In an effort to understand the role of sediment of South San Francisco Bay (South Bay) salt ponds, an acoustic seabed classification was performed with the condition of over two hundred sediment samples. The success of the large-scale tidal wetland restoration of up to 15,000 acres of South Bay partly depends on the ability of the converted ponds to acquire and retain enough sediment to support marsh growth. Determining the distribution of South Bay's seabed sediment types and understanding their potential erosive properties helps answer critical planning questions about sediment budgets and sediment transportation.
\nAcoustic seabed classification is the organization of the seafloor into discrete units based on the characteristics of the acoustic response generated by an echosounder. Acoustic diversity is considered a proxy for geoacoustical parameters including acoustic impedance contrast, scatter and volume reverberation which all vary with sediment type. In addition, biological and anthropogenic features can influence the acoustic response.
\nData for an acoustic seabed classification were collected as a part of a California Coastal Conservancy funded bathymetric survey of South Bay in early 2005. A QTC VIEW seabed classification system recorded echoes from a sungle bean 50 kHz echosounder. Approximately 450,000 seabed classification records were generated from an are of of about 30 sq. miles. Ten district acoustic classes were identified through an unsupervised classification system using principle component and cluster analyses. One hundred and sixty-one grab samples and forty-five benthic community composition data samples collected in the study area shortly before and after the seabed classification survey, further refined the ten classes into groups based on grain size. A preliminary map of surficial grain size of South Bay was developed from the combination of the seabed classification and the grab and benthic samples. The initial seabed classification map, the grain size map, and locations of sediment samples will be displayed along with the methods of acousitc seabed classification.
","language":"English","usgsCitation":"Fregoso, T.A., Jaffe, B., Rathwell, G., Collins, W., Rhynas, K., Tomlin, V., and Sullivan, S., 2006, Mapping South San Francisco Bay's seabed diversity for use in wetland restoration planning, 1 p.","productDescription":"1 p.","numberOfPages":"1","onlineOnly":"N","additionalOnlineFiles":"N","costCenters":[{"id":5079,"text":"Pacific Regional Director's Office","active":true,"usgs":true}],"links":[{"id":325980,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":325978,"rank":1,"type":{"id":11,"text":"Document"},"url":"https://www.southbayrestoration.org/pdf_files/science%20symposium/2006%20Science%20Symposium%20Poster%20Abstracts.pdf","text":"South Bay Pond Restoration Project","size":"275 KB","linkFileType":{"id":1,"text":"pdf"},"description":"South Bay Pond Restoration Project"}],"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"57a1c430e4b006cb45552c25","contributors":{"authors":[{"text":"Fregoso, Theresa A. 0000-0001-7802-5812 tfregoso@usgs.gov","orcid":"https://orcid.org/0000-0001-7802-5812","contributorId":2571,"corporation":false,"usgs":true,"family":"Fregoso","given":"Theresa","email":"tfregoso@usgs.gov","middleInitial":"A.","affiliations":[{"id":520,"text":"Pacific Coastal and Marine Science Center","active":true,"usgs":true},{"id":186,"text":"Coastal and Marine Geology Program","active":true,"usgs":true}],"preferred":true,"id":644368,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Jaffe, B.","contributorId":78517,"corporation":false,"usgs":true,"family":"Jaffe","given":"B.","affiliations":[],"preferred":false,"id":644369,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Rathwell, G.","contributorId":67453,"corporation":false,"usgs":true,"family":"Rathwell","given":"G.","affiliations":[],"preferred":false,"id":644370,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Collins, W.","contributorId":29359,"corporation":false,"usgs":true,"family":"Collins","given":"W.","affiliations":[],"preferred":false,"id":644371,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Rhynas, K.","contributorId":56599,"corporation":false,"usgs":true,"family":"Rhynas","given":"K.","affiliations":[],"preferred":false,"id":644372,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Tomlin, V.","contributorId":173349,"corporation":false,"usgs":false,"family":"Tomlin","given":"V.","email":"","affiliations":[],"preferred":false,"id":644373,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Sullivan, S.","contributorId":173350,"corporation":false,"usgs":false,"family":"Sullivan","given":"S.","affiliations":[],"preferred":false,"id":644374,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ,{"id":70160307,"text":"70160307 - 2006 - Assessing vaccination as a control strategy in an ongoing epidemic: Bovine tuberculosis in African buffalo","interactions":[],"lastModifiedDate":"2021-03-18T15:14:31.57442","indexId":"70160307","displayToPublicDate":"2015-08-04T00:00:00","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1458,"text":"Ecological Modelling","active":true,"publicationSubtype":{"id":10}},"title":"Assessing vaccination as a control strategy in an ongoing epidemic: Bovine tuberculosis in African buffalo","docAbstract":"Bovine tuberculosis (BTB) is an exotic disease invading the buffalo population (Syncerus caffer) of the Kruger National Park (KNP), South Africa. We used a sex and age-structured epidemiological model to assess the effectiveness of a vaccination program and define important research directions. The model allows for dispersal between a focal herd and background population and was parameterized with a combination of published data and analyses of over 130 radio-collared buffalo in the central region of the KNP. Radio-tracking data indicated that all sex and age categories move between mixed herds, and males over 8 years old had higher mortality and dispersal rates than any other sex or age category. In part due to the high dispersal rates of buffalo, sensitivity analyses indicate that disease prevalence in the background population accounts for the most variability in the BTB prevalence and quasi-eradication within the focal herd. Vaccination rate and the transmission coefficient were the second and third most important parameters of the sensitivity analyses. Further analyses of the model without dispersal suggest that the amount of vaccination necessary for quasi-eradication (i.e. prevalence < 5%) depends upon the duration that a vaccine grants protection. Vaccination programs are more efficient (i.e. fewer wasted doses) when they focus on younger individuals. However, even with a lifelong vaccine and a closed population, the model suggests that >70% of the calf population would have to be vaccinated every year to reduce the prevalence to less than 1%. If the half-life of the vaccine is less than 5 years, even vaccinating every calf for 50 years may not eradicate BTB. Thus, although vaccination provides a means of controlling BTB prevalence it should be combined with other control measures if eradication is the objective.
","language":"English","publisher":"Elselvier","doi":"10.1016/j.ecolmodel.2006.02.009","usgsCitation":"Cross, P.C., and Getz, W.M., 2006, Assessing vaccination as a control strategy in an ongoing epidemic: Bovine tuberculosis in African buffalo: Ecological Modelling, v. 196, no. 3-4, p. 494-504, https://doi.org/10.1016/j.ecolmodel.2006.02.009.","productDescription":"11 p.","startPage":"494","endPage":"504","onlineOnly":"N","additionalOnlineFiles":"N","costCenters":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"links":[{"id":312384,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"South Africa","otherGeospatial":"Kruger National Park","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n 31.865844726562504,\n -23.956136333969273\n ],\n [\n 31.75048828125,\n -23.87076873182047\n ],\n [\n 31.6680908203125,\n -23.61432859499168\n ],\n [\n 31.569213867187496,\n -23.478362362272495\n ],\n [\n 31.5472412109375,\n -23.185813175302915\n ],\n [\n 31.26708984375,\n -22.37039634432004\n ],\n [\n 31.0638427734375,\n -22.329752304376473\n ],\n [\n 30.9814453125,\n -22.52270570348246\n ],\n [\n 30.8880615234375,\n -22.710322842052246\n ],\n [\n 31.019897460937504,\n -22.735656852206482\n ],\n [\n 30.871582031249996,\n -23.0443526637918\n ],\n [\n 31.096801757812496,\n -23.649556122147732\n ],\n [\n 31.1572265625,\n -24.021379342900296\n ],\n [\n 30.805664062500004,\n -24.15176601231297\n ],\n [\n 31.26708984375,\n -24.602074737077242\n ],\n [\n 31.580200195312496,\n -24.63203814959688\n ],\n [\n 31.327514648437496,\n -24.72188526321623\n ],\n [\n 31.179199218749996,\n -25.000994300028946\n ],\n [\n 31.338500976562496,\n -25.547397663603167\n ],\n [\n 32.0086669921875,\n -25.423431426334222\n ],\n [\n 32.0196533203125,\n -24.8864364907877\n ],\n [\n 32.0196533203125,\n -24.467150664738988\n ],\n [\n 31.9921875,\n -24.302046975036543\n ],\n [\n 31.904296874999996,\n -24.166802085303225\n ],\n [\n 31.865844726562504,\n -23.956136333969273\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"196","issue":"3-4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"56729942e4b01a7f82451d9d","contributors":{"authors":[{"text":"Cross, Paul C. 0000-0001-8045-5213 pcross@usgs.gov","orcid":"https://orcid.org/0000-0001-8045-5213","contributorId":2709,"corporation":false,"usgs":true,"family":"Cross","given":"Paul","email":"pcross@usgs.gov","middleInitial":"C.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":582493,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Getz, Wayne M.","contributorId":64563,"corporation":false,"usgs":true,"family":"Getz","given":"Wayne","email":"","middleInitial":"M.","affiliations":[],"preferred":false,"id":582494,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70160232,"text":"70160232 - 2006 - Natural glide slab avalanches, Glacier National Park, USA: A unique hazard and forecasting challenge","interactions":[],"lastModifiedDate":"2015-12-14T13:26:26","indexId":"70160232","displayToPublicDate":"2015-08-02T12:15:00","publicationYear":"2006","noYear":false,"publicationType":{"id":24,"text":"Conference Paper"},"publicationSubtype":{"id":19,"text":"Conference Paper"},"title":"Natural glide slab avalanches, Glacier National Park, USA: A unique hazard and forecasting challenge","docAbstract":"In a museum of avalanche phenomena, glide cracks and glide avalanches might be housed in the “strange but true” section. These oddities are uncommon in most snow climates and tend to be isolated to specific terrain features such as bedrock slabs. Many glide cracks never result in avalanches, and when they do, the wide range of time between crack formation and slab failure makes them highly unpredictable. Despite their relative rarity, glide cracks and glide avalanches pose a regular threat and complex forecasting challenge during the annual spring opening of the Going-to-the-Sun Road in Glacier National Park, U.S.A. During the 2006 season, a series of unusual glide cracks delayed snow removal operations by over a week and provided a unique opportunity to record detailed observations of glide avalanches and characterize their occurrence and associated weather conditions. Field observations were from snowpits, crown profiles and where possible, measurements of slab thickness, bed surface slope angle, substrate and other physical characteristics. Weather data were recorded at one SNOTEL site and two automated stations located from 0.6-10 km of observed glide slab avalanches. Nearly half (43%) of the 35 glide slab avalanches recorded were Class D2-2.5, with 15% Class D3-D3.5. The time between glide crack opening and failure ranged from 2 days to over six weeks, and the avalanches occurred in cycles associated with loss of snow water equivalent and spikes in temperature and radiation. We conclude with suggest ions for further study.
