs20143073","displayToPublicDate":"2015-03-09T11:45:00","publicationYear":"2015","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":313,"text":"Fact Sheet","code":"FS","onlineIssn":"2327-6932","printIssn":"2327-6916","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"2014-3073","title":"Aquatics Systems Branch: transdisciplinary research to address water-related environmental problems","docAbstract":"The Aquatic Systems Branch at the Fort Collins Science Center is a group of scientists dedicated to advancing interdisciplinary science and providing science support to solve water-related environmental issues. Natural resource managers have an increasing need for scientific information and stakeholders face enormous challenges of increasing and competing demands for water. Our scientists are leaders in ecological flows, riparian ecology, hydroscape ecology, ecosystem management, and contaminant biology. The Aquatic Systems Branch employs and develops state-of-the-science approaches in field investigations, laboratory experiments, remote sensing, simulation and predictive modeling, and decision support tools. We use the aquatic experimental laboratory, the greenhouse, the botanical garden and other advanced facilities to conduct unique research. Our scientists pursue research on the ground, in the rivers, and in the skies, generating and testing hypotheses and collecting quantitative information to support planning and design in natural resource management and aquatic restoration.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/fs20143073","usgsCitation":"Dong, Q., and Walters, K.D., 2015, Aquatics Systems Branch: transdisciplinary research to address water-related environmental problems: U.S. Geological Survey Fact Sheet 2014-3073, 4 p., https://doi.org/10.3133/fs20143073.","productDescription":"4 p.","numberOfPages":"4","onlineOnly":"Y","additionalOnlineFiles":"N","ipdsId":"IP-056937","costCenters":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"links":[{"id":298370,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/fs20143073.jpg"},{"id":298368,"rank":1,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/fs/2014/3073/"},{"id":298369,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/fs/2014/3073/pdf/fs2014-3073.pdf","text":"Report","size":"8.18 MB","linkFileType":{"id":1,"text":"pdf"},"description":"Report"}],"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"54feb619e4b02419550deb99","contributors":{"authors":[{"text":"Dong, Quan 0000-0003-0571-5884 qdong@usgs.gov","orcid":"https://orcid.org/0000-0003-0571-5884","contributorId":4506,"corporation":false,"usgs":true,"family":"Dong","given":"Quan","email":"qdong@usgs.gov","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":true,"id":542021,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Walters, Katie D. waltersk@usgs.gov","contributorId":741,"corporation":false,"usgs":true,"family":"Walters","given":"Katie","email":"waltersk@usgs.gov","middleInitial":"D.","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":false,"id":542022,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70142635,"text":"70142635 - 2015 - Integrated climate and land use change scenarios for California rangeland ecosystem services: wildlife habitat, soil carbon, and water supply","interactions":[],"lastModifiedDate":"2018-09-13T14:44:28","indexId":"70142635","displayToPublicDate":"2015-03-09T02:45:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2602,"text":"Landscape Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Integrated climate and land use change scenarios for California rangeland ecosystem services: wildlife habitat, soil carbon, and water supply","docAbstract":"In addition to biodiversity conservation, California rangelands generate multiple ecosystem services including livestock production, drinking and irrigation water, and carbon sequestration. California rangeland ecosystems have experienced substantial conversion to residential land use and more intensive agriculture.
\nTo understand the potential impacts to rangeland ecosystem services, we developed six spatially explicit (250 m) climate/land use change scenarios for the Central Valley of California and surrounding foothills consistent with three Intergovernmental Panel on Climate Change emission scenario narratives.
\nWe quantified baseline and projected change in wildlife habitat, soil organic carbon (SOC), and water supply (recharge and runoff). For six case study watersheds we quantified the interactions of future development and changing climate on recharge, runoff and streamflow, and precipitation thresholds where dominant watershed hydrological processes shift through analysis of covariance.
\nThe scenarios show that across the region, habitat loss is expected to occur predominantly in grasslands, primarily due to future development (up to a 37 % decline by 2100), however habitat loss in priority conservation errors will likely be due to cropland and hay/pasture expansion (up to 40 % by 2100). Grasslands in the region contain approximately 100 teragrams SOC in the top 20 cm, and up to 39 % of this SOC is subject to conversion by 2100. In dryer periods recharge processes typically dominate runoff. Future development lowers the precipitation value at which recharge processes dominate runoff, and combined with periods of drought, reduces the opportunity for recharge, especially on deep soils.
\nResults support the need for climate-smart land use planning that takes recharge areas into account, which will provide opportunities for water storage in dry years. Given projections for agriculture, more modeling is needed on feedbacks between agricultural expansion on rangelands and water supply.
","language":"English","publisher":"Springer","doi":"10.1007/s10980-015-0159-7","usgsCitation":"Byrd, K.B., Flint, L.E., Alvarez, P., Casey, F., Sleeter, B.M., Soulard, C.E., Flint, A.L., and Sohl, T.L., 2015, Integrated climate and land use change scenarios for California rangeland ecosystem services: wildlife habitat, soil carbon, and water supply: Landscape Ecology, v. 30, no. 4, p. 729-750, https://doi.org/10.1007/s10980-015-0159-7.","productDescription":"22 p.","startPage":"729","endPage":"750","numberOfPages":"22","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-059547","costCenters":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true},{"id":222,"text":"Earth Resources Observation and Science (EROS) Center","active":true,"usgs":true},{"id":657,"text":"Western Geographic Science Center","active":true,"usgs":true}],"links":[{"id":472218,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1007/s10980-015-0159-7","text":"Publisher Index Page"},{"id":298389,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"California","otherGeospatial":"Central Valley","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -120.574951171875,\n 34.379712580462204\n ],\n [\n -122.37670898437499,\n 36.99377838872517\n ],\n [\n -123.81591796875,\n 38.90813299596705\n ],\n [\n -124.024658203125,\n 40.74725696280421\n ],\n [\n -121.981201171875,\n 40.76390128094589\n ],\n [\n -121.62963867187499,\n 40.287906612507406\n ],\n [\n -120.904541015625,\n 39.257778150283336\n ],\n [\n -118.57543945312501,\n 36.60670888641815\n ],\n [\n -118.5205078125,\n 34.397844946449865\n ],\n [\n -120.574951171875,\n 34.379712580462204\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"30","issue":"4","publishingServiceCenter":{"id":14,"text":"Menlo Park PSC"},"noUsgsAuthors":false,"publicationDate":"2015-02-05","publicationStatus":"PW","scienceBaseUri":"54feb61be4b02419550deb9b","contributors":{"authors":[{"text":"Byrd, Kristin B. 0000-0002-5725-7486 kbyrd@usgs.gov","orcid":"https://orcid.org/0000-0002-5725-7486","contributorId":3814,"corporation":false,"usgs":true,"family":"Byrd","given":"Kristin","email":"kbyrd@usgs.gov","middleInitial":"B.","affiliations":[{"id":657,"text":"Western Geographic Science Center","active":true,"usgs":true}],"preferred":true,"id":542067,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Flint, Lorraine E. 0000-0002-7868-441X lflint@usgs.gov","orcid":"https://orcid.org/0000-0002-7868-441X","contributorId":1184,"corporation":false,"usgs":true,"family":"Flint","given":"Lorraine","email":"lflint@usgs.gov","middleInitial":"E.","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":542068,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Alvarez, Pelayo","contributorId":139613,"corporation":false,"usgs":false,"family":"Alvarez","given":"Pelayo","email":"","affiliations":[{"id":12808,"text":"California Rangeland Conservation Coalition","active":true,"usgs":false}],"preferred":false,"id":542069,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Casey, Frank ccasey@usgs.gov","contributorId":4188,"corporation":false,"usgs":true,"family":"Casey","given":"Frank","email":"ccasey@usgs.gov","affiliations":[{"id":436,"text":"National Research Program - Eastern Branch","active":true,"usgs":true}],"preferred":false,"id":542070,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Sleeter, Benjamin M. 0000-0003-2371-9571 bsleeter@usgs.gov","orcid":"https://orcid.org/0000-0003-2371-9571","contributorId":3479,"corporation":false,"usgs":true,"family":"Sleeter","given":"Benjamin","email":"bsleeter@usgs.gov","middleInitial":"M.","affiliations":[{"id":657,"text":"Western Geographic Science Center","active":true,"usgs":true},{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"preferred":true,"id":542071,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Soulard, Christopher E. 0000-0002-5777-9516 csoulard@usgs.gov","orcid":"https://orcid.org/0000-0002-5777-9516","contributorId":2642,"corporation":false,"usgs":true,"family":"Soulard","given":"Christopher","email":"csoulard@usgs.gov","middleInitial":"E.","affiliations":[{"id":657,"text":"Western Geographic Science Center","active":true,"usgs":true}],"preferred":true,"id":542072,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Flint, Alan L. 0000-0002-5118-751X aflint@usgs.gov","orcid":"https://orcid.org/0000-0002-5118-751X","contributorId":1492,"corporation":false,"usgs":true,"family":"Flint","given":"Alan","email":"aflint@usgs.gov","middleInitial":"L.","affiliations":[{"id":657,"text":"Western Geographic Science Center","active":true,"usgs":true},{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":542073,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Sohl, Terry L. 0000-0002-9771-4231 sohl@usgs.gov","orcid":"https://orcid.org/0000-0002-9771-4231","contributorId":648,"corporation":false,"usgs":true,"family":"Sohl","given":"Terry","email":"sohl@usgs.gov","middleInitial":"L.","affiliations":[{"id":223,"text":"Earth Resources Observation and Science (EROS) Center (Geography)","active":false,"usgs":true},{"id":222,"text":"Earth Resources Observation and Science (EROS) Center","active":true,"usgs":true}],"preferred":true,"id":542074,"contributorType":{"id":1,"text":"Authors"},"rank":8}]}} ,{"id":70138865,"text":"70138865 - 2015 - Adaptive harvest management for the Svalbard population of Pink-Footed Geese: 2014 progress summary","interactions":[],"lastModifiedDate":"2015-12-21T14:59:55","indexId":"70138865","displayToPublicDate":"2015-03-09T00:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":9,"text":"Other Report"},"title":"Adaptive harvest management for the Svalbard population of Pink-Footed Geese: 2014 progress summary","docAbstract":"This document describes progress to date on the development of an adaptive harvest-management strategy for maintaining the Svalbard population of pink-footed geese (Anser brachyrhynchus) near their agreed target level (60 thousand) by providing for sustainable harvests in Norway and Denmark. Specifically, this report provides an assessment of the most recent monitoring information and its implications for the harvest management strategy.
\nThe development of a passively adaptive harvest management strategy requires specification of four elements: (a) a set of alternative population models, describing the effects of harvest and other relevant environmental factors; (b) a set of probabilities describing the relative credibility of the alternative models, which are updated each year based on a comparison of model predictions and monitoring information; (c) a set of alternative harvest quotas, from which a 3-year quota is chosen; and (d) an objective function, by which alternative harvest strategies can be evaluated and an optimal strategy chosen.
\nBy combining varying hypotheses about survival and reproduction, a suite of nine models have been developed that represent a wide range of possibilities concerning the extent to which demographic rates are density dependent or independent, and the extent to which spring temperatures are important. Five of the models incorporate density-dependent mechanisms that would maintain the population near a carrying capacity (i.e., in the absence of harvest) of 65k – 129k depending on the specific model. The remaining four models are density independent and predict an exponentially growing population even with moderate levels of harvest.
\nThe most current set of monitoring information was used to update model weights for the period 1991 – 2013. Current model weights suggest little or no evidence for density-dependent survival and reproduction. These results suggest that the pink-footed goose population may have recently experienced a release from density-dependent mechanisms, corresponding to the period of most rapid growth in population size. There was equivocal evidence for the effect of May temperature days (number of days with temperatures above freezing: TempDays) on survival and on reproduction.
\nDuring the summer of 2013 we computed an optimal harvest strategy for the 3-year period 2013 – 2015. The strategy suggested that the appropriate annual harvest quota is 15 thousand. The 1-year harvest strategy calculated to determine whether an emergency closure of the hunting season is required this year suggested an allowable harvest of 25.0 thousand; thus, a hunting-season closure is not warranted. If the harvest quota of 15 thousand were met in the coming hunting season, the next population count would be expected to be 71.0 thousand. If only the most recent 4-year mean harvest were realized (11.3 thousand), a population size of 74.8 thousand would be expected. Simulations suggest that it will take approximately seven years at current harvest levels to reduce population size to the goal of 60 thousand. However, it is possible that the extension of the forthcoming hunting season in Denmark could result in a total harvest approaching 15 thousand; in this case, simulations suggest it would only take about three years to reach the goal.