","largerWorkType":{"id":24,"text":"Conference Paper"},"largerWorkTitle":"Proceedings of 2006 International Snow Science Workshop","largerWorkSubtype":{"id":19,"text":"Conference Paper"},"conferenceTitle":"2006 International Snow Science Workshop","conferenceDate":"October 1-6, 2006","conferenceLocation":"Telluride, CO","language":"English","usgsCitation":"Reardon, B., Fagre, D.B., Dundas, M., and Lundy, C., 2006, Natural glide slab avalanches, Glacier National Park, USA: A unique hazard and forecasting challenge, in Proceedings of 2006 International Snow Science Workshop, Telluride, CO, October 1-6, 2006, p. 778-785.","productDescription":"8 p.","startPage":"778","endPage":"785","numberOfPages":"8","onlineOnly":"N","additionalOnlineFiles":"N","costCenters":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"links":[{"id":312259,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":312258,"rank":1,"type":{"id":15,"text":"Index Page"},"url":"https://arc.lib.montana.edu/snow-science/item.php?id=500"}],"country":"United States","state":"Montana","otherGeospatial":"Glacier National Park","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -114.7576904296875,\n 47.94946583788702\n ],\n [\n -114.7576904296875,\n 49.005447494058096\n ],\n [\n -112.39562988281249,\n 49.005447494058096\n ],\n [\n -112.39562988281249,\n 47.94946583788702\n ],\n [\n -114.7576904296875,\n 47.94946583788702\n ]\n ]\n ]\n }\n }\n ]\n}","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"566ff654e4b09cfe53ca79b1","contributors":{"authors":[{"text":"Reardon, Blase","contributorId":150198,"corporation":false,"usgs":true,"family":"Reardon","given":"Blase","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":false,"id":582115,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Fagre, Daniel B. 0000-0001-8552-9461 dan_fagre@usgs.gov","orcid":"https://orcid.org/0000-0001-8552-9461","contributorId":2036,"corporation":false,"usgs":true,"family":"Fagre","given":"Daniel","email":"dan_fagre@usgs.gov","middleInitial":"B.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":582116,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Dundas, Mark","contributorId":150560,"corporation":false,"usgs":false,"family":"Dundas","given":"Mark","email":"","affiliations":[{"id":16272,"text":"National Park Service, Glacier National Park, West Glacier, MT","active":true,"usgs":false}],"preferred":false,"id":582117,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Lundy, Chris","contributorId":150424,"corporation":false,"usgs":false,"family":"Lundy","given":"Chris","email":"","affiliations":[{"id":16272,"text":"National Park Service, Glacier National Park, West Glacier, MT","active":true,"usgs":false}],"preferred":false,"id":582118,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70120871,"text":"70120871 - 2006 - Overview of selected surrogate technologies for continuous suspended-sediment monitoring","interactions":[],"lastModifiedDate":"2014-08-18T10:46:52","indexId":"70120871","displayToPublicDate":"2013-08-18T10:35:00","publicationYear":"2006","noYear":false,"publicationType":{"id":24,"text":"Conference Paper"},"publicationSubtype":{"id":19,"text":"Conference Paper"},"title":"Overview of selected surrogate technologies for continuous suspended-sediment monitoring","docAbstract":"Surrogate technologies for inferring selected characteristics of suspended sediments in surface waters are being tested by the U.S. Geological Survey and several partners with the ultimate goal of augmenting or replacing traditional monitoring methods. Optical properties of water such as turbidity and optical backscatter are the most commonly used surrogates for suspended-sediment concentration, but use of other techniques such as those based on acoustic backscatter, laser diffraction, digital photo-optic, and pressure-difference principles is increasing for concentration and, in some cases, particle-size distribution and flux determinations. The potential benefits of these technologies include acquisition of automated, continuous, quantifiably accurate data obtained with increased safety and at less expense. When suspended-sediment surrogate data meet consensus accuracy criteria and appropriate sediment-record computation techniques are applied, these technologies have the potential to revolutionize the way fluvial-sediment data are collected, analyzed, and disseminated.
","largerWorkType":{"id":4,"text":"Book"},"largerWorkTitle":"Proceedings of the Eighth Federal Interagency Sedimentation Conference (8thFISC), April2-6, 2006, Reno, NV, USA","largerWorkSubtype":{"id":12,"text":"Conference publication"},"language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","usgsCitation":"Gray, J.R., and Gartner, J.W., 2006, Overview of selected surrogate technologies for continuous suspended-sediment monitoring, in Proceedings of the Eighth Federal Interagency Sedimentation Conference (8thFISC), April2-6, 2006, Reno, NV, USA, p. 337-344.","productDescription":"8 p.","startPage":"337","endPage":"344","costCenters":[{"id":502,"text":"Office of Surface Water","active":true,"usgs":true}],"links":[{"id":292394,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":292396,"type":{"id":15,"text":"Index Page"},"url":"https://acwi.gov/8thFISC-ordering-revised.html"},{"id":292397,"type":{"id":11,"text":"Document"},"url":"https://acwi.gov/sos/pubs/8thFISC/Session%204C-1_Gray.pdf"}],"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"53f25feae4b033341871893f","contributors":{"authors":[{"text":"Gray, J. R.","contributorId":63372,"corporation":false,"usgs":true,"family":"Gray","given":"J.","email":"","middleInitial":"R.","affiliations":[],"preferred":false,"id":498520,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Gartner, J. W.","contributorId":81903,"corporation":false,"usgs":false,"family":"Gartner","given":"J.","email":"","middleInitial":"W.","affiliations":[],"preferred":false,"id":498521,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70045364,"text":"70045364 - 2006 - Highly Pathogenic Avian Influenza Early Detection Data System (HEDDS)","interactions":[],"lastModifiedDate":"2018-04-12T10:00:11","indexId":"70045364","displayToPublicDate":"2013-01-01T00:00:00","publicationYear":"2006","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":6,"text":"USGS Unnumbered Series"},"seriesTitle":{"id":359,"text":"Fact Sheet","active":false,"publicationSubtype":{"id":6}},"title":"Highly Pathogenic Avian Influenza Early Detection Data System (HEDDS)","docAbstract":"HEDDS offers a unique opportunity for multiagency cooperation for data sharing and visualization.","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/70045364","usgsCitation":"Worrest, R., and Dein, F.J., 2006, Highly Pathogenic Avian Influenza Early Detection Data System (HEDDS): Fact Sheet, 2 p., https://doi.org/10.3133/70045364.","productDescription":"2 p.","onlineOnly":"Y","additionalOnlineFiles":"N","costCenters":[{"id":408,"text":"National Biological Information Infrastructure","active":false,"usgs":true},{"id":456,"text":"National Wildlife Health Center","active":true,"usgs":true}],"links":[{"id":270819,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/unnumbered/70045364/70045364-infosheet.pdf","text":"Report","linkFileType":{"id":1,"text":"pdf"}},{"id":270820,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/unnumbered/70045364/coverthb.jpg","size":"303 KB"}],"contact":"Director, National Wildlife Health Center
U.S. Geological Survey
6006 Schroeder Road
Madison, WI 53711
The population of dusky Canada geese (Branta canadensis occidentalis; hereafter duskies) breeding on the Copper River Delta (CRD), Alaska, USA, has been in long-term decline, largely as a result of reduced productivity. Estimates of renesting rates by duskies may be useful for adjusting estimates of the size of the breeding population derived from aerial surveys and for understanding population dynamics. We used a marked population of dusky females to obtain estimates of renesting propensity and renesting interval on the CRD, 1999–2000. Continuation nests, replacement nests initiated without a break in the laying sequence, resulted only after first nests were destroyed in the laying stage with ≤4 eggs laid. Renesting propensity declined with nest age from 72% in mid-laying to 30% in early incubation. Between first nests and renests, mean interval was 11.9 ± 0.6 days, mean distance was 74.5 m (range 0–214 m), and clutch size declined 0.9 ± 0.4 eggs. We incorporated our renesting estimates and available estimates of other nesting parameters into an individual-based model to predict the proportion of first nests, continuation nests, and renests, and to examine female success on the CRD, 1997–2000. Our model predicted that 19–36% of nests each year were continuation nests and renests. Also, through 15 May (the approx. date of breeding ground surveys), 1.1–1.3 nests were initiated per female. Thus, the number of nests per female would have a significant, though relatively consistent, effect on adjusting the relation between numbers of nests found on ground surveys versus numbers of birds seen during aerial surveys. We also suggest a method that managers could use to predict nests per female using nest success of early nests. Our model predicted that relative to observed estimates of nest success, female success was 32–100% greater, due to replacement nests. Thus, although nest success remains low, production for duskies was higher than previously thought. For dusky Canada geese, managers need to consider both continuation nests and renests in designing surveys and in calculating adjustment factors for the expansion of aerial survey data using nest densities.
","language":"English","publisher":"The Wildlife Society","publisherLocation":"Bethesda, MD","doi":"10.2193/0022-541X(2006)70[955:RBDCGO]2.0.CO;2","usgsCitation":"Fondell, T.F., Grand, J.B., Miller, D.A., and Anthony, R.M., 2006, Renesting by dusky Canada geese on the Copper River Delta, Alaska: Journal of Wildlife Management, v. 70, no. 4, p. 955-964, https://doi.org/10.2193/0022-541X(2006)70[955:RBDCGO]2.0.CO;2.","productDescription":"10 p.","startPage":"955","endPage":"964","onlineOnly":"N","additionalOnlineFiles":"N","costCenters":[{"id":114,"text":"Alaska Science Center","active":true,"usgs":true}],"links":[{"id":258069,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":258065,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.2193/0022-541X(2006)70[955:RBDCGO]2.0.CO;2","linkFileType":{"id":5,"text":"html"}}],"country":"United States","state":"Alaska","otherGeospatial":"Copper River Delta","volume":"70","issue":"4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505aa73fe4b0c8380cd852e3","contributors":{"authors":[{"text":"Fondell, Thomas F. tfondell@usgs.gov","contributorId":50771,"corporation":false,"usgs":true,"family":"Fondell","given":"Thomas","email":"tfondell@usgs.gov","middleInitial":"F.","affiliations":[],"preferred":false,"id":355613,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Grand, J. Barry 0000-0002-3576-4567 barry_grand@usgs.gov","orcid":"https://orcid.org/0000-0002-3576-4567","contributorId":579,"corporation":false,"usgs":true,"family":"Grand","given":"J.","email":"barry_grand@usgs.gov","middleInitial":"Barry","affiliations":[{"id":198,"text":"Coop Res Unit Atlanta","active":true,"usgs":true}],"preferred":true,"id":355610,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Miller, David A.W. davidmiller@usgs.gov","contributorId":4043,"corporation":false,"usgs":true,"family":"Miller","given":"David","email":"davidmiller@usgs.gov","middleInitial":"A.W.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true},{"id":7260,"text":"Pennsylvania State University","active":true,"usgs":false}],"preferred":false,"id":355611,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Anthony, R. Michael","contributorId":16057,"corporation":false,"usgs":true,"family":"Anthony","given":"R.","email":"","middleInitial":"Michael","affiliations":[],"preferred":false,"id":355612,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70006417,"text":"70006417 - 2006 - Modeling approaches in avian conservation and the role of field biologists","interactions":[],"lastModifiedDate":"2012-07-14T01:01:39","indexId":"70006417","displayToPublicDate":"2012-01-01T14:23:00","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2965,"text":"Ornithological Monographs","active":true,"publicationSubtype":{"id":10}},"title":"Modeling approaches in avian conservation and the role of field biologists","docAbstract":"This review grew out of our realization that models play an increasingly important role in conservation but are rarely used in the research of most avian biologists. Modelers are creating models that are more complex and mechanistic and that can incorporate more of the knowledge acquired by field biologists. Such models require field biologists to provide more specific information, larger sample sizes, and sometimes new kinds of data, such as habitat-specific demography and dispersal information. Field biologists need to support model development by testing key model assumptions and validating models. The best conservation decisions will occur where cooperative interaction enables field biologists, modelers, statisticians, and managers to contribute effectively. We begin by discussing the general form of ecological models—heuristic or mechanistic, \"scientific\" or statistical—and then highlight the structure, strengths, weaknesses, and applications of six types of models commonly used in avian conservation: (1) deterministic single-population matrix models, (2) stochastic population viability analysis (PVA) models for single populations, (3) metapopulation models, (4) spatially explicit models, (5) genetic models, and (6) species distribution models. We end by considering their unique attributes, determining whether the assumptions that underlie the structure are valid, and testing the ability of the model to predict the future correctly.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Ornithological Monographs","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","publisher":"University of California Press","publisherLocation":"Berkeley, CA","collaboration":"None","usgsCitation":"Beissinger, S.R., Walters, J.R., Catanzaro, D., Smith, K.G., Dunning, J., Haig, S.M., Noon, B., and Stith, B., 2006, Modeling approaches in avian conservation and the role of field biologists: Ornithological Monographs, v. 59, p. iii-56.","productDescription":"61 p.","startPage":"iii","endPage":"56","numberOfPages":"56","costCenters":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"links":[{"id":258886,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":258872,"rank":100,"type":{"id":15,"text":"Index Page"},"url":"https://www.jstor.org/stable/40166820","linkFileType":{"id":5,"text":"html"}}],"volume":"59","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505a5bdde4b0c8380cd6f86c","contributors":{"authors":[{"text":"Beissinger, Steven R.","contributorId":100534,"corporation":false,"usgs":true,"family":"Beissinger","given":"Steven","email":"","middleInitial":"R.","affiliations":[],"preferred":false,"id":354465,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Walters, J. R.","contributorId":91061,"corporation":false,"usgs":true,"family":"Walters","given":"J.","email":"","middleInitial":"R.","affiliations":[],"preferred":false,"id":354464,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Catanzaro, D.G.","contributorId":17085,"corporation":false,"usgs":true,"family":"Catanzaro","given":"D.G.","email":"","affiliations":[],"preferred":false,"id":354460,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Smith, Kimberly G.","contributorId":47720,"corporation":false,"usgs":true,"family":"Smith","given":"Kimberly","email":"","middleInitial":"G.","affiliations":[],"preferred":false,"id":354462,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Dunning, J.B.","contributorId":23373,"corporation":false,"usgs":true,"family":"Dunning","given":"J.B.","affiliations":[],"preferred":false,"id":354461,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Haig, Susan M. 0000-0002-6616-7589 susan_haig@usgs.gov","orcid":"https://orcid.org/0000-0002-6616-7589","contributorId":719,"corporation":false,"usgs":true,"family":"Haig","given":"Susan","email":"susan_haig@usgs.gov","middleInitial":"M.","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":354458,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Noon, Barry","contributorId":64934,"corporation":false,"usgs":true,"family":"Noon","given":"Barry","affiliations":[],"preferred":false,"id":354463,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Stith, Bradley bstith@usgs.gov","contributorId":3596,"corporation":false,"usgs":true,"family":"Stith","given":"Bradley","email":"bstith@usgs.gov","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"preferred":true,"id":354459,"contributorType":{"id":1,"text":"Authors"},"rank":8}]}} ,{"id":79238,"text":"ds151 - 2006 - Geochemical data for mercury, methylmercury, and other constituents in sediments from Englebright Lake, California, 2002","interactions":[],"lastModifiedDate":"2020-03-21T11:55:07","indexId":"ds151","displayToPublicDate":"2012-01-01T00:00:00","publicationYear":"2006","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":310,"text":"Data Series","code":"DS","onlineIssn":"2327-638X","printIssn":"2327-0271","active":false,"publicationSubtype":{"id":5}},"seriesNumber":"151","title":"Geochemical data for mercury, methylmercury, and other constituents in sediments from Englebright Lake, California, 2002","docAbstract":"This report presents geochemical data from two 2002 sampling campaigns conducted in Englebright Lake on the Yuba River in northern California. A deep coring campaign was done in May-June 2002 and a shallow sampling campaign was completed in October 2002. This work assessed the chemical composition of material deposited in the reservoir between 1940, the year Englebright Dam was completed, and 2002 as part of the Upper Yuba River Studies Program, an effort designed to evaluate the feasibility of introducing anadromous fish, including steelhead and spring-run Chinook salmon, upstream from Englebright Dam. Results of analyses of total mercury (HgT) in 444 subsamples, methylmercury (MeHg) in 243 subsamples, and other trace and major elements in 202 subsamples are presented. Data quality was evaluated on the basis of analyses of replicate pairs of subsamples, standard reference materials, blanks, and spike additions.Deep coring penetrated the full thickness of material deposited after 1940 at six locations in the reservoir; the cores reached a maximum depth of 32.8 meters below the reservoir floor. At the three deep coring sites closest to Englebright Dam, concentrations of HgT (dry basis) were consistently in the range of 100 to 500 ng/g (nanogram per gram), in sediment dominantly of silt size (median grain size of 0.004 to 0.063 mm [millimeter]). At the deep coring sites located farther upstream, the upper parts of the profile had lower concentrations of HgT, generally ranging from 2 to 100 ng/g, in sediment dominantly of sand size (median grain size from 0.063 to 2 mm). The lower part of the vertical profiles at three upstream coring sites had higher concentrations of HgT than the upper and middle parts of these profiles, and had finer median grain size. The highest median concentration of MeHg (1.1 ng/g) was in the top 2 cm (centimeter) of the shallow box cores. This vertical interval also had the highest value of the ratio of MeHg to HgT, 0.41 percent. Median concentrations of MeHg and median values of MeHg/HgT decreased systematically with depth from 0-4 to 4-8 to 8-12 cm in the shallow cores. However, similar systematic decreases were not observed at the meter scale in the deep cores of the MEM (MEthylMercury) series. The overall median of the ratio MeHg/HgT in the deep cores was 0.25 percent, not much less than the overall median value for the shallow cores (0.33 percent). Mercury-203 radiotracer divalent inorganic mercury (203Hg(II)) was used to determine microbial mercury-methylation potential rates for 11 samples collected from three reservoir locations and various depths in the sediment profile. For the five shallow mercury-methylation subsamples, ancillary geochemical parameters were assayed, including microbial sulfate reduction rates, sulfur speciation (sediment acid volatile sulfide, total reduced sulfur, and pore-water sulfate), iron speciation (sediment acid extractable iron(II), amorphous iron(III), crystalline iron(III) and pore-water iron(II)), pore-water chloride and dissolved organic carbon, and pH, oxidation-reduction potential (Eh) and whole-sediment organic content. The highest potential rates of microbial mercury methylation were measured in shallow (0 to 8 cm depth) sediments (5 to 30 nanograms of mercury per gram dry sediment per day), whereas potential rates for subsamples collected from depths greater than 500 cm were consistently below the detection limit of the radiotracer method (< 0.02 nanogram of mercury per gram dry sediment per day). Chemical analyses of trace and major elements in bed sediment are presented for 202 samples from deep cores from five locations in Englebright Lake. The mean values and standard deviations for selected trace elements were as follows (in micrograms per gram): antimony, 2.4 ± 1.6; arsenic, 69 ± 48; chromium, 134 ± 23; lead, 33 ± 25; and nickel, 87 ± 24. Concentrated samples of heavy-mineral grains, prepared using nine large-volume composite samples from","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ds151","collaboration":"Prepared in cooperation with the CALFED Ecosystem Restoration Program California Bay--Delta Authority and the California Resources Agency","usgsCitation":"Alpers, C.N., Hunerlach, M.P., Marvin-DePasquale, M.C., Antweiler, R.C., Lasorsa, B.K., De Wild, J.F., and Snyder, N., 2006, Geochemical data for mercury, methylmercury, and other constituents in sediments from Englebright Lake, California, 2002: U.S. Geological Survey Data Series 151, 107 p., https://doi.org/10.3133/ds151.","productDescription":"107 p.","numberOfPages":"107","onlineOnly":"Y","additionalOnlineFiles":"Y","temporalStart":"2002-01-01","temporalEnd":"2002-12-31","costCenters":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true},{"id":589,"text":"Toxic Substances Hydrology Program","active":true,"usgs":true}],"links":[{"id":190683,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/usgs_thumb.jpg"},{"id":274140,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/ds/2006/151/ds_151.pdf","text":"Report"},{"id":274139,"rank":3,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/ds/2006/151/"}],"country":"United States","state":"California","otherGeospatial":"Englebright Lake","geographicExtents":"{ \"type\": \"FeatureCollection\", \"features\": [ { \"type\": \"Feature\", \"properties\": {}, \"geometry\": { \"type\": \"Polygon\", \"coordinates\": [ [ [ -121.27121,39.24487 ], [ -121.27121,39.29387 ], [ -121.21188,39.29387 ], [ -121.21188,39.24487 ], [ -121.27121,39.24487 ] ] ] } } ] }","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4b23e4b07f02db6ae387","contributors":{"authors":[{"text":"Alpers, Charles N. 0000-0001-6945-7365 cnalpers@usgs.gov","orcid":"https://orcid.org/0000-0001-6945-7365","contributorId":411,"corporation":false,"usgs":true,"family":"Alpers","given":"Charles","email":"cnalpers@usgs.gov","middleInitial":"N.","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":512523,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Hunerlach, Michael P.","contributorId":66668,"corporation":false,"usgs":true,"family":"Hunerlach","given":"Michael","email":"","middleInitial":"P.","affiliations":[],"preferred":false,"id":512529,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Marvin-DePasquale, Mark C.","contributorId":38655,"corporation":false,"usgs":true,"family":"Marvin-DePasquale","given":"Mark","email":"","middleInitial":"C.","affiliations":[],"preferred":false,"id":512526,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Antweiler, Ronald C. 0000-0001-5652-6034 antweil@usgs.gov","orcid":"https://orcid.org/0000-0001-5652-6034","contributorId":1481,"corporation":false,"usgs":true,"family":"Antweiler","given":"Ronald","email":"antweil@usgs.gov","middleInitial":"C.","affiliations":[{"id":5044,"text":"National Research Program - Central Branch","active":true,"usgs":true}],"preferred":true,"id":512524,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Lasorsa, Brenda K.","contributorId":45398,"corporation":false,"usgs":true,"family":"Lasorsa","given":"Brenda","email":"","middleInitial":"K.","affiliations":[],"preferred":false,"id":512528,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"De Wild, John