","language":"English","publisher":"Aarhus University; Danish Center for Environment and Energy","usgsCitation":"Johnson, F.A., and Madsen, J., 2015, Adaptive harvest management for the Svalbard population of Pink-Footed Geese: 2014 progress summary, no. 40, 22 p.","productDescription":"22 p.","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-057797","costCenters":[{"id":566,"text":"Southeast Ecological Science Center","active":true,"usgs":true}],"links":[{"id":312648,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":312647,"rank":1,"type":{"id":15,"text":"Index Page"},"url":"https://dce.au.dk/udgivelser/tr/nr-1-49/abstracts/no-40-adaptive-harvest-management-for-the-svalbard-population-of-pink-footed-geese-2014-progress-summary/"}],"country":"Norway","otherGeospatial":"Svalbard","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n 16.2158203125,\n 80.77471572295197\n ],\n [\n 33.57421875,\n 80.71818333779603\n ],\n [\n 34.1015625,\n 78.16157013950931\n ],\n [\n 19.51171875,\n 74.06786624952264\n ],\n [\n 15.6005859375,\n 74.8793566119438\n ],\n [\n 8.96484375,\n 78.7163161518392\n ],\n [\n 8.26171875,\n 79.60821469998169\n ],\n [\n 15.380859374999998,\n 80.66130757742846\n ],\n [\n 16.2158203125,\n 80.77471572295197\n ]\n ]\n ]\n }\n }\n ]\n}","issue":"40","publishingServiceCenter":{"id":8,"text":"Raleigh PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"567930bde4b0da412f4fb52e","contributors":{"authors":[{"text":"Johnson, Fred A. 0000-0002-5854-3695 fjohnson@usgs.gov","orcid":"https://orcid.org/0000-0002-5854-3695","contributorId":2773,"corporation":false,"usgs":true,"family":"Johnson","given":"Fred","email":"fjohnson@usgs.gov","middleInitial":"A.","affiliations":[{"id":455,"text":"National Wetlands Research Center","active":true,"usgs":true},{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true},{"id":566,"text":"Southeast Ecological Science Center","active":true,"usgs":true}],"preferred":true,"id":539104,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Madsen, J.","contributorId":31921,"corporation":false,"usgs":true,"family":"Madsen","given":"J.","email":"","affiliations":[],"preferred":false,"id":583041,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70144493,"text":"70144493 - 2015 - Using near-real-time monitoring data from Pu'u 'Ō'ō vent at Kīlauea Volcano for training and educational purposes","interactions":[],"lastModifiedDate":"2015-03-31T11:50:05","indexId":"70144493","displayToPublicDate":"2015-03-08T00:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3841,"text":"Journal of Applied Volcanology","active":true,"publicationSubtype":{"id":10}},"title":"Using near-real-time monitoring data from Pu'u 'Ō'ō vent at Kīlauea Volcano for training and educational purposes","docAbstract":"Training non-scientists in the use of volcano-monitoring data is critical preparation in advance of a volcanic crisis, but it is currently unclear which methods are most effective for improving the content-knowledge of non-scientists to help bridge communications between volcano experts and non-experts. We measured knowledge gains for beginning-(introductory-level students) and novice-level learners (students with a basic understanding of geologic concepts) engaged in the Volcanoes Exploration Program: Pu‘u ‘Ō‘ō (VEPP) “Monday Morning Meeting at the Hawaiian Volcano Observatory” classroom activity that incorporates authentic Global Positioning System (GPS), tilt, seismic, and webcam data from the Pu‘u ‘Ō‘ō eruptive vent on Kīlauea Volcano, Hawai‘i (NAGT website, 2010), as a means of exploring methods for effectively advancing non-expert understanding of volcano monitoring. Learner groups consisted of students in introductory and upper-division college geology courses at two different institutions. Changes in their content knowledge and confidence in the use of data were assessed before and after the activity using multiple-choice and open-ended questions. Learning assessments demonstrated that students who took part in the exercise increased their understanding of volcano-monitoring practices and implications, with beginners reaching a novice stage, and novices reaching an advanced level (akin to students who have completed an upper-division university volcanology class). Additionally, participants gained stronger confidence in their ability to understand the data. These findings indicate that training modules like the VEPP: Monday Morning Meeting classroom activity that are designed to prepare non-experts for responding to volcanic activity and interacting with volcano scientists should introduce real monitoring data prior to proceeding with role-paying scenarios that are commonly used in such courses. The learning gains from the combined approach will help improve effective communications between volcano experts and non-experts during times of crisis, thereby reducing the potential for confusion and misinterpretation of data.
","language":"English","publisher":"Springer","doi":"10.1186/s13617-015-0026-x","usgsCitation":"Teasdale, R., Kraft, K.V., and Poland, M.P., 2015, Using near-real-time monitoring data from Pu'u 'Ō'ō vent at Kīlauea Volcano for training and educational purposes: Journal of Applied Volcanology, v. 4, no. 11, 16 p., https://doi.org/10.1186/s13617-015-0026-x.","productDescription":"16 p.","numberOfPages":"16","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-055760","costCenters":[{"id":617,"text":"Volcano Science Center","active":true,"usgs":true}],"links":[{"id":472219,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1186/s13617-015-0026-x","text":"Publisher Index Page"},{"id":299209,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Hawaii","otherGeospatial":"Kīlauea Volcano","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -155.3075408935547,\n 19.38888634723281\n ],\n [\n -155.3075408935547,\n 19.442636882017393\n ],\n [\n -155.2338981628418,\n 19.442636882017393\n ],\n [\n -155.2338981628418,\n 19.38888634723281\n ],\n [\n -155.3075408935547,\n 19.38888634723281\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"4","issue":"11","publishingServiceCenter":{"id":14,"text":"Menlo Park PSC"},"noUsgsAuthors":false,"publicationDate":"2015-03-08","publicationStatus":"PW","scienceBaseUri":"551bc52ee4b0323842783a5c","contributors":{"authors":[{"text":"Teasdale, Rachel","contributorId":102388,"corporation":false,"usgs":false,"family":"Teasdale","given":"Rachel","email":"","affiliations":[],"preferred":false,"id":543660,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kraft, Katrien van der Hoeven","contributorId":139983,"corporation":false,"usgs":false,"family":"Kraft","given":"Katrien","email":"","middleInitial":"van der Hoeven","affiliations":[{"id":13342,"text":"Mesa Community College","active":true,"usgs":false}],"preferred":false,"id":543661,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Poland, Michael P. 0000-0001-5240-6123 mpoland@usgs.gov","orcid":"https://orcid.org/0000-0001-5240-6123","contributorId":127857,"corporation":false,"usgs":true,"family":"Poland","given":"Michael","email":"mpoland@usgs.gov","middleInitial":"P.","affiliations":[{"id":617,"text":"Volcano Science Center","active":true,"usgs":true}],"preferred":false,"id":543659,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70141879,"text":"70141879 - 2015 - A Laurentian margin back-arc: the Ordovician Wedowee-Emuckfaw-Dahlonega basin","interactions":[],"lastModifiedDate":"2015-08-03T10:10:44","indexId":"70141879","displayToPublicDate":"2015-03-06T08:45:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1724,"text":"GSA Field Guides","active":true,"publicationSubtype":{"id":10}},"title":"A Laurentian margin back-arc: the Ordovician Wedowee-Emuckfaw-Dahlonega basin","docAbstract":"Independent researchers working in the Talladega belt, Ashland-Wedowee-Emuckfaw belt, and Opelika Complex of Alabama, as well as the Dahlonega gold belt and western Inner Piedmont of Alabama, Georgia, and the Carolinas, have mapped stratigraphic sequences unique to each region. Although historically considered distinct terranes of disparate origin, a synthesis of data suggests that each includes lithologic units that formed in an Ordovician back-arc basin (Wedowee-Emuckfaw-Dahlonega basin—WEDB). Rocks in these terranes include varying proportions of metamorphosed mafic and bimodal volcanic rock suites interlayered with deep-water metasedimentary rock sequences. Metavolcanic rocks yield ages that are Early–Middle Ordovician (480–460 Ma) and interlayered metasedimentary units are populated with both Grenville and Early–Middle Ordovician detrital zircons. Metamafic rocks display geochemical trends ranging from mid-oceanic-ridge basalt to arc affinity, similar to modern back-arc basalts. The collective data set limits formation of the WEDB to a suprasubduction system built on and adjacent to upper Neoproterozoic–lower Paleozoic rocks of the passive Laurentian margin at the trailing edge of Iapetus, specifically in a continental margin back-arc setting. Overwhelmingly, the geologic history of the southern Appalachians, including rocks of the WEDB described here, indicates that the Ordovician Taconic orogeny in the southern Appalachians developed in an accretionary orogenic setting instead of the traditional collisional orogenic setting attributed to subduction of the Laurentian margin beneath an exotic or peri-Laurentian arc. Well-studied Cenozoic accretionary orogens provide excellent analogs for Taconic orogenesis, and an accretionary orogenic model for the southern Appalachian Taconic orogeny can account for aspects of Ordovician tectonics not easily explained through collisional orogenesis.
","language":"English","publisher":"Geological Society of America","publisherLocation":"Boulder, CO","doi":"10.1130/2015.0039(02)","usgsCitation":"Barineau, C.I., Tull, J.F., and Holm-Denoma, C.S., 2015, A Laurentian margin back-arc: the Ordovician Wedowee-Emuckfaw-Dahlonega basin: GSA Field Guides, v. 39, p. 21-78, https://doi.org/10.1130/2015.0039(02).","productDescription":"58 p.","startPage":"21","endPage":"78","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-061407","costCenters":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"links":[{"id":298316,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Alabama, Georgia, North Carolina, South Carolina","otherGeospatial":"Appalachian Mountains","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {\n \"stroke\": \"#555555\",\n \"stroke-width\": 2,\n \"stroke-opacity\": 1,\n \"fill\": \"#555555\",\n \"fill-opacity\": 0.5\n },\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -86.98974609375,\n 33.358061612778876\n ],\n [\n -84.00146484374999,\n 37.10776507118514\n ],\n [\n -77.6513671875,\n 37.055177106660814\n ],\n [\n -83.6279296875,\n 31.74685416292141\n ],\n [\n -87.01171875,\n 31.728167146023935\n ],\n [\n -86.98974609375,\n 33.358061612778876\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"39","publishingServiceCenter":{"id":2,"text":"Denver PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"54facfa9e4b02419550db6c8","contributors":{"authors":[{"text":"Barineau, Clinton I.","contributorId":139194,"corporation":false,"usgs":false,"family":"Barineau","given":"Clinton","email":"","middleInitial":"I.","affiliations":[{"id":12692,"text":"Columbus State University","active":true,"usgs":false}],"preferred":false,"id":541419,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Tull, James F.","contributorId":139458,"corporation":false,"usgs":false,"family":"Tull","given":"James","email":"","middleInitial":"F.","affiliations":[{"id":7092,"text":"Florida State University","active":true,"usgs":false}],"preferred":false,"id":541420,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Holm-Denoma, Christopher S. 0000-0003-3229-5440 cholm-denoma@usgs.gov","orcid":"https://orcid.org/0000-0003-3229-5440","contributorId":2442,"corporation":false,"usgs":true,"family":"Holm-Denoma","given":"Christopher","email":"cholm-denoma@usgs.gov","middleInitial":"S.","affiliations":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":541418,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70155916,"text":"70155916 - 2015 - Urgent need for warming experiments in tropical forests","interactions":[],"lastModifiedDate":"2020-09-01T14:27:41.041637","indexId":"70155916","displayToPublicDate":"2015-03-06T03:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1837,"text":"Global Change Biology","active":true,"publicationSubtype":{"id":10}},"title":"Urgent need for warming experiments in tropical forests","docAbstract":"Although tropical forests account for only a fraction of the planet's terrestrial surface, they exchange more carbon dioxide with the atmosphere than any other biome on Earth, and thus play a disproportionate role in the global climate. In the next 20 years, the tropics will experience unprecedented warming, yet there is exceedingly high uncertainty about their potential responses to this imminent climatic change. Here, we prioritize research approaches given both funding and logistical constraints in order to resolve major uncertainties about how tropical forests function and also to improve predictive capacity of earth system models. We investigate overall model uncertainty of tropical latitudes and explore the scientific benefits and inevitable trade-offs inherent in large-scale manipulative field experiments. With a Coupled Model Intercomparison Project Phase 5 analysis, we found that model variability in projected net ecosystem production was nearly 3 times greater in the tropics than for any other latitude. Through a review of the most current literature, we concluded that manipulative warming experiments are vital to accurately predict future tropical forest carbon balance, and we further recommend the establishment of a network of comparable studies spanning gradients of precipitation, edaphic qualities, plant types, and/or land use change. We provide arguments for long-term, single-factor warming experiments that incorporate warming of the most biogeochemically active ecosystem components (i.e. leaves, roots, soil microbes). Hypothesis testing of underlying mechanisms should be a priority, along with improving model parameterization and constraints. No single tropical forest is representative of all tropical forests; therefore logistical feasibility should be the most important consideration for locating large-scale manipulative experiments. Above all, we advocate for multi-faceted research programs, and we offer arguments for what we consider the most powerful and urgent way forward in order to improve our understanding of tropical forest responses to climate change.