F.","contributorId":31800,"corporation":false,"usgs":true,"family":"De Wild","given":"John","email":"","middleInitial":"F.","affiliations":[],"preferred":false,"id":512525,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Snyder, Noah P.","contributorId":43848,"corporation":false,"usgs":true,"family":"Snyder","given":"Noah P.","affiliations":[],"preferred":false,"id":512527,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ,{"id":70003890,"text":"70003890 - 2006 - Predicting woodrat (Neotoma) responses to anthropogenic warming from studies of the palaeomidden record","interactions":[],"lastModifiedDate":"2012-02-10T00:12:00","indexId":"70003890","displayToPublicDate":"2011-11-04T00:00:00","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2193,"text":"Journal of Biogeography","active":true,"publicationSubtype":{"id":10}},"title":"Predicting woodrat (Neotoma) responses to anthropogenic warming from studies of the palaeomidden record","docAbstract":"Aim The influence of anthropogenic climate change on organisms is an area of great scientific concern. Increasingly there is recognition that abrupt climate transitions have occurred over the late Quaternary; studies of these shifts may yield insights into likely biotic responses to contemporary warming. Here, we review research undertaken over the past decade investigating the response of Neotoma (woodrats) body size and distribution to climate change over the late Quaternary (the last 40,000 years). By integrating information from woodrat palaeomiddens, historical museum specimens and field studies of modern populations, we identify potential evolutionary responses to climate change occurring over a variety of temporal and spatial scales. Specifically, we characterize climatic thresholds in the past that led to local species extirpation and/or range alterations rather than in situ adaptation, and apply them to anticipate potential biotic responses to anthropogenic climate change. Location Middens were collected at about 55 sites scattered across the western United States, ranging from about 34 to 46° N and about 104 to 116° W, respectively. Data for modern populations were drawn from studies conducted in Death Valley, California, Missoula, Montana and the Sevilleta LTER site in central New Mexico. Methods We analysed faecal pellets from midden series collected at numerous cave sites across the western United States. From these we estimated body mass using techniques validated in earlier studies. We compared body size fluctuations at different elevations in different regions and integrated these results with studies investigating temperature–body size tradeoffs in modern animals. We also quantify the rapidity of the size changes over the late Quaternary to estimate the evolutionary capacity of woodrats to deal with predicted rates of anthropogenic climate change over the next century. Results We find remarkable similarities across the geographical range to late Quaternary climate change. In the middle of the geographical range woodrats respond in accordance to Bergmann's rule: colder climatic conditions select for larger body size and warmer conditions select for smaller body size. Patterns are more complicated at range boundaries, and local environmental conditions influence the observed response. In general, woodrat body size fluctuates with approximately the same amplitude and frequency as climate; there is a significant and positive correlation between woodrat body size and generalized climate proxies (such as ice core records). Woodrats have achieved evolutionary rates of change equal to or greater than those needed to adapt in situ to anthropogenic climate change. Main conclusions In situ body size evolution is a likely outcome of climate change, and such shifts are part of a normal spectrum of adaptation. Woodrats appear to be subject to ongoing body size selection in response to fluctuating environmental conditions. Allometric considerations suggest that these shifts in body size lead to substantial changes in the physiology, life history and ecology of woodrats, and on their direct and indirect interactions with other organisms in the ecosystem. Our work highlights the importance of a finely resolved and long-term record in understanding biotic responses to climatic shifts.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Journal of Biogeography","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","publisher":"Wiley","publisherLocation":"Hoboken, NJ","usgsCitation":"Smith, F., and Betancourt, J.L., 2006, Predicting woodrat (Neotoma) responses to anthropogenic warming from studies of the palaeomidden record: Journal of Biogeography, v. 33, no. 12, p. 2061-2076.","productDescription":"16 p.","startPage":"2061","endPage":"2076","costCenters":[{"id":148,"text":"Branch of Regional Research-Western Region","active":false,"usgs":true}],"links":[{"id":204257,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":94669,"rank":300,"type":{"id":11,"text":"Document"},"url":"https://wwwpaztcn.wr.usgs.gov/julio_pdf/Smith_Betancourt2006.pdf","linkFileType":{"id":1,"text":"pdf"}}],"country":"United States","geographicExtents":"{ \"type\": \"FeatureCollection\", \"features\": [ { \"type\": \"Feature\", \"properties\": {}, \"geometry\": { \"type\": \"Polygon\", \"coordinates\": [ [ [ -116,34 ], [ -116,46 ], [ -104,46 ], [ -104,34 ], [ -116,34 ] ] ] } } ] }","volume":"33","issue":"12","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4acce4b07f02db67e7f2","contributors":{"authors":[{"text":"Smith, Felisa A.","contributorId":9389,"corporation":false,"usgs":true,"family":"Smith","given":"Felisa A.","affiliations":[],"preferred":false,"id":349322,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Betancourt, Julio L. 0000-0002-7165-0743 jlbetanc@usgs.gov","orcid":"https://orcid.org/0000-0002-7165-0743","contributorId":3376,"corporation":false,"usgs":true,"family":"Betancourt","given":"Julio","email":"jlbetanc@usgs.gov","middleInitial":"L.","affiliations":[{"id":554,"text":"Science and Decisions Center","active":true,"usgs":true},{"id":436,"text":"National Research Program - Eastern Branch","active":true,"usgs":true},{"id":438,"text":"National Research Program - Western Branch","active":true,"usgs":true}],"preferred":true,"id":349321,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70170256,"text":"70170256 - 2006 - Identifying suitable sites for Florida panther reintroduction","interactions":[],"lastModifiedDate":"2017-05-18T11:25:25","indexId":"70170256","displayToPublicDate":"2010-12-13T00:00:00","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2508,"text":"Journal of Wildlife Management","active":true,"publicationSubtype":{"id":10}},"title":"Identifying suitable sites for Florida panther reintroduction","docAbstract":"A major objective of the 1995 Florida Panther (Puma concolor cory) Recovery Plan is the establishment of 2 additional panther populations within the historic range. Our goal was to identify prospective sites for Florida panther reintroduction within the historic range based on quantitative landscape assessments. First, we delineated 86 panther home ranges using telemetry data collected from 1981 to 2001 in south Florida to develop a Mahalanobis distance (D2) habitat model, using 4 anthropogenic variables and 3 landscape variables mapped at a 500-m resolution. From that analysis, we identified 9 potential reintroduction sites of sufficient size to support a panther population. We then developed a similar D2 model at a higher spatial resolution to quantify the area of favorable panther habitat at each site. To address potential for the population to expand, we calculated the amount of favorable habitat adjacent to each prospective reintroduction site within a range of dispersal distances of female panthers. We then added those totals to the contiguous patches to estimate the total amount of effective panther habitat at each site. Finally, we developed an expert-assisted model to rank and incorporate potentially important habitat variables that were not appropriate for our empirical analysis (e.g., area of public lands, livestock density). Anthropogenic factors heavily influenced both the landscape and the expert-assisted models. Of the 9 areas we identified, the Okefenokee National Wildlife Refuge, Ozark National Forest, and Felsenthal National Wildlife Refuge regions had the highest combination of effective habitat area and expert opinion scores. Sensitivity analyses indicated that variability among key model parameters did not affect the high ranking of those sites. Those sites should be considered as starting points for the field evaluation of potential reintroduction sites.
","language":"English","publisher":"Wildlife Society","doi":"10.2193/0022-541X(2006)70[752:ISSFFP]2.0.CO;2","usgsCitation":"Thatcher, C.A., van Manen, F.T., and Clark, J.D., 2006, Identifying suitable sites for Florida panther reintroduction: Journal of Wildlife Management, v. 70, no. 3, p. 752-763, https://doi.org/10.2193/0022-541X(2006)70[752:ISSFFP]2.0.CO;2.","productDescription":"12 p.","startPage":"752","endPage":"763","onlineOnly":"N","additionalOnlineFiles":"N","costCenters":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"links":[{"id":320035,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Florida","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -82.803955078125,\n 29.152161283318915\n ],\n [\n -82.584228515625,\n 29.1233732108192\n ],\n [\n -82.298583984375,\n 29.104176683949984\n ],\n [\n -82.001953125,\n 29.075375179558346\n ],\n [\n -81.8701171875,\n 29.152161283318915\n ],\n [\n -81.7822265625,\n 29.305561325527698\n ],\n [\n -81.62841796875,\n 29.401319510041485\n ],\n [\n -81.45263671875,\n 29.46829664171322\n ],\n [\n -81.18896484375,\n 29.477861195816843\n ],\n [\n -80.980224609375,\n 29.334298230315675\n ],\n [\n -80.67260742187499,\n 28.738763971370293\n ],\n [\n -80.48583984375,\n 28.497660832963472\n ],\n [\n -80.5078125,\n 28.17855984939698\n ],\n [\n -80.2001953125,\n 27.42053815128712\n ],\n [\n -79.98046875,\n 27.039556602163195\n ],\n [\n -79.95849609375,\n 26.401710528707707\n ],\n [\n -80.04638671875,\n 25.750424835909385\n ],\n [\n -80.244140625,\n 25.512700007620513\n ],\n [\n -80.39794921875,\n 25.21488107113259\n ],\n [\n -80.68359375,\n 25.11544539706194\n ],\n [\n -80.9912109375,\n 25.055745117015316\n ],\n [\n -81.221923828125,\n 25.11544539706194\n ],\n [\n -81.221923828125,\n 25.37380917154398\n ],\n [\n -81.34277343749999,\n 25.572175556682115\n ],\n [\n -81.441650390625,\n 25.770213848960275\n ],\n [\n -81.771240234375,\n 25.78999956287362\n ],\n [\n -81.903076171875,\n 26.125850185680356\n ],\n [\n -82.012939453125,\n 26.362342068998764\n ],\n [\n -82.298583984375,\n 26.441065564038418\n ],\n [\n -82.33154296875,\n 26.755420897359123\n ],\n [\n -82.628173828125,\n 27.196014383173306\n ],\n [\n -82.7490234375,\n 27.527758206861886\n ],\n [\n -82.90283203125,\n 27.732160709580906\n ],\n [\n -82.94677734375,\n 27.98470011861268\n ],\n [\n -82.85888671875,\n 28.246327971048842\n ],\n [\n -82.79296874999999,\n 28.44937385955666\n ],\n [\n -82.7490234375,\n 28.632746799225856\n ],\n [\n -82.77099609375,\n 28.767659105691255\n ],\n [\n -82.8369140625,\n 28.93124697186731\n ],\n [\n -82.869873046875,\n 29.05616970274342\n ],\n [\n -82.803955078125,\n 29.152161283318915\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"70","issue":"3","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"570f6db5e4b0ef3b7ca3568e","contributors":{"authors":[{"text":"Thatcher, Cindy A. 0000-0003-0331-071X thatcherc@usgs.gov","orcid":"https://orcid.org/0000-0003-0331-071X","contributorId":2868,"corporation":false,"usgs":true,"family":"Thatcher","given":"Cindy","email":"thatcherc@usgs.gov","middleInitial":"A.","affiliations":[{"id":455,"text":"National Wetlands Research Center","active":true,"usgs":true},{"id":242,"text":"Eastern Geographic Science Center","active":true,"usgs":true},{"id":423,"text":"National Geospatial Program","active":true,"usgs":true}],"preferred":false,"id":626646,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"van Manen, Frank T. 0000-0001-5340-8489 fvanmanen@usgs.gov","orcid":"https://orcid.org/0000-0001-5340-8489","contributorId":2267,"corporation":false,"usgs":true,"family":"van Manen","given":"Frank","email":"fvanmanen@usgs.gov","middleInitial":"T.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":626647,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Clark, Joseph D. 0000-0002-8547-8112 jclark1@usgs.gov","orcid":"https://orcid.org/0000-0002-8547-8112","contributorId":2265,"corporation":false,"usgs":true,"family":"Clark","given":"Joseph","email":"jclark1@usgs.gov","middleInitial":"D.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true},{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":true,"id":626648,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70170257,"text":"70170257 - 2006 - Growth and sustainability of black bears at White River National Wildlife Refuge, Arkansas","interactions":[],"lastModifiedDate":"2016-04-13T15:11:22","indexId":"70170257","displayToPublicDate":"2010-12-07T00:00:00","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2508,"text":"Journal of Wildlife Management","active":true,"publicationSubtype":{"id":10}},"title":"Growth and sustainability of black bears at White River National Wildlife Refuge, Arkansas","docAbstract":"The black bear (Ursus americanus) population at White River National Wildlife Refuge is isolated and genetically distinct, but hunting occurs adjacent to refuge boundaries and females with cubs are removed annually for a reintroduction project. We trapped and radiotracked bears to determine level of exploitation and compare methods for estimating population growth and sustainability. We captured 260 bears (113 M:147 F), 414 times, from 1998 through 2003. Survival estimates based on radiotracking and mark–recapture indicated that hunting and translocations were significant sources of loss. Based on mark–recapture data (Pradel estimator), the annual population growth rate (λ) averaged 1.066 (SE = 0.077) when translocation removals occurred and averaged 0.961 (SE = 0.155) when both harvest and translocations occurred. Estimates of λ based on a population simulation model (program RISKMAN) averaged 1.061 (SD = 0.104) and 1.100 (SD = 0.111) when no removals occurred, 1.003 (SD = 0.097) and 1.046 (SD = 0.102) when translocations occurred, and 0.973 (SD = 0.096) and 1.006 (SD = 0.099) when both harvest and translocations occurred, depending on the survival rate estimates we used. The probability of population decline by >25% over a 10-year period ranged from 13.8 to 68.8%, given our estimated removal rates. We conclude that hunting and translocation losses are at or exceed the maximum the population is capable of sustaining. Although extinction risks of this important bear population are low over the near term, it should continue to be closely monitored by state and federal agencies. The mark–recapture method we used to estimate λ proved to be a reliable alternative to more costly population modeling methods.
","language":"English","publisher":"Wildlife Society","doi":"10.2193/0022-541X(2006)70[1094:GASOBB]2.0.CO;2","usgsCitation":"Clark, J.D., and Eastridge, R., 2006, Growth and sustainability of black bears at White River National Wildlife Refuge, Arkansas: Journal of Wildlife Management, v. 70, no. 4, p. 1094-1101, https://doi.org/10.2193/0022-541X(2006)70[1094:GASOBB]2.0.CO;2.","productDescription":"8 p.","startPage":"1094","endPage":"1101","costCenters":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"links":[{"id":320036,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Arkansas","county":"Arkansas county, Desha county, Monroe county, Phillips county","otherGeospatial":"White River National Wildlife Refuge","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -91.18515014648438,\n 34.00428898114395\n ],\n [\n -91.2469482421875,\n 34.01055023831342\n ],\n [\n -91.24076843261719,\n 34.03729768165775\n ],\n [\n -91.241455078125,\n 34.057210513510306\n ],\n [\n -91.23458862304688,\n 34.068587174791965\n ],\n [\n -91.24282836914062,\n 34.085080620514844\n ],\n [\n -91.25312805175781,\n 34.099865116851994\n ],\n [\n -91.22840881347655,\n 34.115783994045756\n ],\n [\n -91.20368957519531,\n 34.14420310897081\n ],\n [\n -91.19956970214844,\n 34.161818161230386\n ],\n [\n -91.19476318359375,\n 34.17147646866661\n ],\n [\n -91.17965698242188,\n 34.179429539103374\n ],\n [\n -91.1700439453125,\n 34.20158056821986\n ],\n [\n -91.14463806152344,\n 34.21180215769026\n ],\n [\n -91.11305236816406,\n 34.21180215769026\n ],\n [\n -91.08901977539062,\n 34.21180215769026\n ],\n [\n -91.05949401855469,\n 34.204420022968065\n ],\n [\n -91.05262756347656,\n 34.186245860011574\n ],\n [\n -91.05262756347656,\n 34.16124999108587\n ],\n [\n -91.05606079101562,\n 34.13226824445654\n ],\n [\n -91.05812072753906,\n 34.0822371521209\n ],\n [\n -91.06979370117188,\n 34.05891711006568\n ],\n [\n -91.07460021972656,\n 34.04241857075928\n ],\n [\n -91.0821533203125,\n 34.028762179464465\n ],\n [\n -91.10069274902344,\n 34.016811033816374\n ],\n [\n -91.15287780761719,\n 34.0219331594475\n ],\n [\n -91.18515014648438,\n 34.00428898114395\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"70","issue":"4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"570f6db4e4b0ef3b7ca35688","contributors":{"authors":[{"text":"Clark, Joseph D. 0000-0002-8547-8112 jclark1@usgs.gov","orcid":"https://orcid.org/0000-0002-8547-8112","contributorId":2265,"corporation":false,"usgs":true,"family":"Clark","given":"Joseph","email":"jclark1@usgs.gov","middleInitial":"D.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true},{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":true,"id":626649,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Eastridge, R.","contributorId":46464,"corporation":false,"usgs":true,"family":"Eastridge","given":"R.","affiliations":[],"preferred":false,"id":626650,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":98862,"text":"ofr20061349 - 2006 - Genetic analyses of captive Alala (Corvus hawaiiensis) using AFLP analyses","interactions":[],"lastModifiedDate":"2013-11-15T14:18:58","indexId":"ofr20061349","displayToPublicDate":"2010-11-04T00:00:00","publicationYear":"2006","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":"2006-1349","title":"Genetic analyses of captive Alala (Corvus hawaiiensis) using AFLP analyses","docAbstract":"Population level studies of genetic diversity can provide information about population structure, individual genetic distinctiveness and former population size. They are especially important for rare and threatened species like the Alala, where they can be used to assess extinction risks and evolutionary potential. In an ideal situation multiple methods should be used to detect variation, and these methods should be comparable across studies. In this report, we discuss AFLP (Amplified Fragment Length Polymorphism) as a genetic approach for detecting variation in the Alala , describe our findings, and discuss these in relation to mtDNA and microsatellite data reported elsewhere in this same population.\n\nAFLP is a technique for DNA fingerprinting that has wide applications. Because little or no prior knowledge of the particular species is required to carry out this method of analysis, AFLP can be used universally across varied taxonomic groups. Within individuals, estimates of diversity or heterozygosity across genomes may be complex because levels of diversity differ between and among genes. One of the more traditional methods of estimating diversity employs the use of codominant markers such as microsatellites. Codominant markers detect each allele at a locus independently. Hence, one can readily distinguish heterozygotes from homozygotes, directly assess allele frequencies and calculate other population level statistics. Dominant markers (for example, AFLP) are scored as either present or absent (null) so heterozygotes cannot be directly distinguished from homozygotes. However, the presence or absence data can be converted to expected heterozygosity estimates which are comparable to those determined by codominant markers. High allelic diversity and heterozygosity inherent in microsatellites make them excellent tools for studies of wild populations and they have been used extensively. One limitation to the use of microsatellites is that heterozygosity estimates are affected by the mutation rate at microsatellite loci, thus introducing a bias. Also, the number of loci that can be studied is frequently limited to fewer than 10. This theoretically represents a maximum of one marker for each of 10 chromosomes. Dominant markers like AFLP allow a larger fraction of the genome to be screened. Large numbers of loci can be screened by AFLP to resolve very small individual differences that can be used for identification of individuals, estimates of pairwise relatedness and, in some cases, for parentage analyses. Since AFLP is a dominant marker (can not distinguish between +/+ homozygote versus +/- heterozygote), it has limitations for parentage analyses. Only when both parents are homozygous for the absence of alleles (-/-) and offspring show a presence (+/+ or +/-) can the parents be excluded. In this case, microsatellites become preferable as they have the potential to exclude individual parents when the other parent is unknown. Another limitation of AFLP is that the loci are generally less polymorphic (only two alleles/locus) than microsatellite loci (often >10 alleles/locus). While generally fewer than 10 highly polymorphic microsatellite loci are enough to exclude and assign parentage, it might require up to 100 or more AFLP loci. While there are pros and cons to different methodologies, the total number of loci evaluated by AFLP generally offsets the limitations imposed due to the dominant nature of this approach and end results between methods are generally comparable.\n\nOverall objectives of this study were to evaluate the level of genetic diversity in the captive population of Alala, to compare genetic data with currently available pedigree information, and to determine the extent of relatedness of mating pairs and among founding individuals.","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ofr20061349","usgsCitation":"Jarvi, S.I., and Bianchi, K.R., 2006, Genetic analyses of captive Alala (Corvus hawaiiensis) using AFLP analyses: U.S. Geological Survey Open-File Report 2006-1349, iii, 37 p., https://doi.org/10.3133/ofr20061349.","productDescription":"iii, 37 p.","numberOfPages":"40","onlineOnly":"Y","additionalOnlineFiles":"N","costCenters":[{"id":521,"text":"Pacific Island Ecosystems Research Center","active":false,"usgs":true}],"links":[{"id":126125,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/ofr_2006_1349.jpg"},{"id":14277,"rank":100,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/of/2006/1349/","linkFileType":{"id":5,"text":"html"}},{"id":279111,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/of/2006/1349/of2006-1349.pdf"}],"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4b24e4b07f02db6aebc0","contributors":{"authors":[{"text":"Jarvi, Susan I.","contributorId":47748,"corporation":false,"usgs":true,"family":"Jarvi","given":"Susan","email":"","middleInitial":"I.","affiliations":[],"preferred":false,"id":306750,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Bianchi, Kiara R.","contributorId":97864,"corporation":false,"usgs":true,"family":"Bianchi","given":"Kiara","email":"","middleInitial":"R.","affiliations":[],"preferred":false,"id":306751,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":98712,"text":"tm11A2 - 2006 - FGDC Digital Cartographic Standard for Geologic Map Symbolization (PostScript Implementation)","interactions":[],"lastModifiedDate":"2024-07-01T18:40:13.69788","indexId":"tm11A2","displayToPublicDate":"2010-09-17T00:00:00","publicationYear":"2006","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":335,"text":"Techniques and Methods","code":"TM","onlineIssn":"2328-7055","printIssn":"2328-7047","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"11-A2","title":"FGDC Digital Cartographic Standard for Geologic Map Symbolization (PostScript Implementation)","docAbstract":"PLEASE NOTE: This now-approved 'FGDC Digital Cartographic Standard for Geologic Map Symbolization (PostScript Implementation)' officially supercedes its earlier (2000) Public Review Draft version (see 'Earlier Versions of the Standard' below). \r\n\r\nIn August 2006, the Digital Cartographic Standard for Geologic Map Symbolization was officially endorsed by the Federal Geographic Data Committee (FGDC) as the national standard for the digital cartographic representation of geologic map features (FGDC Document Number FGDC-STD-013-2006). Presented herein is the PostScript Implementation of the standard, which will enable users to directly apply the symbols in the standard to geologic maps and illustrations prepared in desktop illustration and (or) publishing software. \r\n\r\nThe FGDC Digital Cartographic Standard for Geologic Map Symbolization contains descriptions, examples, cartographic specifications, and notes on usage for a wide variety of symbols that may be used on typical, general-purpose geologic maps and related products such as cross sections. The standard also can be used for different kinds of special-purpose or derivative map products and databases that may be focused on a specific geoscience topic (for example, slope stability) or class of features (for example, a fault map). The standard is scale-independent, meaning that the symbols are appropriate for use with geologic mapping compiled or published at any scale. It will be useful to anyone who either produces or uses geologic map information, whether in analog or digital form. \r\n\r\nPlease be aware that this standard is not intended to be used inflexibly or in a manner that will limit one's ability to communicate the observations and interpretations gained from geologic mapping. In certain situations, a symbol or its usage might need to be modified in order to better represent a particular feature on a geologic map or cross section. This standard allows the use of any symbol that doesn't conflict with others in the standard, provided that it is clearly explained on the map and in the database. In addition, modifying the size, color, and (or) lineweight of an existing symbol to suit the needs of a particular map or output device also is permitted, provided that the modified symbol's appearance is not too similar to another symbol on the map. Be aware, however, that reducing lineweights below .125 mm (.005 inch) may cause symbols to plot incorrectly if output at higher resolutions (1800 dpi or higher). \r\n\r\nFor guidelines on symbol usage, as well as on color design and map labeling, please refer to the standard's introductory text. Also found there are informational sections covering concepts of geologic mapping and some definitions of geologic map features, as well as sections on the newly defined concepts and terminology for the scientific confidence and locational accuracy of geologic map features. \r\n\r\nMore information on both the past development and the future maintenance of the FGDC Digital Cartographic Standard for Geologic Map Symbolization can be found at the FGDC Geologic Data Subcommittee website (http://ngmdb.usgs.gov/fgdc_gds/). \r\n\r\nEarlier Versions of the Standard","language":"ENGLISH","publisher":"U.S. Geological Survey","doi":"10.3133/tm11A2","collaboration":"Prepared in cooperation with the Geologic Data Subcommittee of the Federal Geographic Data Committee","usgsCitation":"U.S. Geological Survey, 2006, FGDC Digital Cartographic Standard for Geologic Map Symbolization (PostScript