","language":"English","publisher":"Wiley","doi":"10.1111/gcb.12860","usgsCitation":"Calaveri, M.A., Reed, S.C., Smith, W., and Wood, T.E., 2015, Urgent need for warming experiments in tropical forests: Global Change Biology, v. 21, no. 6, p. 2111-2121, https://doi.org/10.1111/gcb.12860.","productDescription":"11 p.","startPage":"2111","endPage":"2121","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-060487","costCenters":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true},{"id":29789,"text":"John Wesley Powell Center for Analysis and Synthesis","active":true,"usgs":true}],"links":[{"id":472220,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1111/gcb.12860","text":"Publisher Index Page"},{"id":306662,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"21","issue":"6","publishingServiceCenter":{"id":14,"text":"Menlo Park PSC"},"noUsgsAuthors":false,"publicationDate":"2015-03-06","publicationStatus":"PW","scienceBaseUri":"55cdbfc0e4b08400b1fe1458","chorus":{"doi":"10.1111/gcb.12860","url":"http://dx.doi.org/10.1111/gcb.12860","publisher":"Wiley-Blackwell","authors":"Cavaleri Molly A., Reed Sasha C., Smith W. Kolby, Wood Tana E.","journalName":"Global Change Biology","publicationDate":"3/6/2015","auditedOn":"4/6/2016"},"contributors":{"authors":[{"text":"Calaveri, Molly A.","contributorId":146258,"corporation":false,"usgs":false,"family":"Calaveri","given":"Molly","email":"","middleInitial":"A.","affiliations":[{"id":16650,"text":"School of Forest Resources & Environmental Science, Michigan Technological University, 1400 Townsend Dr., Houghton, MI 49931","active":true,"usgs":false}],"preferred":false,"id":566816,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Reed, Sasha C. 0000-0002-8597-8619 screed@usgs.gov","orcid":"https://orcid.org/0000-0002-8597-8619","contributorId":462,"corporation":false,"usgs":true,"family":"Reed","given":"Sasha","email":"screed@usgs.gov","middleInitial":"C.","affiliations":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"preferred":true,"id":566815,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Smith, W. Kolby","contributorId":9933,"corporation":false,"usgs":false,"family":"Smith","given":"W. Kolby","affiliations":[{"id":7089,"text":"University of Montana, Missoula, MT","active":true,"usgs":false}],"preferred":false,"id":566817,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Wood, Tana E.","contributorId":33193,"corporation":false,"usgs":true,"family":"Wood","given":"Tana","email":"","middleInitial":"E.","affiliations":[],"preferred":false,"id":566818,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70156251,"text":"70156251 - 2015 - Heterogeneous movement of insectivorous Amazonian birds through primary and secondary forest: A case study using multistate models with radiotelemetry data","interactions":[],"lastModifiedDate":"2022-11-10T16:36:18.01769","indexId":"70156251","displayToPublicDate":"2015-03-06T00:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1015,"text":"Biological Conservation","active":true,"publicationSubtype":{"id":10}},"title":"Heterogeneous movement of insectivorous Amazonian birds through primary and secondary forest: A case study using multistate models with radiotelemetry data","docAbstract":"Given rates of deforestation, disturbance, and secondary forest accumulation in tropical rainforests, there is a great need to quantify habitat use and movement among different habitats. This need is particularly pronounced for animals most sensitive to disturbance, such as insectivorous understory birds. Here we use multistate capture–recapture models with radiotelemetry data to determine the successional stage at which within-day movement probabilities of Amazonian birds in secondary forest are similar to those in primary forest. We radio-tracked three common understory insectivore species in primary and secondary forest at the Biological Dynamics of Forest Fragments project near Manaus, Brazil: two woodcreepers, Glyphorynchus spirurus (n = 19) andXiphorhynchus pardalotus (n = 18), and the terrestrial antthrush Formicarius colma(n = 19). Forest age was a strong predictor of fidelity to a given habitat. All three species showed greater fidelity to primary forest than to 8–14-year-old secondary forest, indicating the latter’s relatively poor quality. The two woodcreeper species used 12–18-year-old secondary forest in a manner comparable to continuous forest, but F. colmaavoided moving even to 27–31-year-old secondary forest—the oldest at our site. Our results suggest that managers concerned with less sensitive species can assume that forest reserves connected by 12–18-year-old secondary forest corridors are effectively connected. On the other hand, >30 years are required after land abandonment before secondary forest serves as a primary forest-like conduit for movement by F. colma; more sensitive terrestrial insectivores may take longer still.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.biocon.2015.01.028","usgsCitation":"Hines, J.E., Powell, L.L., Wolfe, J.D., Johnson, E.L., Nichols, J., and Stouffer, P.C., 2015, Heterogeneous movement of insectivorous Amazonian birds through primary and secondary forest: A case study using multistate models with radiotelemetry data: Biological Conservation, v. 188, p. 100-108, https://doi.org/10.1016/j.biocon.2015.01.028.","productDescription":"8 p.","startPage":"100","endPage":"108","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-064220","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":306824,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Brazil","city":"Manaus","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -61.384530576017966,\n -1.6981363640401668\n ],\n [\n -61.384530576017966,\n -4.235218153320815\n ],\n [\n -58.61166836481719,\n -4.235218153320815\n ],\n [\n -58.61166836481719,\n -1.6981363640401668\n ],\n [\n -61.384530576017966,\n -1.6981363640401668\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"188","publishingServiceCenter":{"id":10,"text":"Baltimore PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"55d305b5e4b0518e35468cfe","contributors":{"authors":[{"text":"Hines, James E. 0000-0001-5478-7230 jhines@usgs.gov","orcid":"https://orcid.org/0000-0001-5478-7230","contributorId":146530,"corporation":false,"usgs":true,"family":"Hines","given":"James","email":"jhines@usgs.gov","middleInitial":"E.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":true,"id":568246,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Powell, Luke L.","contributorId":146576,"corporation":false,"usgs":false,"family":"Powell","given":"Luke","email":"","middleInitial":"L.","affiliations":[],"preferred":false,"id":568338,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Wolfe, Jared D.","contributorId":146577,"corporation":false,"usgs":false,"family":"Wolfe","given":"Jared","email":"","middleInitial":"D.","affiliations":[],"preferred":false,"id":568339,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Johnson, Erik l.","contributorId":146578,"corporation":false,"usgs":false,"family":"Johnson","given":"Erik","email":"","middleInitial":"l.","affiliations":[],"preferred":false,"id":568340,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Nichols, James D. 0000-0002-7631-2890 jnichols@usgs.gov","orcid":"https://orcid.org/0000-0002-7631-2890","contributorId":405,"corporation":false,"usgs":true,"family":"Nichols","given":"James D.","email":"jnichols@usgs.gov","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":568341,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Stouffer, Phillip C.","contributorId":146579,"corporation":false,"usgs":false,"family":"Stouffer","given":"Phillip","email":"","middleInitial":"C.","affiliations":[],"preferred":false,"id":568342,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70142429,"text":"70142429 - 2015 - The Mw6.0 24 August 2014 South Napa earthquake","interactions":[],"lastModifiedDate":"2017-11-27T12:57:58","indexId":"70142429","displayToPublicDate":"2015-03-05T14:30:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3372,"text":"Seismological Research Letters","onlineIssn":"1938-2057","printIssn":"0895-0695","active":true,"publicationSubtype":{"id":10}},"title":"The Mw6.0 24 August 2014 South Napa earthquake","docAbstract":"The Mw 6.0 South Napa earthquake, which occurred at 10:20 UTC 24 August 2014 was the largest earthquake to strike the greater San Francisco Bay area since the Mw 6.9 1989 Loma Prieta earthquake. The rupture from this right‐lateral earthquake propagated mostly unilaterally to the north and up‐dip, directing the strongest shaking toward the city of Napa, where peak ground accelerations (PGAs) between 45%g and 61%g were recorded and modified Mercalli intensities (MMIs) of VII–VIII were reported. Tectonic surface rupture with dextral slip of up to 46 cm was observed on a 12.5 km long segment, some of which was along a previously mapped strand of the West Napa fault system, although the rupture extended to the north of the mapped Quaternary strand. Modeling of seismic and geodetic data suggests an average coseismic slip of 50 cm, with a maximum slip of about 1 m at depths of 10–11 km. We observed up to 35 cm of afterslip along the surface trace in the week following the mainshock, primarily along the southern half of the surface rupture that experienced relatively little coseismic offset. Relocation of the sparse aftershock sequence suggests en echelon southwest‐ and northeast‐dipping fault planes, reflective of the complex fault geometry in this region. The Napa basin and historic and late Holocene alluvial flood deposits in downtown Napa amplified the ground motions there. Few ground failures were mapped, reflecting the dry season (as well as a persistent drought that had lowered the groundwater table) and the short duration of strong shaking in the epicentral area.
","language":"English","publisher":"Seismological Society of America","doi":"10.1785/0220150004","usgsCitation":"Brocher, T.M., Baltay Sundstrom, A.S., Hardebeck, J.L., Pollitz, F., Murray, J.R., Llenos, A., Schwartz, D.P., Blair, J.L., Ponti, D.J., Lienkaemper, J., Langenheim, V., Dawson, T.E., Hudnut, K.W., Shelly, D.R., Dreger, D.S., Boatwright, J., Aagaard, B.T., Wald, D.J., Allen, R.M., Barnhart, W.D., Knudsen, K.L., Brooks, B.A., and Scharer, K.M., 2015, The Mw6.0 24 August 2014 South Napa earthquake: Seismological Research Letters, v. 86, no. 2A, p. 309-326, https://doi.org/10.1785/0220150004.","productDescription":"18 p.","startPage":"309","endPage":"326","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-062228","costCenters":[{"id":237,"text":"Earthquake Science Center","active":true,"usgs":true}],"links":[{"id":298312,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"California","otherGeospatial":"Napa Valley","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -122.83264160156251,\n 37.83798775896515\n ],\n [\n -122.83264160156251,\n 38.74337300148126\n ],\n [\n -121.75598144531251,\n 38.74337300148126\n ],\n [\n -121.75598144531251,\n 37.83798775896515\n ],\n [\n -122.83264160156251,\n 37.83798775896515\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"86","issue":"2A","publishingServiceCenter":{"id":14,"text":"Menlo Park PSC"},"noUsgsAuthors":false,"publicationDate":"2015-03-04","publicationStatus":"PW","scienceBaseUri":"54f97e2de4b02419550d9b60","contributors":{"authors":[{"text":"Brocher, Thomas M. 0000-0002-9740-839X brocher@usgs.gov","orcid":"https://orcid.org/0000-0002-9740-839X","contributorId":262,"corporation":false,"usgs":true,"family":"Brocher","given":"Thomas","email":"brocher@usgs.gov","middleInitial":"M.","affiliations":[{"id":237,"text":"Earthquake Science Center","active":true,"usgs":true}],"preferred":true,"id":541874,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Baltay Sundstrom, Annemarie S. 0000-0002-6514-852X abaltay@usgs.gov","orcid":"https://orcid.org/0000-0002-6514-852X","contributorId":4932,"corporation":false,"usgs":true,"family":"Baltay Sundstrom","given":"Annemarie","email":"abaltay@usgs.gov","middleInitial":"S.","affiliations":[{"id":237,"text":"Earthquake Science Center","active":true,"usgs":true},{"id":234,"text":"Earthquake Hazards Program","active":true,"usgs":true}],"preferred":true,"id":541875,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Hardebeck, Jeanne L. 0000-0002-6737-7780 jhardebeck@usgs.gov","orcid":"https://orcid.org/0000-0002-6737-7780","contributorId":841,"corporation":false,"usgs":true,"family":"Hardebeck","given":"Jeanne","email":"jhardebeck@usgs.gov","middleInitial":"L.","affiliations":[{"id":234,"text":"Earthquake Hazards Program","active":true,"usgs":true},{"id":237,"text":"Earthquake Science Center","active":true,"usgs":true}],"preferred":true,"id":541876,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Pollitz, Fred F. fpollitz@usgs.gov","contributorId":2408,"corporation":false,"usgs":true,"family":"Pollitz","given":"Fred F.","email":"fpollitz@usgs.gov","affiliations":[{"id":237,"text":"Earthquake Science Center","active":true,"usgs":true}],"preferred":false,"id":541877,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Murray, Jessica R. 0000-0002-6144-1681 jrmurray@usgs.gov","orcid":"https://orcid.org/0000-0002-6144-1681","contributorId":2759,"corporation":false,"usgs":true,"family":"Murray","given":"Jessica","email":"jrmurray@usgs.gov","middleInitial":"R.","affiliations":[{"id":237,"text":"Earthquake Science Center","active":true,"usgs":true}],"preferred":true,"id":541878,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Llenos, Andrea L. allenos@usgs.gov","contributorId":139572,"corporation":false,"usgs":true,"family":"Llenos","given":"Andrea L.","email":"allenos@usgs.gov","affiliations":[{"id":237,"text":"Earthquake Science Center","active":true,"usgs":true}],"preferred":false,"id":541879,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Schwartz, David P. 0000-0001-5193-9200 dschwartz@usgs.gov","orcid":"https://orcid.org/0000-0001-5193-9200","contributorId":1940,"corporation":false,"usgs":true,"family":"Schwartz","given":"David","email":"dschwartz@usgs.gov","middleInitial":"P.","affiliations":[{"id":237,"text":"Earthquake Science Center","active":true,"usgs":true}],"preferred":true,"id":541880,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Blair, J. 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Throughout the Fort Irwin National Training Center area, 111 samples from both cored boreholes and surface outcrops were collected and processed for laboratory measurements. These samples represent various lithologic types that include plutonic and metamorphic (basement) rocks, lava flows, consolidated sedimentary rocks, and unconsolidated sedimentary deposits that formed in a series of intermountain basins. Basement rocks, lava flows, and some lithified tuffs are generally resistive (≥100 ohm-meters [Ω·m]) when saturated. Saturated unconsolidated samples are moderately conductive to conductive, with resistivities generally less than 100 Ω·m, and many of these samples are less than 50 Ω·m. The unconsolidated samples can further be separated into two broad groups: (1) younger sediments that are moderately conductive, owing to their limited clay content, and (2) older, more conductive sediments with a higher clay content that reflects substantial amounts of originally glassy volcanic ash subsequently altered to clay. The older sediments are believed to be Tertiary. Time-domain electromagnetic (TEM) data were acquired near most of the boreholes, and, on the whole, close agreements between laboratory measurements and resistivity models were found.