Implementation) (Version 1.0): U.S. Geological Survey Techniques and Methods 11-A2, HTML Page; PDF Files, https://doi.org/10.3133/tm11A2.","productDescription":"HTML Page; PDF Files","onlineOnly":"Y","additionalOnlineFiles":"Y","costCenters":[],"links":[{"id":14120,"rank":2,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/tm/2006/11A02/","linkFileType":{"id":5,"text":"html"}},{"id":115934,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/tm_11_A2.jpg"}],"edition":"Version 1.0","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e49a0e4b07f02db5bddac","contributors":{"authors":[{"text":"U.S. Geological Survey","contributorId":147999,"corporation":true,"usgs":false,"organization":"U.S. Geological Survey","id":905333,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":5224642,"text":"5224642 - 2006 - Comparative dynamics of avian communities across edges and interiors of North American ecoregions","interactions":[],"lastModifiedDate":"2012-02-02T00:15:33","indexId":"5224642","displayToPublicDate":"2010-06-16T12:18:55","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2193,"text":"Journal of Biogeography","active":true,"publicationSubtype":{"id":10}},"title":"Comparative dynamics of avian communities across edges and interiors of North American ecoregions","docAbstract":"Aim Based on a priori hypotheses, we developed predictions about how avian communities might differ at the edges vs. interiors of ecoregions. Specifically, we predicted lower species richness and greater local turnover and extinction probabilities for regional edges. We tested these predictions using North American Breeding Bird Survey (BBS) data across nine ecoregions over a 20-year time period. Location Data from 2238 BBS routes within nine ecoregions of the United States were used. Methods The estimation methods used accounted for species detection probabilities < 1. Parameter estimates for species richness, local turnover and extinction probabilities were obtained using the program COMDYN. We examined the difference in community-level parameters estimated from within exterior edges (the habitat interface between ecoregions), interior edges (the habitat interface between two bird conservation regions within the same ecoregion) and interior (habitat excluding interfaces). General linear models were constructed to examine sources of variation in community parameters for five ecoregions (containing all three habitat types) and all nine ecoregions (containing two habitat types). Results Analyses provided evidence that interior habitats and interior edges had on average higher bird species richness than exterior edges, providing some evidence of reduced species richness near habitat edges. Lower average extinction probabilities and turnover rates in interior habitats (five-region analysis) provided some support for our predictions about these quantities. However, analyses directed at all three response variables, i.e. species richness, local turnover, and local extinction probability, provided evidence of an interaction between habitat and region, indicating that the relationships did not hold in all regions. Main conclusions The overall predictions of lower species richness, higher local turnover and extinction probabilities in regional edge habitats, as opposed to interior habitats, were generally supported. However, these predicted tendencies did not hold in all regions.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Journal of Biogeography","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"6552_Karanth.pdf","usgsCitation":"Karanth, K., Nichols, J., Sauer, J., and Hines, J., 2006, Comparative dynamics of avian communities across edges and interiors of North American ecoregions: Journal of Biogeography, v. 33, no. 4, p. 674-682.","productDescription":"674-682","startPage":"674","endPage":"682","numberOfPages":"9","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":17564,"rank":200,"type":{"id":11,"text":"Document"},"url":"https://www3.interscience.wiley.com/journal/118728870/abstract","linkFileType":{"id":5,"text":"html"}},{"id":201930,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"33","issue":"4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4b24e4b07f02db6ae56b","contributors":{"authors":[{"text":"Karanth, K.K.","contributorId":65964,"corporation":false,"usgs":true,"family":"Karanth","given":"K.K.","email":"","affiliations":[],"preferred":false,"id":342208,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Nichols, J.D. 0000-0002-7631-2890","orcid":"https://orcid.org/0000-0002-7631-2890","contributorId":14332,"corporation":false,"usgs":true,"family":"Nichols","given":"J.D.","affiliations":[],"preferred":false,"id":342206,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Sauer, J.R. 0000-0002-4557-3019","orcid":"https://orcid.org/0000-0002-4557-3019","contributorId":66197,"corporation":false,"usgs":true,"family":"Sauer","given":"J.R.","affiliations":[],"preferred":false,"id":342209,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Hines, J.E. 0000-0001-5478-7230","orcid":"https://orcid.org/0000-0001-5478-7230","contributorId":36885,"corporation":false,"usgs":true,"family":"Hines","given":"J.E.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":342207,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":5224639,"text":"5224639 - 2006 - Estimating species richness and accumulation by modeling species occurrence and detectability","interactions":[],"lastModifiedDate":"2012-02-02T00:15:30","indexId":"5224639","displayToPublicDate":"2010-06-16T12:18:55","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1465,"text":"Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Estimating species richness and accumulation by modeling species occurrence and detectability","docAbstract":"A statistical model is developed for estimating species richness and accumulation by formulating these community-level attributes as functions of model-based estimators of species occurrence while accounting for imperfect detection of individual species. The model requires a sampling protocol wherein repeated observations are made at a collection of sample locations selected to be representative of the community. This temporal replication provides the data needed to resolve the ambiguity between species absence and nondetection when species are unobserved at sample locations. Estimates of species richness and accumulation are computed for two communities, an avian community and a butterfly community. Our model-based estimates suggest that detection failures in many bird species were attributed to low rates of occurrence, as opposed to simply low rates of detection. We estimate that the avian community contains a substantial number of uncommon species and that species richness greatly exceeds the number of species actually observed in the sample. In fact, predictions of species accumulation suggest that even doubling the number of sample locations would not have revealed all of the species in the community. In contrast, our analysis of the butterfly community suggests that many species are relatively common and that the estimated richness of species in the community is nearly equal to the number of species actually detected in the sample. Our predictions of species accumulation suggest that the number of sample locations actually used in the butterfly survey could have been cut in half and the asymptotic richness of species still would have been attained. Our approach of developing occurrence-based summaries of communities while allowing for imperfect detection of species is broadly applicable and should prove useful in the design and analysis of surveys of biodiversity.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Ecology","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"6549_Dorazio.pdf","usgsCitation":"Dorazio, R., Royle, J., Soderstrom, B., and Glimskarc, A., 2006, Estimating species richness and accumulation by modeling species occurrence and detectability: Ecology, v. 87, no. 4, p. 842-854.","productDescription":"842-854","startPage":"842","endPage":"854","numberOfPages":"13","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":17561,"rank":200,"type":{"id":11,"text":"Document"},"url":"https://www.esajournals.org/doi/abs/10.1890/0012-9658(2006)87%5B842%3AESRAAB%5D2.0.CO%3B2","linkFileType":{"id":5,"text":"html"}},{"id":202079,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"87","issue":"4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4a0ce4b07f02db5fc858","contributors":{"authors":[{"text":"Dorazio, R.M. 0000-0003-2663-0468","orcid":"https://orcid.org/0000-0003-2663-0468","contributorId":23475,"corporation":false,"usgs":true,"family":"Dorazio","given":"R.M.","affiliations":[],"preferred":false,"id":342196,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Royle, J. Andrew 0000-0003-3135-2167","orcid":"https://orcid.org/0000-0003-3135-2167","contributorId":96221,"corporation":false,"usgs":true,"family":"Royle","given":"J. Andrew","affiliations":[],"preferred":false,"id":342198,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Soderstrom, B.","contributorId":73318,"corporation":false,"usgs":true,"family":"Soderstrom","given":"B.","email":"","affiliations":[],"preferred":false,"id":342197,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Glimskarc, A.","contributorId":22885,"corporation":false,"usgs":true,"family":"Glimskarc","given":"A.","email":"","affiliations":[],"preferred":false,"id":342195,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":5222542,"text":"5222542 - 2006 - Surface elevation dynamics in vegetated Spartina marshes versus unvegetated tidal ponds along the mid-Atlantic coast, USA, with implications to waterbirds","interactions":[],"lastModifiedDate":"2016-08-16T15:49:11","indexId":"5222542","displayToPublicDate":"2010-06-16T12:18:55","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1584,"text":"Estuaries and Coasts","active":true,"publicationSubtype":{"id":10}},"title":"Surface elevation dynamics in vegetated Spartina marshes versus unvegetated tidal ponds along the mid-Atlantic coast, USA, with implications to waterbirds","docAbstract":"Mid Atlantic coastal salt marshes contain a matrix of vegetation diversified by tidal pools, pannes, and creeks, providing habitats of varying importance to many species of breeding, migrating, and wintering waterbirds. We hypothesized that changes in marsh elevation were not sufficient to keep pace with those of sea level in both vegetated and unvegetated Spartina alterniflora sites at a number of mid lagoon marsh areas along the Atlantic coast. We also predicted that northern areas would suffer less of a deficit than would southern sites. Beginning in August 1998, we installed surface elevation tables at study sites on Cape Cod, Massachusetts, southern New Jersey, and two locations along Virginia's eastern shore. We compared these elevation changes over the 4-4.5 yr record with the long-term (> 50 yr) tidal records for each locale. We also collected data on waterbird use of these sites during all seasons of the year, based on ground surveys and replicated surveys from observation platforms. Three patterns of marsh elevation change were found. At Nauset Marsh, Cape Cod, the Spartina marsh surface tracked the pond surface, both keeping pace with regional sea-level rise rates. In New Jersey, the ponds are becoming deeper while marsh surface elevation remains unchanged from the initial reading. This may result in a submergence of the marsh in the future, assuming sea-level rise continues at current rates. Ponds at both Virginia sites are filling in, while marsh surface elevation rates do not seem to be keeping pace with local sea-level rise. An additional finding at all sites was that subsidence in the vegetated marsh surfaces was less than in unvegetated areas, reflecting the importance of the root mat in stabilizing sediments. The implications to migratory waterbirds are significant. Submergence of much of the lagoonal marsh area in Virginia and New Jersey over the next century could have major negative (i.e., flooding) effects on nesting populations of marsh-dependent seaside sparrows Ammodramus maritimus, saltmarsh sharp-tailed sparrows A. caudacutus, black rails Laterallus jamaicensis, clapper rails Rallus longirostris, Forster's terns Sterna forsteri, common terns Sterna hirundo, and gull-billed terns Sterna nilotica. Although short-term inundation of many lagoonal marshes may benefit some open-water feeding ducks, geese, and swans during winter, the long-term ecosystem effects may be detrimental, as wildlife resources will be lost or displaced. With the reduction in area of emergent marsh, estuarine secondary productivity and biotic diversity will also be reduced.