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Geology, Minerals, Energy, & Geophysics Science Center—Menlo Park
U.S. Geological Survey
345 Middlefield Road
Menlo Park, CA 94025-3591
The contribution of science to the development and implementation of policy is typically neither direct nor transparent. In 1995, the U.S. Fish and Wildlife Service (FWS) made a decision that was unprecedented in natural resource management, turning to an unused and unproven decision process to carry out trust responsibilities mandated by an international treaty. The decision process was adopted for the establishment of annual sport hunting regulations for the most economically important duck population in North America, the 6 to 11 million mallards Anas platyrhynchos breeding in the mid-continent region of north-central United States and central Canada. The key idea underlying the adopted decision process was to formally embed within it a scientific process designed to reduce uncertainty (learn) and thus make better decisions in the future. The scientific process entails use of models to develop predictions of competing hypotheses about system response to the selected action at each decision point. These prediction not only are used to select the optimal management action, but also are compared with the subsequent estimates of system state variables, providing evidence for modifying degrees of confidence in, and hence relative influence of, these models at the next decision point. Science and learning in one step are formally and directly incorporated into the next decision, contrasting with the usual ad hoc and indirect use of scientific results in policy development and decision-making. Application of this approach over the last 20 years has led to a substantial reduction in uncertainty, as well as to an increase in transparency and defensibility of annual decisions and a decrease in the contentiousness of the decision process. As resource managers are faced with increased uncertainty associated with various components of global change, this approach provides a roadmap for the future scientific management of natural resources.
","language":"English","publisher":"Wiley","doi":"10.1111/1365-2664.12406","usgsCitation":"Nichols, J., Johnson, F.A., Williams, B., and Boomer, G.S., 2015, On formally integrating science and policy: walking the walk: Journal of Applied Ecology, v. 52, no. 3, p. 539-543, https://doi.org/10.1111/1365-2664.12406.","productDescription":"5 p.","startPage":"539","endPage":"543","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-056557","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":298301,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Canada, United States","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -141.328125,\n 24.846565348219734\n ],\n [\n -141.328125,\n 69.7181066990676\n ],\n [\n -51.15234375,\n 69.7181066990676\n ],\n [\n -51.15234375,\n 24.846565348219734\n ],\n [\n -141.328125,\n 24.846565348219734\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"52","issue":"3","publishingServiceCenter":{"id":10,"text":"Baltimore PSC"},"noUsgsAuthors":false,"publicationDate":"2015-02-26","publicationStatus":"PW","scienceBaseUri":"54f97e2de4b02419550d9b5e","chorus":{"doi":"10.1111/1365-2664.12406","url":"http://dx.doi.org/10.1111/1365-2664.12406","publisher":"Wiley-Blackwell","authors":"Nichols James D., Johnson Fred A., Williams Byron K., Boomer G. Scott","journalName":"Journal of Applied Ecology","publicationDate":"2/26/2015"},"contributors":{"authors":[{"text":"Nichols, James D. 0000-0002-7631-2890 jnichols@usgs.gov","orcid":"https://orcid.org/0000-0002-7631-2890","contributorId":405,"corporation":false,"usgs":true,"family":"Nichols","given":"James D.","email":"jnichols@usgs.gov","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":541844,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Johnson, Fred A. 0000-0002-5854-3695 fjohnson@usgs.gov","orcid":"https://orcid.org/0000-0002-5854-3695","contributorId":2773,"corporation":false,"usgs":true,"family":"Johnson","given":"Fred","email":"fjohnson@usgs.gov","middleInitial":"A.","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true},{"id":566,"text":"Southeast Ecological Science Center","active":true,"usgs":true},{"id":455,"text":"National Wetlands Research Center","active":true,"usgs":true}],"preferred":true,"id":541845,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Williams, Byron K.","contributorId":139564,"corporation":false,"usgs":false,"family":"Williams","given":"Byron K.","affiliations":[{"id":12801,"text":"The Wildlife Society","active":true,"usgs":false}],"preferred":false,"id":541846,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Boomer, G. 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The prevailing assumption that laboratory-derived isotopic parameters apply to free-living animals is largely untested. We used stable carbon isotopes (δ13C) in whole blood from migratory Dunlin (Calidris alpina arcticola) to estimate an in situ turnover rate and individual diet-switch dates. Our in situ results indicated that turnover rates were higher in free-living birds, in comparison to the results of an experimental study on captive Dunlin and estimates derived from a theoretical allometric model. Diet-switch dates from all 3 methods were then used to estimate arrival dates to the Arctic; arrival dates calculated with the in situ turnover rate were later than those with the other turnover-rate estimates, substantially so in some cases. These later arrival dates matched dates when local snow conditions would have allowed Dunlin to settle, and agreed with anticipated arrival dates of Dunlin tracked with light-level geolocators. Our study presents a novel method for accurately estimating arrival dates for individuals of migratory species in which return dates are difficult to document. This may be particularly appropriate for species in which extrinsic tracking devices cannot easily be employed because of cost, body size, or behavioral constraints, and in habitats that do not allow individuals to be detected easily upon first arrival. Thus, this isotopic method offers an exciting alternative approach to better understand how species may be altering their arrival dates in response to changing climatic conditions.
","language":"English","publisher":"American Ornithological Society","doi":"10.1642/AUK-14-227.1","usgsCitation":"Doll, A.C., Lanctot, R.B., Stricker, C.A., Yezerinac, S.M., and Wunder, M., 2015, Improved arrival-date estimates of Arctic-breeding Dunlin (Calidris alpina arcticola): The Auk, v. 132, no. 2, p. 408-421, https://doi.org/10.1642/AUK-14-227.1.","productDescription":"14 p.","startPage":"408","endPage":"421","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-055980","costCenters":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"links":[{"id":472221,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1642/auk-14-227.1","text":"Publisher Index Page"},{"id":298300,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"otherGeospatial":"Arctic","volume":"132","issue":"2","publishingServiceCenter":{"id":2,"text":"Denver PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"54f97e2be4b02419550d9b56","contributors":{"authors":[{"text":"Doll, Andrew C.","contributorId":139566,"corporation":false,"usgs":false,"family":"Doll","given":"Andrew","email":"","middleInitial":"C.","affiliations":[{"id":6674,"text":"Department of Integrative Biology, University of Colorado Denver","active":true,"usgs":false}],"preferred":false,"id":541855,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Lanctot, Richard B.","contributorId":31894,"corporation":false,"usgs":true,"family":"Lanctot","given":"Richard","email":"","middleInitial":"B.","affiliations":[{"id":7029,"text":"Queen's University, Kingston, Ontario, Canada","active":true,"usgs":false},{"id":6987,"text":"U.S. Fish and Wildlife Sevice","active":true,"usgs":false},{"id":17786,"text":"Carleton University","active":true,"usgs":false},{"id":135,"text":"Biological Resources Division","active":false,"usgs":true}],"preferred":false,"id":541856,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Stricker, Craig A. 0000-0002-5031-9437 cstricker@usgs.gov","orcid":"https://orcid.org/0000-0002-5031-9437","contributorId":1097,"corporation":false,"usgs":true,"family":"Stricker","given":"Craig","email":"cstricker@usgs.gov","middleInitial":"A.","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":true,"id":541854,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Yezerinac, Stephen M.","contributorId":139567,"corporation":false,"usgs":false,"family":"Yezerinac","given":"Stephen","email":"","middleInitial":"M.","affiliations":[{"id":12803,"text":"Mount Allison University","active":true,"usgs":false}],"preferred":false,"id":541857,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Wunder, Michael B.","contributorId":80599,"corporation":false,"usgs":false,"family":"Wunder","given":"Michael B.","affiliations":[{"id":6674,"text":"Department of Integrative Biology, University of Colorado Denver","active":true,"usgs":false}],"preferred":false,"id":541858,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70180868,"text":"70180868 - 2015 - A new approach for continuous estimation of baseflow using discrete water quality data: Method description and comparison with baseflow estimates from two existing approaches","interactions":[],"lastModifiedDate":"2017-05-03T13:36:22","indexId":"70180868","displayToPublicDate":"2015-03-05T00:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2342,"text":"Journal of Hydrology","active":true,"publicationSubtype":{"id":10}},"title":"A new approach for continuous estimation of baseflow using discrete water quality data: Method description and comparison with baseflow estimates from two existing approaches","docAbstract":"Understanding how watershed characteristics and climate influence the baseflow component of stream discharge is a topic of interest to both the scientific and water management communities. Therefore, the development of baseflow estimation methods is a topic of active research. Previous studies have demonstrated that graphical hydrograph separation (GHS) and conductivity mass balance (CMB) methods can be applied to stream discharge data to estimate daily baseflow. While CMB is generally considered to be a more objective approach than GHS, its application across broad spatial scales is limited by a lack of high frequency specific conductance (SC) data. We propose a new method that uses discrete SC data, which are widely available, to estimate baseflow at a daily time step using the CMB method. The proposed approach involves the development of regression models that relate discrete SC concentrations to stream discharge and time. Regression-derived CMB baseflow estimates were more similar to baseflow estimates obtained using a CMB approach with measured high frequency SC data than were the GHS baseflow estimates at twelve snowmelt dominated streams and rivers. There was a near perfect fit between the regression-derived and measured CMB baseflow estimates at sites where the regression models were able to accurately predict daily SC concentrations. We propose that the regression-derived approach could be applied to estimate baseflow at large numbers of sites, thereby enabling future investigations of watershed and climatic characteristics that influence the baseflow component of stream discharge across large spatial scales.
","language":"English","publisher":"Elsevier","publisherLocation":"Amsterdam","doi":"10.1016/j.jhydrol.2014.12.039","usgsCitation":"Miller, M.P., Johnson, H.M., Susong, D.D., and Wolock, D.M., 2015, A new approach for continuous estimation of baseflow using discrete water quality data: Method description and comparison with baseflow estimates from two existing approaches: Journal of Hydrology, v. 522, p. 203-210, https://doi.org/10.1016/j.jhydrol.2014.12.039.","productDescription":"8 p.","startPage":"203","endPage":"210","ipdsId":"IP-057375","costCenters":[{"id":353,"text":"Kansas Water Science Center","active":false,"usgs":true},{"id":451,"text":"National Water Quality Assessment Program","active":true,"usgs":true},{"id":610,"text":"Utah Water Science Center","active":true,"usgs":true}],"links":[{"id":334804,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Arizona, Colorado, New Mexico, Utah, 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Center","active":true,"usgs":true}],"preferred":true,"id":662641,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Wolock, David M. 0000-0002-6209-938X dwolock@usgs.gov","orcid":"https://orcid.org/0000-0002-6209-938X","contributorId":540,"corporation":false,"usgs":true,"family":"Wolock","given":"David","email":"dwolock@usgs.gov","middleInitial":"M.","affiliations":[{"id":353,"text":"Kansas Water Science Center","active":false,"usgs":true},{"id":27111,"text":"National Water Quality Program","active":true,"usgs":true},{"id":451,"text":"National Water Quality Assessment Program","active":true,"usgs":true},{"id":503,"text":"Office of Water Quality","active":true,"usgs":true},{"id":37778,"text":"WMA - Integrated Modeling and Prediction Division","active":true,"usgs":true}],"preferred":true,"id":662642,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70182712,"text":"70182712 - 2015 - Life history strategies of fish species and biodiversity in eastern USA streams","interactions":[],"lastModifiedDate":"2018-09-25T09:40:22","indexId":"70182712","displayToPublicDate":"2015-03-05T00:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1528,"text":"Environmental Biology of Fishes","active":true,"publicationSubtype":{"id":10}},"title":"Life history strategies of fish species and biodiversity in eastern USA streams","docAbstract":"Predictive models have been used to determine fish species that occur less frequently than expected (decreasers) and those that occur more frequently than expected (increasers) in streams in the eastern U.S. Coupling life history traits with 51 decreaser and 38 increaser fish species provided the opportunity to examine potential mechanisms associated with predicted changes in fish species distributions in eastern streams. We assigned six life history traits – fecundity, longevity, maturation age, maximum total length, parental care, and spawning season duration – to each fish species. Decreaser species were significantly smaller in size and shorter-lived with reduced fecundity and shorter spawning seasons compared to increaser species. Cluster analysis of traits revealed correspondence with a life history model defining equilibrium (low fecundity, high parental care), opportunistic (early maturation, low parental care), and periodic (late maturation, high fecundity, low parental care) end-point strategies. Nearly 50 % of decreaser species were associated with an intermediate opportunistic-periodic strategy, suggesting that abiotic factors such as habitat specialization and streamflow alteration may serve as important influences on life history traits and strategies of decreaser species. In contrast, the percent of increaser species among life history strategy groups ranged from 21 to 32 %, suggesting that life history strategies of increaser species were more diverse than those of decreaser species. This study highlights the utility of linking life history theory to biodiversity to better understand mechanisms that contribute to fish species distributions in the eastern U.S.
","language":"English","doi":"10.1007/s10641-014-0304-1","usgsCitation":"Meador, M., and Brown, L.M., 2015, Life history strategies of fish species and biodiversity in eastern USA streams: Environmental Biology of Fishes, v. 98, no. 2, p. 663-677, https://doi.org/10.1007/s10641-014-0304-1.","productDescription":"15 p.","startPage":"663","endPage":"677","ipdsId":"IP-051004","costCenters":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true},{"id":451,"text":"National Water Quality Assessment Program","active":true,"usgs":true}],"links":[{"id":336247,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","volume":"98","issue":"2","publishingServiceCenter":{"id":9,"text":"Reston PSC"},"noUsgsAuthors":false,"publicationDate":"2014-07-02","publicationStatus":"PW","scienceBaseUri":"58b548c2e4b01ccd54fddfca","contributors":{"authors":[{"text":"Meador, Michael R. mrmeador@usgs.gov","contributorId":615,"corporation":false,"usgs":true,"family":"Meador","given":"Michael R.","email":"mrmeador@usgs.gov","affiliations":[{"id":451,"text":"National Water Quality Assessment Program","active":true,"usgs":true}],"preferred":true,"id":673389,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Brown, Larry M.","contributorId":184044,"corporation":false,"usgs":false,"family":"Brown","given":"Larry","email":"","middleInitial":"M.","affiliations":[],"preferred":false,"id":673390,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70141749,"text":"70141749 - 2015 - Geotechnical aspects in the epicentral region of the 2011, Mw5.8 Mineral, Virginia earthquake","interactions":[],"lastModifiedDate":"2017-04-14T10:22:17","indexId":"70141749","displayToPublicDate":"2015-03-04T15:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1727,"text":"GSA Special Papers","active":true,"publicationSubtype":{"id":10}},"title":"Geotechnical aspects in the epicentral region of the 2011, Mw5.8 Mineral, Virginia earthquake","docAbstract":"A reconnaissance team documented the geotechnical and geological aspects in the epicentral region of the Mw (moment magnitude) 5.8 Mineral, Virginia (USA), earthquake of 23 August 2011. Tectonically and seismically induced ground deformations, evidence of liquefaction, rock slides, river bank slumps, ground subsidence, performance of earthen dams, damage to public infrastructure and lifelines, and other effects of the earthquake were documented. This moderate earthquake provided the rare opportunity to collect data to help assess current geoengineering practices in the region, as well as to assess seismic performance of the aging infrastructure in the region. Ground failures included two marginal liquefaction sites, a river bank slump, four minor rockfalls, and a ~4-m-wide, ~12-m-long, ~0.3-m-deep subsidence on a residential property. Damage to lifelines included subsidence of the approaches for a bridge and a water main break to a heavily corroded, 5-cm-diameter valve in Mineral, Virginia. Observed damage to dams, landfills, and public-use properties included a small, shallow slide in the temporary (“working”) clay cap of the county landfill, damage to two earthen dams (one in the epicentral region and one further away near Bedford, Virginia), and substantial structural damage to two public school buildings.
","language":"English","publisher":"Geological Society of America","doi":"10.1130/2014.2509(09)","usgsCitation":"Green, R.A., Lasley, S., Carter, M.W., Munsey, J.W., Maurer, B.W., and Tuttle, M.P., 2015, Geotechnical aspects in the epicentral region of the 2011, Mw5.8 Mineral, Virginia earthquake: GSA Special Papers, v. 509, p. 151-172, https://doi.org/10.1130/2014.2509(09).","productDescription":"22 p.","startPage":"151","endPage":"172","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-054097","costCenters":[{"id":243,"text":"Eastern Geology and Paleoclimate Science Center","active":true,"usgs":true}],"links":[{"id":298295,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Virginia","city":"Mineral","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -84.495849609375,\n 36.10237644873644\n ],\n [\n -84.495849609375,\n 39.918162846609455\n ],\n [\n -74.77294921875,\n 39.918162846609455\n ],\n [\n -74.77294921875,\n 36.10237644873644\n ],\n [\n -84.495849609375,\n 36.10237644873644\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"509","publishingServiceCenter":{"id":9,"text":"Reston PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"54f82cafe4b02419550d99de","contributors":{"authors":[{"text":"Green, Russell A.","contributorId":94708,"corporation":false,"usgs":false,"family":"Green","given":"Russell","email":"","middleInitial":"A.","affiliations":[],"preferred":false,"id":540989,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Lasley, Samuel","contributorId":139385,"corporation":false,"usgs":false,"family":"Lasley","given":"Samuel","email":"","affiliations":[{"id":12694,"text":"Virginia Tech","active":true,"usgs":false}],"preferred":false,"id":540990,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Carter, Mark W. 0000-0003-0460-7638 mcarter@usgs.gov","orcid":"https://orcid.org/0000-0003-0460-7638","contributorId":4808,"corporation":false,"usgs":true,"family":"Carter","given":"Mark","email":"mcarter@usgs.gov","middleInitial":"W.","affiliations":[{"id":40020,"text":"Florence Bascom Geoscience Center","active":true,"usgs":true},{"id":245,"text":"Eastern Mineral and Environmental Resources Science Center","active":true,"usgs":true},{"id":243,"text":"Eastern Geology and Paleoclimate Science Center","active":true,"usgs":true}],"preferred":true,"id":540988,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Munsey, Jeffrey W.","contributorId":139386,"corporation":false,"usgs":false,"family":"Munsey","given":"Jeffrey","email":"","middleInitial":"W.","affiliations":[{"id":12759,"text":"TVA","active":true,"usgs":false}],"preferred":false,"id":540991,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Maurer, Brett W.","contributorId":139387,"corporation":false,"usgs":false,"family":"Maurer","given":"Brett","email":"","middleInitial":"W.","affiliations":[{"id":12694,"text":"Virginia Tech","active":true,"usgs":false}],"preferred":false,"id":540992,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Tuttle, Martitia P.","contributorId":139388,"corporation":false,"usgs":false,"family":"Tuttle","given":"Martitia","email":"","middleInitial":"P.","affiliations":[{"id":12760,"text":"Tuttle and Associates","active":true,"usgs":false}],"preferred":false,"id":540993,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70140105,"text":"70140105 - 2015 - Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia","interactions":[],"lastModifiedDate":"2017-06-29T12:13:27","indexId":"70140105","displayToPublicDate":"2015-03-04T12:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1325,"text":"Conservation Genetics Resources","active":true,"publicationSubtype":{"id":10}},"title":"Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia","docAbstract":"Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan (Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated from two three-hour runs on the Ion Torrent PGM can generate a sufficient number of nuclear and mitochondrial markers to improve understanding of the evolutionary and ecological dynamics of non-model and in particular, invasive species.
","language":"English","publisher":"Springer","publisherLocation":"Netherlands","doi":"10.1007/s12686-015-0430-x","usgsCitation":"King, T.L., Eackles, M.S., and Reshetnikov, A.N., 2015, Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia: Conservation Genetics Resources, v. 7, no. 2, p. 363-368, https://doi.org/10.1007/s12686-015-0430-x.","productDescription":"6 p.","startPage":"363","endPage":"368","numberOfPages":"6","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-060630","costCenters":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"links":[{"id":310265,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Russia","otherGeospatial":"European Russia","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n 26.71875,\n 42.032974332441405\n ],\n [\n 26.71875,\n 76.84081641443098\n ],\n [\n 91.23046875,\n 76.84081641443098\n ],\n [\n 91.23046875,\n 42.032974332441405\n ],\n [\n 26.71875,\n 42.032974332441405\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"7","issue":"2","publishingServiceCenter":{"id":10,"text":"Baltimore PSC"},"noUsgsAuthors":false,"publicationDate":"2015-03-04","publicationStatus":"PW","scienceBaseUri":"5628b73fe4b0d158f5926c49","contributors":{"authors":[{"text":"King, Tim L. tlking@usgs.gov","contributorId":3520,"corporation":false,"usgs":true,"family":"King","given":"Tim","email":"tlking@usgs.gov","middleInitial":"L.","affiliations":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":true,"id":539793,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Eackles, Michael S. meackles@usgs.gov","contributorId":4371,"corporation":false,"usgs":true,"family":"Eackles","given":"Michael","email":"meackles@usgs.gov","middleInitial":"S.","affiliations":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":true,"id":539794,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Reshetnikov, Andrey N.","contributorId":149329,"corporation":false,"usgs":false,"family":"Reshetnikov","given":"Andrey","email":"","middleInitial":"N.","affiliations":[{"id":12617,"text":"A.N. Severtsov Ecology & Evolution Institute, Leninskiy 33, Moscow 119071, Russia","active":true,"usgs":false}],"preferred":false,"id":577989,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70142328,"text":"70142328 - 2015 - Stochastic reservoir simulation for the modeling of uncertainty in coal seam degasification","interactions":[],"lastModifiedDate":"2015-03-04T10:53:51","indexId":"70142328","displayToPublicDate":"2015-03-04T10:45:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1709,"text":"Fuel","active":true,"publicationSubtype":{"id":10}},"title":"Stochastic reservoir simulation for the modeling of uncertainty in coal seam degasification","docAbstract":"Coal seam degasification improves coal mine safety by reducing the gas content of coal seams and also by generating added value as an energy source. Coal seam reservoir simulation is one of the most effective ways to help with these two main objectives. As in all modeling and simulation studies, how the reservoir is defined and whether observed productions can be predicted are important considerations.
\nUsing geostatistical realizations as spatial maps of different coal reservoir properties is a more realistic approach than assuming uniform properties across the field. In fact, this approach can help with simultaneous history matching of multiple wellbores to enhance the confidence in spatial models of different coal properties that are pertinent to degasification. The problem that still remains is the uncertainty in geostatistical simulations originating from the partial sampling of the seam that does not properly reflect the stochastic nature of coal property realizations. Stochastic simulations and using individual realizations, rather than E-type, make evaluation of uncertainty possible.
\nThis work is an advancement over Karacan et al. (2014) in the sense of assessing uncertainty that stems from geostatistical maps. In this work, we batched 100 individual realizations of 10 coal properties that were randomly generated to create 100 bundles and used them in 100 separate coal seam reservoir simulations for simultaneous history matching. We then evaluated the history matching errors for each bundle and defined the single set of realizations that would minimize the error for all wells. We further compared the errors with those of E-type and the average realization of the best matches. Unlike in Karacan et al. (2014), which used E-type maps and average of quantile maps, using these 100 bundles created 100 different history match results from separate simulations, and distributions of results for in-place gas quantity, for example, from which uncertainty in coal property realizations could be evaluated.