","language":"English","publisher":"Springer","doi":"10.1007/BF02784702","usgsCitation":"Erwin, R.M., Cahoon, D.R., Prosser, D.J., Sanders, G., and Hensel, P., 2006, Surface elevation dynamics in vegetated Spartina marshes versus unvegetated tidal ponds along the mid-Atlantic coast, USA, with implications to waterbirds: Estuaries and Coasts, v. 29, no. 1, p. 96-106, https://doi.org/10.1007/BF02784702.","productDescription":"11 p.","startPage":"96","endPage":"106","onlineOnly":"N","additionalOnlineFiles":"N","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":194132,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"29","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4afee4b07f02db697554","contributors":{"authors":[{"text":"Erwin, R. Michael 0000-0003-2108-9502","orcid":"https://orcid.org/0000-0003-2108-9502","contributorId":57125,"corporation":false,"usgs":true,"family":"Erwin","given":"R.","email":"","middleInitial":"Michael","affiliations":[],"preferred":false,"id":336455,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Cahoon, Donald R. 0000-0002-2591-5667 dcahoon@usgs.gov","orcid":"https://orcid.org/0000-0002-2591-5667","contributorId":3791,"corporation":false,"usgs":true,"family":"Cahoon","given":"Donald","email":"dcahoon@usgs.gov","middleInitial":"R.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":true,"id":336458,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Prosser, Diann J. 0000-0002-5251-1799 dprosser@usgs.gov","orcid":"https://orcid.org/0000-0002-5251-1799","contributorId":2389,"corporation":false,"usgs":true,"family":"Prosser","given":"Diann","email":"dprosser@usgs.gov","middleInitial":"J.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":true,"id":336457,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Sanders, Geoffrey","contributorId":85841,"corporation":false,"usgs":true,"family":"Sanders","given":"Geoffrey","affiliations":[],"preferred":false,"id":336459,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Hensel, Philippe","contributorId":26009,"corporation":false,"usgs":true,"family":"Hensel","given":"Philippe","affiliations":[],"preferred":false,"id":336456,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":5224640,"text":"5224640 - 2006 - Fish-assemblage variation between geologically defined regions and across a longitudinal gradient in the Monkey River Basin, Belize","interactions":[],"lastModifiedDate":"2021-05-16T17:10:36.407508","indexId":"5224640","displayToPublicDate":"2010-06-16T12:18:55","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2564,"text":"Journal of the North American Benthological Society","onlineIssn":"1937-237X","printIssn":"0887-3593","active":true,"publicationSubtype":{"id":10}},"title":"Fish-assemblage variation between geologically defined regions and across a longitudinal gradient in the Monkey River Basin, Belize","docAbstract":"Linkages between geology and fish assemblages have been inferred in many regions throughout the world, but no studies have yet investigated whether fish assemblages differ across geologies in Mesoamerica. The goals of our study were to: 1) compare physicochemical conditions and fish-assemblage structure across 2 geologic types in headwaters of the Monkey River Basin, Belize, and 2) describe basin-scale patterns in fish community composition and structure for the benefit of conservation efforts. We censused headwater-pool fishes by direct observation, and assessed habitat size, structure, and water chemistry to compare habitat and fish richness, diversity, evenness, and density between streams in the variably metamorphosed sedimentary geologic type typical of 80% of Belize’s Maya Mountains (the Santa Rosa Group), and an anomalous extrusive geologic formation in the same area (the Bladen Volcanic Member). We also collected species-presence data from 20 sites throughout the basin for analyses of compositional patterns from the headwaters to the top of the estuary. Thirty-nine fish species in 21 families were observed. Poeciliids were numerically dominant, making up 39% of individuals captured, followed by characins (25%), and cichlids (20%). Cichlidae was the most species-rich family (7 spp.), followed by Poeciliidae (6 spp.). Habitat size and water chemistry differed strongly between geologic types, but habitat diversity did not. Major fish-assemblage differences also were not obvious between geologies, despite a marked difference in the presence of the aquatic macrophyte, Marathrum oxycarpum (Podostemaceae), which covered 37% of the stream bottom in high-nutrient streams draining the Santa Rosa Group, and did not occur in the low-P streams draining the Bladen Volcanic Member. Correlation analyses suggested that distance from the sea and amount of cover within pools are important to fish-assemblage structure, but that differing abiotic factors may influence assemblage structure within each geologic type. The fauna showed weak compositional zonation into 3 groups (headwaters, coastal plain, and nearshore). Nearly 20% of the fish species collected have migratory life cycles (including Joturuspichardi, Agonostomusmonticola, and Gobiomorusdormitor) that use freshwater and marine habitats. Some of these species probably rely on a natural flow regime and longitudinal connectivity for reproduction and dispersal of young, and natural flow regime and longitudinal connectivity are important factors for maintenance of functional linkages between the uplands and the coast in the ridge-to-reef corridor where the Monkey River is located. Therefore, we suggest that the viability of migratory fish populations may be a good biological indicator of upland-to-estuary connectivity important both to fishes and coastal ecosystem function. We recommend follow-up studies to substantiate the relative strengths of relationships between community structure and abiotic factors in contrasting geologies and to examine potential bottom−up responses of stream biota to the higher nutrient levels that were observed in stream waters draining the Santa Rosa Group geologic type.
","language":"English","publisher":"University of Chicago Press Journals","doi":"10.1899/0887-3593(2006)25[142:FVBGDR]2.0.CO;2","usgsCitation":"Esselman, P., Freeman, M.C., and Pringle, C.M., 2006, Fish-assemblage variation between geologically defined regions and across a longitudinal gradient in the Monkey River Basin, Belize: Journal of the North American Benthological Society, v. 25, no. 1, p. 142-156, https://doi.org/10.1899/0887-3593(2006)25[142:FVBGDR]2.0.CO;2.","productDescription":"15 p.","startPage":"142","endPage":"156","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":385663,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Belize","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -89.20898437499999,\n 15.961329081596647\n ],\n [\n -87.7587890625,\n 15.961329081596647\n ],\n [\n -87.7587890625,\n 18.35452552912664\n ],\n [\n -89.20898437499999,\n 18.35452552912664\n ],\n [\n -89.20898437499999,\n 15.961329081596647\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"25","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e49f3e4b07f02db5ef492","contributors":{"authors":[{"text":"Esselman, P.C.","contributorId":35044,"corporation":false,"usgs":true,"family":"Esselman","given":"P.C.","email":"","affiliations":[],"preferred":false,"id":342199,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Freeman, Mary C. 0000-0001-7615-6923","orcid":"https://orcid.org/0000-0001-7615-6923","contributorId":99659,"corporation":false,"usgs":true,"family":"Freeman","given":"Mary","email":"","middleInitial":"C.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":342201,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Pringle, C. M.","contributorId":72902,"corporation":false,"usgs":false,"family":"Pringle","given":"C.","email":"","middleInitial":"M.","affiliations":[],"preferred":false,"id":342200,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":5224627,"text":"5224627 - 2006 - Combining multistate capture-recapture data with tag recoveries to estimate demographic parameters","interactions":[],"lastModifiedDate":"2012-02-02T00:15:04","indexId":"5224627","displayToPublicDate":"2010-06-16T12:18:55","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1465,"text":"Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Combining multistate capture-recapture data with tag recoveries to estimate demographic parameters","docAbstract":"Matrix population models that allow an animal to occupy more than one state over time are important tools for population and evolutionary ecologists. Definition of state can vary, including location for metapopulation models and breeding state for life history models. For populations whose members can be marked and subsequently re-encountered, multistate mark-recapture models are available to estimate the survival and transition probabilities needed to construct population models. Multistate models have proved extremely useful in this context, but they often require a substantial amount of data and restrict estimation of transition probabilities to those areas or states subjected to formal sampling effort. At the same time, for many species, there are considerable tag recovery data provided by the public that could be modeled in order to increase precision and to extend inference to a greater number of areas or states. Here we present a statistical model for combining multistate capture-recapture data (e.g., from a breeding ground study) with multistate tag recovery data (e.g., from wintering grounds). We use this method to analyze data from a study of Canada Geese (Branta canadensis) in the Atlantic Flyway of North America. Our analysis produced marginal improvement in precision, due to relatively few recoveries, but we demonstrate how precision could be further improved with increases in the probability that a retrieved tag is reported.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Ecology","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"6533_Kendall.pdf","usgsCitation":"Kendall, W., Conn, P., and Hines, J., 2006, Combining multistate capture-recapture data with tag recoveries to estimate demographic parameters: Ecology, v. 87, no. 1, p. 169-177.","productDescription":"169-177","startPage":"169","endPage":"177","numberOfPages":"9","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":17556,"rank":200,"type":{"id":11,"text":"Document"},"url":"https://www.esajournals.org/doi/abs/10.1890/05-0637","linkFileType":{"id":5,"text":"html"}},{"id":198191,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"87","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4b24e4b07f02db6ae6d4","contributors":{"authors":[{"text":"Kendall, W. L. 0000-0003-0084-9891","orcid":"https://orcid.org/0000-0003-0084-9891","contributorId":32880,"corporation":false,"usgs":true,"family":"Kendall","given":"W. L.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":342146,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Conn, P.B.","contributorId":73974,"corporation":false,"usgs":true,"family":"Conn","given":"P.B.","email":"","affiliations":[],"preferred":false,"id":342148,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Hines, J.E. 0000-0001-5478-7230","orcid":"https://orcid.org/0000-0001-5478-7230","contributorId":36885,"corporation":false,"usgs":true,"family":"Hines","given":"J.E.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":342147,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":5224629,"text":"5224629 - 2006 - Site occupancy models with heterogeneous detection probabilities","interactions":[],"lastModifiedDate":"2012-02-02T00:15:31","indexId":"5224629","displayToPublicDate":"2010-06-16T12:18:55","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1039,"text":"Biometrics","active":true,"publicationSubtype":{"id":10}},"title":"Site occupancy models with heterogeneous detection probabilities","docAbstract":"Models for estimating the probability of occurrence of a species in the presence of imperfect detection are important in many ecological disciplines. In these ?site occupancy? models, the possibility of heterogeneity in detection probabilities among sites must be considered because variation in abundance (and other factors) among sampled sites induces variation in detection probability (p). In this article, I develop occurrence probability models that allow for heterogeneous detection probabilities by considering several common classes of mixture distributions for p. For any mixing distribution, the likelihood has the general form of a zero-inflated binomial mixture for which inference based upon integrated likelihood is straightforward. A recent paper by Link (2003, Biometrics 59, 1123?1130) demonstrates that in closed population models used for estimating population size, different classes of mixture distributions are indistinguishable from data, yet can produce very different inferences about population size. I demonstrate that this problem can also arise in models for estimating site occupancy in the presence of heterogeneous detection probabilities. The implications of this are discussed in the context of an application to avian survey data and the development of animal monitoring programs.