\nThe study helped to determine the realization bundle that consisted of the spatial maps of coal properties, which resulted in minimum error. In addition, it was shown that both E-type and the average of realizations that gave the best match for invidual approximated the same properties resonably. Moreover, the determined realization bundle showed that the study field initially had 151.5 million m3 (cubic meter) of gas and 1.04 million m3 water in the coal, corresponding to Q90 of the entire range of probability for gas and close to Q75 for water. In 2013, in-place fluid amounts decreased to 138.9 million m3 and 0.997 million m3 for gas and water, respectively.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.fuel.2015.01.046","usgsCitation":"Karacan, C., and Olea, R., 2015, Stochastic reservoir simulation for the modeling of uncertainty in coal seam degasification: Fuel, v. 148, p. 87-97, https://doi.org/10.1016/j.fuel.2015.01.046.","productDescription":"11 p.","startPage":"87","endPage":"97","numberOfPages":"11","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-062278","costCenters":[{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true}],"links":[{"id":472223,"rank":0,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"http://doi.org/10.1016/j.fuel.2015.01.046","text":"External Repository"},{"id":298276,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Indiana","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -87.54592895507812,\n 39.00851330385611\n ],\n [\n -87.54592895507812,\n 39.089034905217474\n ],\n [\n -87.41134643554688,\n 39.089034905217474\n ],\n [\n -87.41134643554688,\n 39.00851330385611\n ],\n [\n -87.54592895507812,\n 39.00851330385611\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"148","publishingServiceCenter":{"id":9,"text":"Reston PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"54f82cb1e4b02419550d99e2","contributors":{"authors":[{"text":"Karacan, C. Özgen 0000-0002-0947-8241","orcid":"https://orcid.org/0000-0002-0947-8241","contributorId":139554,"corporation":false,"usgs":true,"family":"Karacan","given":"C. Özgen","affiliations":[{"id":12800,"text":"National Institute for Occupational Safety and Health (NIOSH)","active":true,"usgs":false}],"preferred":false,"id":541822,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Olea, Ricardo A. 0000-0003-4308-0808 rolea@usgs.gov","orcid":"https://orcid.org/0000-0003-4308-0808","contributorId":1401,"corporation":false,"usgs":true,"family":"Olea","given":"Ricardo A.","email":"rolea@usgs.gov","affiliations":[{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true}],"preferred":false,"id":541821,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70136492,"text":"sir20145235 - 2015 - Simulation of groundwater flow and streamflow depletion in the Branch Brook, Merriland River, and parts of the Mousam River watersheds in southern Maine","interactions":[],"lastModifiedDate":"2015-03-04T10:40:00","indexId":"sir20145235","displayToPublicDate":"2015-03-04T10:30:00","publicationYear":"2015","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":334,"text":"Scientific Investigations Report","code":"SIR","onlineIssn":"2328-0328","printIssn":"2328-031X","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"2014-5235","title":"Simulation of groundwater flow and streamflow depletion in the Branch Brook, Merriland River, and parts of the Mousam River watersheds in southern Maine","docAbstract":"Watersheds of three streams, the Mousam River, Branch Brook, and Merriland River in southeastern Maine were investigated from 2010 through 2013 under a cooperative project between the U.S. Geological Survey and the Maine Geological Survey. The Branch Brook watershed previously had been deemed “at risk” by the Maine Geological Survey because of the proportionally large water withdrawals compared to estimates of the in-stream flow requirements for habitat protection. The primary groundwater withdrawals in the study area include a water-supply well in the headwaters of the system and three water-supply wells in the coastal plain near the downstream end of the system. A steady-state groundwater flow model was used to understand the movement of water within the system, to evaluate the water budget and the effect of groundwater withdrawals on streamflows, and to understand streamflow depletion in relation to the State of Maine’s requirements to maintain in-stream flows for habitat protection.
\nDelineation of the simulated groundwater divides compared to the surface-water divides suggests that the groundwater divides in the headwater areas do not exactly correspond to the surface-water divides. Under both pumping and non-pumping conditions, groundwater flows from the headwaters of the Branch Brook watershed into the Mousam River watershed. Pumping in the Mousam River watershed captures a small amount of groundwater from the Branch Brook basin.
\nThe cumulative effect of groundwater withdrawals on base flows in two rivers in the study area (Branch Brook and the Merriland River) was evaluated using the groundwater flow model. Streamflow depletion in the headwaters of Branch Brook was 0.12 cubic feet per second (ft3/s) for the steady-state simulation, or about 10 percent of the average base flow at that location. Downstream on Branch Brook, the total streamflow depletion from all the wells was 0.59 ft3/s, or 3 percent of the average base flow at that location. In the Merriland River downstream from the Merriland River well, the total amount of streamflow depletion was 0.6 ft3/s, or about 7 percent of the average base flow.
\nThe groundwater model was used to evaluate several different scenarios that could affect streamflow and groundwater discharging to the rivers and streams in the study area. The scenarios were (1) no pumping from the water-supply wells; (2) current pumping from the water-supply wells, but simulated drought conditions (25 percent reduction in recharge); (3) current recharge, but with increased pumping from the large water-supply wells; and (4) drought conditions and increased pumping combined.
\nSimulations of increased pumping in the water-supply wells resulted in streamflow depletion in the headwaters of Branch Brook increasing to 16 percent of the headwater base flow. Simulated increases in the pumping in the coastal plain wells increased the amount of streamflow depletion to 6 percent of the flow in Branch Brook and to 8 percent of the flow in the Merriland River. The additional stress of a drought imposed on the model (25 percent less recharge) had a substantial impact on streamflows, as expected. If the simulated drought occurred simultaneously with an increase in pumping, the base flows would be reduced 48 percent in the headwaters of Branch Brook, compared to the no-pumping scenario. Downstream in Branch Brook, the total reduction in flow would be 29 percent of the simulated base flows in the no-pumping scenario, and in the Merriland River, the reduction would be 33 percent of the base flows in the no-pumping scenario.
\nThe study evaluated two different methods of calculating in-stream flow requirements for Branch Brook and the Merriland River—a set of statewide equations used to calculate monthly median flows and the MOVE.1 record-extension technique used on site-specific streamflow measurements. The August median in-stream flow requirement in the Merriland River was calculated as 7.18 ft3/s using the statewide equations but was 3.07 ft3/s using the MOVE.1 analysis. In Branch Brook, the August median in-stream flow requirements were calculated as 20.3 ft3/s using the statewide equations and 11.8 ft3/s using the MOVE.1 analysis. In each case, using site-specific data yields an estimate of in-stream flow that is much lower than an estimate the statewide equations provide.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/sir20145235","collaboration":"Prepared in cooperation with the Maine Geological Survey","usgsCitation":"Nielsen, M.G., and Locke, D.B., 2015, Simulation of groundwater flow and streamflow depletion in the Branch Brook, Merriland River, and parts of the Mousam River watersheds in southern Maine: U.S. Geological Survey Scientific Investigations Report 2014-5235, x, 78 p., https://doi.org/10.3133/sir20145235.","productDescription":"x, 78 p.","numberOfPages":"92","onlineOnly":"Y","additionalOnlineFiles":"N","ipdsId":"IP-057435","costCenters":[{"id":371,"text":"Maine Water Science Center","active":true,"usgs":true}],"links":[{"id":298274,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/sir20145235.jpg"},{"id":298272,"rank":1,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/sir/2014/5235/"},{"id":298273,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/sir/2014/5235/pdf/sir2014-5235.pdf","text":"Report","size":"9.83 MB","linkFileType":{"id":1,"text":"pdf"},"description":"Report"}],"projection":"Universal Transverse Mercator projection","datum":"North American Datum of 1988","country":"United States","state":"Maine","otherGeospatial":"Branch Brook, Merriland River, Mousam River","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -70.7571029663086,\n 43.303944586803205\n ],\n [\n -70.7571029663086,\n 43.4576541092803\n ],\n [\n -70.49789428710938,\n 43.4576541092803\n ],\n [\n -70.49789428710938,\n 43.303944586803205\n ],\n [\n -70.7571029663086,\n 43.303944586803205\n ]\n ]\n ]\n }\n }\n ]\n}","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"54f82cb0e4b02419550d99e0","contributors":{"authors":[{"text":"Nielsen, Martha G. 0000-0003-3038-9400 mnielsen@usgs.gov","orcid":"https://orcid.org/0000-0003-3038-9400","contributorId":4169,"corporation":false,"usgs":true,"family":"Nielsen","given":"Martha","email":"mnielsen@usgs.gov","middleInitial":"G.","affiliations":[{"id":37947,"text":"Upper Midwest Water Science Center","active":true,"usgs":true}],"preferred":true,"id":537485,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Locke, Daniel B.","contributorId":131153,"corporation":false,"usgs":false,"family":"Locke","given":"Daniel","email":"","middleInitial":"B.","affiliations":[{"id":7257,"text":"Maine Geological Survey","active":true,"usgs":false}],"preferred":false,"id":537486,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70142212,"text":"ofr20151039 - 2015 - Estimation of occupancy, breeding success, and predicted abundance of golden eagles (Aquila chrysaetos) in the Diablo Range, California, 2014","interactions":[],"lastModifiedDate":"2017-11-27T14:28:27","indexId":"ofr20151039","displayToPublicDate":"2015-03-04T10:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":330,"text":"Open-File Report","code":"OFR","onlineIssn":"2331-1258","printIssn":"0196-1497","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"2015-1039","title":"Estimation of occupancy, breeding success, and predicted abundance of golden eagles (Aquila chrysaetos) in the Diablo Range, California, 2014","docAbstract":"We used a multistate occupancy sampling design to estimate occupancy, breeding success, and abundance of territorial pairs of golden eagles (Aquila chrysaetos) in the Diablo Range, California, in 2014. This method uses the spatial pattern of detections and non-detections over repeated visits to survey sites to estimate probabilities of occupancy and successful reproduction while accounting for imperfect detection of golden eagles and their young during surveys. The estimated probability of detecting territorial pairs of golden eagles and their young was less than 1 and varied with time of the breeding season, as did the probability of correctly classifying a pair’s breeding status. Imperfect detection and breeding classification led to a sizeable difference between the uncorrected, naïve estimate of the proportion of occupied sites where successful reproduction was observed (0.20) and the model-based estimate (0.30). The analysis further indicated a relatively high overall probability of landscape occupancy by pairs of golden eagles (0.67, standard error = 0.06), but that areas with the greatest occupancy and reproductive potential were patchily distributed. We documented a total of 138 territorial pairs of golden eagles during surveys completed in the 2014 breeding season, which represented about one-half of the 280 pairs we estimated to occur in the broader 5,169-square kilometer region sampled. The study results emphasize the importance of accounting for imperfect detection and spatial heterogeneity in studies of site occupancy, breeding success, and abundance of golden eagles.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ofr20151039","usgsCitation":"Wiens, J.D., Kolar, P.S., Fuller, M.R., Hunt, W.G., and Hunt, T., 2015, Estimation of occupancy, breeding success, and predicted abundance of golden eagles (Aquila chrysaetos) in the Diablo Range, California, 2014: U.S. Geological Survey Open-File Report 2015-1039, iv, 23 p., https://doi.org/10.3133/ofr20151039.","productDescription":"iv, 23 p.","numberOfPages":"32","onlineOnly":"Y","additionalOnlineFiles":"N","temporalStart":"2014-01-01","temporalEnd":"2014-12-31","ipdsId":"IP-061706","costCenters":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"links":[{"id":298266,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/ofr20151039.jpg"},{"id":298265,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/of/2015/1039/pdf/ofr2015-1039.pdf","text":"Report","size":"1.9 MB","linkFileType":{"id":1,"text":"pdf"},"description":"Report"},{"id":298264,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/of/2015/1039/"}],"country":"United States","state":"California","otherGeospatial":"Diablo Range","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -122.39593505859376,\n 38.026458711461245\n ],\n [\n -121.431884765625,\n 36.923547681089296\n ],\n [\n -121.025390625,\n 37.14937133266766\n ],\n [\n -121.16271972656249,\n 37.49229399862877\n ],\n [\n -121.92901611328125,\n 38.06106741381199\n ],\n [\n -122.39593505859376,\n 38.026458711461245\n ]\n ]\n ]\n }\n }\n ]\n}","publishingServiceCenter":{"id":12,"text":"Tacoma PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"54f82ca9e4b02419550d99d8","contributors":{"authors":[{"text":"Wiens, J. David 0000-0002-2020-038X jwiens@usgs.gov","orcid":"https://orcid.org/0000-0002-2020-038X","contributorId":468,"corporation":false,"usgs":true,"family":"Wiens","given":"J.","email":"jwiens@usgs.gov","middleInitial":"David","affiliations":[{"id":289,"text":"Forest and Rangeland Ecosys Science Center","active":true,"usgs":true}],"preferred":false,"id":541813,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kolar, Patrick S. 0000-0002-0076-7565","orcid":"https://orcid.org/0000-0002-0076-7565","contributorId":139543,"corporation":false,"usgs":true,"family":"Kolar","given":"Patrick","email":"","middleInitial":"S.","affiliations":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":541814,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Fuller, Mark R. 0000-0001-7459-1729 mark_fuller@usgs.gov","orcid":"https://orcid.org/0000-0001-7459-1729","contributorId":2296,"corporation":false,"usgs":true,"family":"Fuller","given":"Mark","email":"mark_fuller@usgs.gov","middleInitial":"R.","affiliations":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true},{"id":289,"text":"Forest and Rangeland Ecosys Science Center","active":true,"usgs":true}],"preferred":true,"id":541815,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Hunt, W. Grainger","contributorId":139544,"corporation":false,"usgs":false,"family":"Hunt","given":"W.","email":"","middleInitial":"Grainger","affiliations":[{"id":12795,"text":"The Peregrine Fund, Inc.","active":true,"usgs":false}],"preferred":false,"id":541816,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Hunt, Teresa","contributorId":139545,"corporation":false,"usgs":false,"family":"Hunt","given":"Teresa","affiliations":[{"id":12795,"text":"The Peregrine Fund, Inc.","active":true,"usgs":false}],"preferred":false,"id":541817,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70175225,"text":"70175225 - 2015 - Empirical evaluation of the conceptual model underpinning a regional aquatic long-term monitoring program using causal modelling","interactions":[],"lastModifiedDate":"2016-08-03T12:49:34","indexId":"70175225","displayToPublicDate":"2015-03-04T06:30:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1456,"text":"Ecological Indicators","active":true,"publicationSubtype":{"id":10}},"title":"Empirical evaluation of the conceptual model underpinning a regional aquatic long-term monitoring program using causal modelling","docAbstract":"Conceptual models are an integral facet of long-term monitoring programs. Proposed linkages between drivers, stressors, and ecological indicators are identified within the conceptual model of most mandated programs. We empirically evaluate a conceptual model developed for a regional aquatic and riparian monitoring program using causal models (i.e., Bayesian path analysis). We assess whether data gathered for regional status and trend estimation can also provide insights on why a stream may deviate from reference conditions. We target the hypothesized causal pathways for how anthropogenic drivers of road density, percent grazing, and percent forest within a catchment affect instream biological condition. We found instream temperature and fine sediments in arid sites and only fine sediments in mesic sites accounted for a significant portion of the maximum possible variation explainable in biological condition among managed sites. However, the biological significance of the direct effects of anthropogenic drivers on instream temperature and fine sediments were minimal or not detected. Consequently, there was weak to no biological support for causal pathways related to anthropogenic drivers’ impact on biological condition. With weak biological and statistical effect sizes, ignoring environmental contextual variables and covariates that explain natural heterogeneity would have resulted in no evidence of human impacts on biological integrity in some instances. For programs targeting the effects of anthropogenic activities, it is imperative to identify both land use practices and mechanisms that have led to degraded conditions (i.e., moving beyond simple status and trend estimation). Our empirical evaluation of the conceptual model underpinning the long-term monitoring program provided an opportunity for learning and, consequently, we discuss survey design elements that require modification to achieve question driven monitoring, a necessary step in the practice of adaptive monitoring. We suspect our situation is not unique and many programs may suffer from the same inferential disconnect. Commonly, the survey design is optimized for robust estimates of regional status and trend detection and not necessarily to provide statistical inferences on the causal mechanisms outlined in the conceptual model, even though these relationships are typically used to justify and promote the long-term monitoring of a chosen ecological indicator. Our application demonstrates a process for empirical evaluation of conceptual models and exemplifies the need for such interim assessments in order for programs to evolve and persist.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.ecolind.2014.10.011","usgsCitation":"Irvine, K.M., Miller, S., Al-Chokhachy, R.K., Archer, E., Roper, B.B., and Kershner, J.L., 2015, Empirical evaluation of the conceptual model underpinning a regional aquatic long-term monitoring program using causal modelling: Ecological Indicators, v. 50, p. 8-23, https://doi.org/10.1016/j.ecolind.2014.10.011.","productDescription":"16 p.","startPage":"8","endPage":"23","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-053097","costCenters":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"links":[{"id":326044,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"California, Colorado, Idaho, Montana, Nevada, Oregon, Utah, Washington, Wyoming","otherGeospatial":"Interior Columbia River Basin, Upper Missouri River Basin","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -104.19433593749999,\n 49.03786794532644\n ],\n [\n -106.2158203125,\n 38.34165619279593\n ],\n [\n -124.5849609375,\n 40.74725696280421\n ],\n [\n -124.541015625,\n 41.60722821271717\n ],\n [\n -124.62890625,\n 42.553080288955826\n ],\n [\n -124.76074218749999,\n 43.16512263158296\n ],\n [\n -124.4091796875,\n 43.96119063892024\n ],\n [\n -124.18945312500001,\n 45.42929873257377\n ],\n [\n -124.1455078125,\n 46.07323062540838\n ],\n [\n -124.45312499999999,\n 47.338822694822\n ],\n [\n -124.93652343749999,\n 48.1367666796927\n ],\n [\n -124.71679687499999,\n 48.45835188280866\n ],\n [\n -123.79394531249999,\n 48.3416461723746\n ],\n [\n -123.134765625,\n 48.48748647988415\n ],\n [\n -123.26660156249999,\n 48.777912755501845\n ],\n [\n -123.04687499999999,\n 48.80686346108517\n ],\n [\n -123.22265625000001,\n 49.03786794532644\n ],\n [\n -104.19433593749999,\n 49.03786794532644\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"50","publishingServiceCenter":{"id":2,"text":"Denver PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"57a315bee4b006cb45558a79","contributors":{"authors":[{"text":"Irvine, Kathryn M. 0000-0002-6426-940X kirvine@usgs.gov","orcid":"https://orcid.org/0000-0002-6426-940X","contributorId":2218,"corporation":false,"usgs":true,"family":"Irvine","given":"Kathryn","email":"kirvine@usgs.gov","middleInitial":"M.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":644411,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Miller, Scott","contributorId":58387,"corporation":false,"usgs":true,"family":"Miller","given":"Scott","affiliations":[],"preferred":false,"id":644412,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Al-Chokhachy, Robert K. 0000-0002-2136-5098 ral-chokhachy@usgs.gov","orcid":"https://orcid.org/0000-0002-2136-5098","contributorId":1674,"corporation":false,"usgs":true,"family":"Al-Chokhachy","given":"Robert","email":"ral-chokhachy@usgs.gov","middleInitial":"K.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":644413,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Archer, Erik","contributorId":173367,"corporation":false,"usgs":false,"family":"Archer","given":"Erik","email":"","affiliations":[{"id":27214,"text":"U.S.D.A. Forest Service, Forest Sciences Lab, 860 North 1200 East, Logan, UT","active":true,"usgs":false}],"preferred":false,"id":644414,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Roper, Brett B.","contributorId":120701,"corporation":false,"usgs":false,"family":"Roper","given":"Brett","email":"","middleInitial":"B.","affiliations":[],"preferred":false,"id":644415,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Kershner, Jeffrey L. 0000-0002-7093-9860 jkershner@usgs.gov","orcid":"https://orcid.org/0000-0002-7093-9860","contributorId":310,"corporation":false,"usgs":true,"family":"Kershner","given":"Jeffrey","email":"jkershner@usgs.gov","middleInitial":"L.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":644416,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70173595,"text":"70173595 - 2015 - Occupancy modeling for improved accuracy and understanding of pathogen prevalence and dynamics","interactions":[],"lastModifiedDate":"2016-06-09T15:53:01","indexId":"70173595","displayToPublicDate":"2015-03-04T00:00:00","publicationYear":"2015","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2980,"text":"PLoS ONE","active":true,"publicationSubtype":{"id":10}},"title":"Occupancy modeling for improved accuracy and understanding of pathogen prevalence and dynamics","docAbstract":"Most pathogen detection tests are imperfect, with a sensitivity < 100%, thereby resulting in the potential for a false negative, where a pathogen is present but not detected. False negatives in a sample inflate the number of non-detections, negatively biasing estimates of pathogen prevalence. Histological examination of tissues as a diagnostic test can be advantageous as multiple pathogens can be examined and providing important information on associated pathological changes to the host. However, it is usually less sensitive than molecular or microbiological tests for specific pathogens. Our study objectives were to 1) develop a hierarchical occupancy model to examine pathogen prevalence in spring Chinook salmonOncorhynchus tshawytscha and their distribution among host tissues 2) use the model to estimate pathogen-specific test sensitivities and infection rates, and 3) illustrate the effect of using replicate within host sampling on sample sizes required to detect a pathogen. We examined histological sections of replicate tissue samples from spring Chinook salmon O. tshawytscha collected after spawning for common pathogens seen in this population:Apophallus/echinostome metacercariae, Parvicapsula minibicornis, Nanophyetus salmincola/metacercariae, and Renibacterium salmoninarum. A hierarchical occupancy model was developed to estimate pathogen and tissue-specific test sensitivities and unbiased estimation of host- and organ-level infection rates. Model estimated sensitivities and host- and organ-level infections rates varied among pathogens and model estimated infection rate was higher than prevalence unadjusted for test sensitivity, confirming that prevalence unadjusted for test sensitivity was negatively biased. The modeling approach provided an analytical approach for using hierarchically structured pathogen detection data from lower sensitivity diagnostic tests, such as histology, to obtain unbiased pathogen prevalence estimates with associated uncertainties. Accounting for test sensitivity using within host replicate samples also required fewer individual fish to be sampled. This approach is useful for evaluating pathogen or microbe community dynamics when test sensitivity is <100%.
","language":"English","publisher":"PLOS One","doi":"10.1371/journal.pone.0116605","usgsCitation":"Colvin, M., Peterson, J., Kent, M.L., and Schreck, C.B., 2015, Occupancy modeling for improved accuracy and understanding of pathogen prevalence and dynamics: PLoS ONE, v. 10, no. 3, https://doi.org/10.1371/journal.pone.0116605.","onlineOnly":"Y","additionalOnlineFiles":"N","ipdsId":"IP-056718","costCenters":[{"id":200,"text":"Coop Res Unit Seattle","active":true,"usgs":true}],"links":[{"id":472225,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1371/journal.pone.0116605","text":"Publisher Index Page"},{"id":323433,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"10","issue":"3","publishingServiceCenter":{"id":12,"text":"Tacoma PSC"},"noUsgsAuthors":false,"publicationDate":"2015-03-04","publicationStatus":"PW","scienceBaseUri":"575a9334e4b04f417c27516c","contributors":{"authors":[{"text":"Colvin, Michael E.","contributorId":140975,"corporation":false,"usgs":false,"family":"Colvin","given":"Michael E.","affiliations":[{"id":6680,"text":"Oregon State University","active":true,"usgs":false}],"preferred":false,"id":638334,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Peterson, James T. 0000-0002-7709-8590 james_peterson@usgs.gov","orcid":"https://orcid.org/0000-0002-7709-8590","contributorId":2111,"corporation":false,"usgs":true,"family":"Peterson","given":"James","email":"james_peterson@usgs.gov","middleInitial":"T.","affiliations":[{"id":200,"text":"Coop Res Unit Seattle","active":true,"usgs":true}],"preferred":true,"id":637383,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Kent, Michael L.","contributorId":16693,"corporation":false,"usgs":true,"family":"Kent","given":"Michael","email":"","middleInitial":"L.","affiliations":[],"preferred":false,"id":638335,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Schreck, Carl B. 0000-0001-8347-1139 carl.schreck@usgs.gov","orcid":"https://orcid.org/0000-0001-8347-1139","contributorId":878,"corporation":false,"usgs":true,"family":"Schreck","given":"Carl","email":"carl.schreck@usgs.gov","middleInitial":"B.","affiliations":[{"id":289,"text":"Forest and Rangeland Ecosys Science Center","active":true,"usgs":true},{"id":200,"text":"Coop Res Unit Seattle","active":true,"usgs":true}],"preferred":true,"id":638336,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70142086,"text":"ofr20151037 - 2015 - Validation of eDNA markers for New Zealand mudsnail surveillance and initial eDNA monitoring at Mississippi River Basin sites","interactions":[],"lastModifiedDate":"2015-03-04T08:41:16","indexId":"ofr20151037","displayToPublicDate":"2015-03-03T17:15:00","publicationYear":"2015","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":330,"text":"Open-File Report","code":"OFR","onlineIssn":"2331-1258","printIssn":"0196-1497","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"2015-1037","title":"Validation of eDNA markers for New Zealand mudsnail surveillance and initial eDNA monitoring at Mississippi River Basin sites","docAbstract":"The performance of newly developed New Zealand mudsnail (Potamopyrgus antipodarum; NZMS) genetic markers for environmental (eDNA) analysis of water were compared across two laboratories. The genetic markers were tested in four quantitative polymerase chain reaction assays targeting two regions of the NZMS mitochondrial genome, specifically the cytochrome c oxidase subunit 1 (coi) and cytochrome b (cytb) genes. In a blind study, analysts tested each sample eight times with each assay. There were 10 expected-negative samples from the Black River in La Crosse, Wisconsin, 10 expected-positive samples from the Black Earth Creek in Black Earth, Wisconsin, and 10 known-positive samples from the Black River spiked with NZMS DNA. Previously extracted samples, kept at the Upper Midwest Environmental Sciences Center, were pooled by sample location and then equal quantities were distributed between the Upper Midwest Environmental Sciences Center and the Molecular Conservation Genetics Laboratory at the University of Wisconsin-Stevens Point for analysis. The assays tested were (1) the assay targeting cytb with a minor groove binder probe described by Goldberg and others (2013), (2) the cytb assay with a modified double-quenched probe, (3) an assay targeting coi with a double-quenched probe, and (4) a duplex reaction combining the modified cytb assay and the coi assay. Samples were considered positive for the presence of NZMS DNA when quantitative polymerase chain reaction amplification and probe signal was higher than the normalized threshold value above baseline fluorescence. For the duplex assay, samples were considered positive only when both probe signals were higher than the normalized threshold value above baseline fluorescence. Positive results were then confirmed by sequencing the products.
\nAll four assays detected the DNA of NZMS in all expected-positive and known-positive samples in both labs. The modified cytb assay, the coi assay, and the duplex assay all failed to detect the DNA of NZMS in all expected-negative samples in both labs. The cytb assay, as described by Goldberg and others (2013), failed to detect the DNA of NZMS in all expected-negative samples for the Molecular Conservation Genetics Laboratory, but some reactions resulted in positive detection in late cycles for 9 of the 10 expected-negative samples at the Upper Midwest Environmental Sciences Center. Amplicons for expected-negative samples with positive reactions were sent for sequencing, and none were confirmed as NZMS. Six amplicons failed to give readable sequences, and three gave sequences without similarity to any known sequence in GenBank. Amplicons from each assay for one representative positive sample were sequenced and identified as NZMS with greater than 99 percent identity.
\nThe duplex assay was chosen as the most efficient assay and was used at the Upper Midwest Environmental Sciences Center to analyze triplicate samples from 29 streams in Wisconsin, 8 streams in Illinois, and 8 streams in Iowa. In order to verify results, additional triplicate samples were collected from two of the streams in Iowa and two of the streams in Wisconsin for analysis at the Molecular Conservation Genetics Laboratory. All samples at all sites were negative for NZMS DNA.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ofr20151037","collaboration":"Prepared in cooperation with Wisconsin Cooperative Fishery Research Unit, Molecular Conservation Genetics Laboratory, College of Natural Resources, University of Wisconsin-Stevens Point","usgsCitation":"Merkes, C.M., Turnquist, K.N., Rees, C.B., and Amberg, J., 2015, Validation of eDNA markers for New Zealand mudsnail surveillance and initial eDNA monitoring at Mississippi River Basin sites: U.S. Geological Survey Open-File Report 2015-1037, Report: vi, 9 p.; Tables 4-7, https://doi.org/10.3133/ofr20151037.","productDescription":"Report: vi, 9 p.; Tables 4-7","numberOfPages":"16","onlineOnly":"Y","additionalOnlineFiles":"Y","ipdsId":"IP-063296","costCenters":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"links":[{"id":298262,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/ofr20151037.jpg"},{"id":298251,"rank":1,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/of/2015/1037/"},{"id":298259,"rank":4,"type":{"id":7,"text":"Companion Files"},"url":"https://pubs.usgs.gov/of/2015/1037/tables/nzms_table5.xlsx","text":"Table 5","size":"30 KB","linkFileType":{"id":3,"text":"xlsx"},"linkHelpText":"Molecular Conservation Genetics Laboratory assay validation results."},{"id":298260,"rank":5,"type":{"id":7,"text":"Companion Files"},"url":"https://pubs.usgs.gov/of/2015/1037/tables/nzms_table6.xlsx","text":"Table 6","size":"20 KB","linkFileType":{"id":3,"text":"xlsx"},"linkHelpText":"Sequencing results."},{"id":298261,"rank":6,"type":{"id":7,"text":"Companion Files"},"url":"https://pubs.usgs.gov/of/2015/1037/tables/nzms_table7.xlsx","text":"Table 7","size":"34 KB","linkFileType":{"id":3,"text":"xlsx"},"linkHelpText":"Monitoring results."},{"id":298258,"rank":3,"type":{"id":7,"text":"Companion Files"},"url":"https://pubs.usgs.gov/of/2015/1037/tables/nzms_table4.xlsx","text":"Table 4","size":"30 KB","linkFileType":{"id":3,"text":"xlsx"},"linkHelpText":"Upper Midwest Environmental Sciences Center assay validation results."},{"id":298257,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/of/2015/1037/pdf/ofr2015-1037.pdf","text":"Report","size":"2631 KB","linkFileType":{"id":1,"text":"pdf"},"description":"OF 2015-1037 Report"}],"country":"United States","state":"Illinois, Iowa, Wisconsin","otherGeospatial":"Mississippi River Basin","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -92.724609375,\n 41.27780646738183\n ],\n [\n -92.724609375,\n 46.164614496897094\n ],\n [\n -88.26416015625,\n 46.164614496897094\n ],\n [\n -88.26416015625,\n 41.27780646738183\n ],\n [\n -92.724609375,\n 41.27780646738183\n ]\n ]\n ]\n }\n }\n ]\n}","publishingServiceCenter":{"id":6,"text":"Columbus PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"54f6db2ee4b02419550d3096","contributors":{"authors":[{"text":"Merkes, Christopher M. 0000-0001-8191-627X cmerkes@usgs.gov","orcid":"https://orcid.org/0000-0001-8191-627X","contributorId":139516,"corporation":false,"usgs":true,"family":"Merkes","given":"Christopher","email":"cmerkes@usgs.gov","middleInitial":"M.","affiliations":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"preferred":true,"id":541782,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Turnquist, Keith N.","contributorId":139517,"corporation":false,"usgs":false,"family":"Turnquist","given":"Keith","email":"","middleInitial":"N.","affiliations":[{"id":12787,"text":"Molecular Conservation Genetics Laboratory, University of Wisconsin-Stevens Point","active":true,"usgs":false}],"preferred":false,"id":541783,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Rees, Christopher B. crees@usgs.gov","contributorId":5500,"corporation":false,"usgs":true,"family":"Rees","given":"Christopher","email":"crees@usgs.gov","middleInitial":"B.","affiliations":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"preferred":true,"id":541784,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Amberg, Jon J. jamberg@usgs.gov","contributorId":139518,"corporation":false,"usgs":true,"family":"Amberg","given":"Jon J.","email":"jamberg@usgs.gov","affiliations":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"preferred":false,"id":541785,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70140639,"text":"ofr20151029 - 2015 - Resilience and risk: a demographic model to inform conservation planning for polar bears","interactions":[],"lastModifiedDate":"2015-03-03T13:45:09","indexId":"ofr20151029","displayToPublicDate":"2015-03-03T14:30:00","publicationYear":"2015","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":330,"text":"Open-File Report","code":"OFR","onlineIssn":"2331-1258","printIssn":"0196-1497","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"2015-1029","title":"Resilience and risk: a demographic model to inform conservation planning for polar bears","docAbstract":"Climate change is having widespread ecological effects, including loss of Arctic sea ice. This has led to listing of the polar bear (Ursus maritimus) and other ice-dependent marine mammals under the U.S. Endangered Species Act (ESA). Methods are needed to evaluate the effects of climate change on population persistence to inform recovery planning for listed species. For polar bears, this includes understanding interactions between climate and secondary factors, such as subsistence harvest, which provide economic, nutritional, or cultural value to humans.
\nWe developed a matrix-based demographic model for polar bears that can be used for population viability analysis and to evaluate the effects of human-caused removals. This model includes density-dependence (the potential for a declining environmental carrying capacity), density-independent limitation, and sex- and age-specific harvest vulnerabilities. We estimated values of adult female survival (0.93–0.96), recruitment (number of yearling cubs per adult female; 0.1–0.3), and carrying capacity (>250 animals) that must be maintained for a hypothetical population to achieve a 90-percent probability of persistence over 100 years.
\nWe also developed a state-dependent management framework, based on harvest theory and the potential biological removal method, by linking the demographic model to simulated population assessments. This framework can be used to estimate the maximum sustainable rate of human-caused removals, including subsistence harvest, which maintains a population at its maximum net productivity level. The framework also can be used to calculate a recommended sustainable harvest rate, which generally is lower than the maximum sustainable rate and depends on management objectives, the precision and frequency of population data, and risk tolerance. The historical standard 4.5-percent harvest rate for polar bears, at a 2:1 male-to-female ratio, is reasonable under many biological and management conditions, although lower or higher rates may be appropriate in some cases.
\nOur modeling results suggest that harvest of polar bears is unlikely to accelerate population declines that result from declining carrying capacity caused by sea-ice loss, provided that several conditions are met: (1) the sustainable harvest rate reflects the population’s intrinsic growth rate, and the corresponding harvest level is obtained by applying this rate to an estimate of population size; (2) the sustainable harvest rate reflects the quality of population data (e.g., lower harvest when data are poor); and (3) the level of human-caused removals can be adjusted. Finally, our results suggest that stopgap measures (e.g., further reduction or cessation of harvest when the population size is less than a critical threshold) may be necessary to minimize the incremental risk associated with harvest, if environmental conditions are deteriorating rapidly. We suggest that the demographic model and approaches presented here can serve as a template for conservation planning for polar bears and other species facing similar challenges.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ofr20151029","collaboration":"Prepared in cooperation with the U.S. Fish and Wildlife Service","usgsCitation":"Regehr, E.V., Wilson, R.H., Rode, K.D., and Runge, M.C., 2015, Resilience and risk: a demographic model to inform conservation planning for polar bears: U.S. Geological Survey Open-File Report 2015-1029, vi, 56 p., https://doi.org/10.3133/ofr20151029.","productDescription":"vi, 56 p.","numberOfPages":"66","onlineOnly":"Y","additionalOnlineFiles":"N","ipdsId":"IP-060795","costCenters":[{"id":116,"text":"Alaska Science Center Biology MFEB","active":true,"usgs":true}],"links":[{"id":298250,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/ofr20151029.jpg"},{"id":298248,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/of/2015/1029/"},{"id":298249,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/of/2015/1029/pdf/ofr2015-1029.pdf","size":"2.1 MB","linkFileType":{"id":1,"text":"pdf"}}],"publishingServiceCenter":{"id":12,"text":"Tacoma PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"54f6db2be4b02419550d3094","contributors":{"authors":[{"text":"Regehr, Eric V. 0000-0003-4487-3105","orcid":"https://orcid.org/0000-0003-4487-3105","contributorId":66364,"corporation":false,"usgs":false,"family":"Regehr","given":"Eric","email":"","middleInitial":"V.","affiliations":[{"id":12428,"text":"U. S. Fish and Wildlife Service","active":true,"usgs":false}],"preferred":false,"id":541774,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Wilson, Ryan H. 0000-0001-7740-7771","orcid":"https://orcid.org/0000-0001-7740-7771","contributorId":130989,"corporation":false,"usgs":false,"family":"Wilson","given":"Ryan","email":"","middleInitial":"H.","affiliations":[{"id":6987,"text":"U.S. Fish and Wildlife Sevice","active":true,"usgs":false}],"preferred":false,"id":541775,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Rode, Karyn D. 0000-0002-3328-8202 krode@usgs.gov","orcid":"https://orcid.org/0000-0002-3328-8202","contributorId":5053,"corporation":false,"usgs":true,"family":"Rode","given":"Karyn","email":"krode@usgs.gov","middleInitial":"D.","affiliations":[{"id":114,"text":"Alaska Science Center","active":true,"usgs":true},{"id":116,"text":"Alaska Science Center Biology MFEB","active":true,"usgs":true}],"preferred":true,"id":541776,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Runge, Michael C. 0000-0002-8081-536X mrunge@usgs.gov","orcid":"https://orcid.org/0000-0002-8081-536X","contributorId":3358,"corporation":false,"usgs":true,"family":"Runge","given":"Michael","email":"mrunge@usgs.gov","middleInitial":"C.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":true,"id":541777,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ]}