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Biometrics","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"6538_Royle.pdf","usgsCitation":"Royle, J., 2006, Site occupancy models with heterogeneous detection probabilities: Biometrics, v. 62, no. 1, p. 97-102.","productDescription":"97-102","startPage":"97","endPage":"102","numberOfPages":"6","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":17558,"rank":200,"type":{"id":11,"text":"Document"},"url":"https://www3.interscience.wiley.com/journal/118626525/abstract","linkFileType":{"id":5,"text":"html"}},{"id":201543,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"62","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4a0be4b07f02db5fbd5f","contributors":{"authors":[{"text":"Royle, J. Andrew 0000-0003-3135-2167","orcid":"https://orcid.org/0000-0003-3135-2167","contributorId":96221,"corporation":false,"usgs":true,"family":"Royle","given":"J. Andrew","affiliations":[],"preferred":false,"id":342155,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":5224638,"text":"5224638 - 2006 - Generalized site occupancy models allowing for false positive and false negative errors","interactions":[],"lastModifiedDate":"2012-02-02T00:15:04","indexId":"5224638","displayToPublicDate":"2010-06-16T12:18:55","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1465,"text":"Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Generalized site occupancy models allowing for false positive and false negative errors","docAbstract":"Site occupancy models have been developed that allow for imperfect species detection or ?false negative? observations. Such models have become widely adopted in surveys of many taxa. The most fundamental assumption underlying these models is that ?false positive? errors are not possible. That is, one cannot detect a species where it does not occur. However, such errors are possible in many sampling situations for a number of reasons, and even low false positive error rates can induce extreme bias in estimates of site occupancy when they are not accounted for. In this paper, we develop a model for site occupancy that allows for both false negative and false positive error rates. This model can be represented as a two-component finite mixture model and can be easily fitted using freely available software. We provide an analysis of avian survey data using the proposed model and present results of a brief simulation study evaluating the performance of the maximum-likelihood estimator and the naive estimator in the presence of false positive errors.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Ecology","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"6548_Royle.pdf","usgsCitation":"Royle, J., and Link, W., 2006, Generalized site occupancy models allowing for false positive and false negative errors: Ecology, v. 87, no. 4, p. 835-841.","productDescription":"835-841","startPage":"835","endPage":"841","numberOfPages":"7","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":17560,"rank":200,"type":{"id":11,"text":"Document"},"url":"https://www.esajournals.org/doi/abs/10.1890/0012-9658(2006)87%5B835%3AGSOMAF%5D2.0.CO%3B2","linkFileType":{"id":5,"text":"html"}},{"id":197895,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"87","issue":"4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4b24e4b07f02db6aec9f","contributors":{"authors":[{"text":"Royle, J. Andrew 0000-0003-3135-2167","orcid":"https://orcid.org/0000-0003-3135-2167","contributorId":96221,"corporation":false,"usgs":true,"family":"Royle","given":"J. Andrew","affiliations":[],"preferred":false,"id":342194,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Link, W.A. 0000-0002-9913-0256","orcid":"https://orcid.org/0000-0002-9913-0256","contributorId":8815,"corporation":false,"usgs":true,"family":"Link","given":"W.A.","affiliations":[],"preferred":false,"id":342193,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":5224606,"text":"5224606 - 2006 - A hierarchical model for regional analysis of population change using Christmas Bird Count data, with application to the American Black Duck","interactions":[],"lastModifiedDate":"2012-02-02T00:15:32","indexId":"5224606","displayToPublicDate":"2010-06-16T12:18:53","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1318,"text":"Condor","active":true,"publicationSubtype":{"id":10}},"title":"A hierarchical model for regional analysis of population change using Christmas Bird Count data, with application to the American Black Duck","docAbstract":"Analysis of Christmas Bird Count (CBC) data is complicated by the need to account for variation in effort on counts and to provide summaries over large geographic regions. We describe a hierarchical model for analysis of population change using CBC data that addresses these needs. The effect of effort is modeled parametrically, with parameter values varying among strata as identically distributed random effects. Year and site effects are modeled hierarchically, accommodating large regional variation in number of samples and precision of estimates. The resulting model is complex, but a Bayesian analysis can be conducted using Markov chain Monte Carlo techniques. We analyze CBC data for American Black Ducks (Anas rubripes), a species of considerable management interest that has historically been monitored using winter surveys. Over the interval 1966-2003, Black Duck populations showed distinct regional patterns of population change. The patterns shown by CBC data are similar to those shown by the Midwinter Waterfowl Inventory for the United States.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Condor","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"6488_Link.pdf","usgsCitation":"Link, W., Sauer, J., and Niven, D., 2006, A hierarchical model for regional analysis of population change using Christmas Bird Count data, with application to the American Black Duck: Condor, v. 108, no. 1, p. 13-24.","productDescription":"13-24","startPage":"13","endPage":"24","numberOfPages":"12","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":202137,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":17496,"rank":200,"type":{"id":11,"text":"Document"},"url":"https://www.bioone.org/doi/abs/10.1650/0010-5422(2006)108%5B0013%3AAHMFRA%5D2.0.CO%3B2","linkFileType":{"id":5,"text":"html"}}],"volume":"108","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4b24e4b07f02db6ae475","contributors":{"authors":[{"text":"Link, W.A. 0000-0002-9913-0256","orcid":"https://orcid.org/0000-0002-9913-0256","contributorId":8815,"corporation":false,"usgs":true,"family":"Link","given":"W.A.","affiliations":[],"preferred":false,"id":342056,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Sauer, J.R. 0000-0002-4557-3019","orcid":"https://orcid.org/0000-0002-4557-3019","contributorId":66197,"corporation":false,"usgs":true,"family":"Sauer","given":"J.R.","affiliations":[],"preferred":false,"id":342058,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Niven, D.K.","contributorId":21247,"corporation":false,"usgs":true,"family":"Niven","given":"D.K.","email":"","affiliations":[],"preferred":false,"id":342057,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":5224731,"text":"5224731 - 2006 - Estimating site occupancy and detection probability parameters for meso- and large mammals in a coastal eosystem","interactions":[],"lastModifiedDate":"2016-10-27T11:12:02","indexId":"5224731","displayToPublicDate":"2010-06-16T12:18:31","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2508,"text":"Journal of Wildlife Management","active":true,"publicationSubtype":{"id":10}},"title":"Estimating site occupancy and detection probability parameters for meso- and large mammals in a coastal eosystem","docAbstract":"Large-scale, multispecies monitoring programs are widely used to assess changes in wildlife populations but they often assume constant detectability when documenting species occurrence. This assumption is rarely met in practice because animal populations vary across time and space. As a result, detectability of a species can be influenced by a number of physical, biological, or anthropogenic factors (e.g., weather, seasonality, topography, biological rhythms, sampling methods). To evaluate some of these influences, we estimated site occupancy rates using species-specific detection probabilities for meso- and large terrestrial mammal species on Cape Cod, Massachusetts, USA. We used model selection to assess the influence of different sampling methods and major environmental factors on our ability to detect individual species. Remote cameras detected the most species (9), followed by cubby boxes (7) and hair traps (4) over a 13-month period. Estimated site occupancy rates were similar among sampling methods for most species when detection probabilities exceeded 0.15, but we question estimates obtained from methods with detection probabilities between 0.05 and 0.15, and we consider methods with lower probabilities unacceptable for occupancy estimation and inference. Estimated detection probabilities can be used to accommodate variation in sampling methods, which allows for comparison of monitoring programs using different protocols. Vegetation and seasonality produced species-specific differences in detectability and occupancy, but differences were not consistent within or among species, which suggests that our results should be considered in the context of local habitat features and life history traits for the target species. We believe that site occupancy is a useful state variable and suggest that monitoring programs for mammals using occupancy data consider detectability prior to making inferences about species distributions or population change.
","language":"English","publisher":"The Wildlife Society","doi":"10.2193/0022-541X(2006)70[1625:ESOADP]2.0.CO;2","usgsCitation":"O’Connell, A.F., Talancy, N.W., Bailey, L., Sauer, J., Cook, R., and Gilbert, A.T., 2006, Estimating site occupancy and detection probability parameters for meso- and large mammals in a coastal eosystem: Journal of Wildlife Management, v. 70, no. 6, p. 1625-1633, https://doi.org/10.2193/0022-541X(2006)70[1625:ESOADP]2.0.CO;2.","productDescription":"9 p.","startPage":"1625","endPage":"1633","numberOfPages":"9","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":202261,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"70","issue":"6","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4a0ce4b07f02db5fc872","contributors":{"authors":[{"text":"O’Connell, Allan F. 0000-0001-7032-7023 aoconnell@usgs.gov","orcid":"https://orcid.org/0000-0001-7032-7023","contributorId":471,"corporation":false,"usgs":true,"family":"O’Connell","given":"Allan","email":"aoconnell@usgs.gov","middleInitial":"F.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":true,"id":342504,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Talancy, Neil W.","contributorId":88454,"corporation":false,"usgs":true,"family":"Talancy","given":"Neil","email":"","middleInitial":"W.","affiliations":[],"preferred":false,"id":342508,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Bailey, Larissa L.","contributorId":93183,"corporation":false,"usgs":true,"family":"Bailey","given":"Larissa L.","affiliations":[],"preferred":false,"id":342506,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Sauer, John R. jrsauer@usgs.gov","contributorId":3737,"corporation":false,"usgs":true,"family":"Sauer","given":"John R.","email":"jrsauer@usgs.gov","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":342507,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Cook, Robert","contributorId":176416,"corporation":false,"usgs":false,"family":"Cook","given":"Robert","affiliations":[],"preferred":false,"id":342505,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Gilbert, Andrew T.","contributorId":100974,"corporation":false,"usgs":true,"family":"Gilbert","given":"Andrew","email":"","middleInitial":"T.","affiliations":[],"preferred":false,"id":342503,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":5224728,"text":"5224728 - 2006 - Assessing recreation impacts to cliffs in Shenandoah National Park: Integrating visitor observation with trail and recreation site measurements","interactions":[],"lastModifiedDate":"2013-03-16T15:51:12","indexId":"5224728","displayToPublicDate":"2010-06-16T12:18:31","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2416,"text":"Journal of Park and Recreation Administration","active":true,"publicationSubtype":{"id":10}},"title":"Assessing recreation impacts to cliffs in Shenandoah National Park: Integrating visitor observation with trail and recreation site measurements","docAbstract":"The rock outcrops and cliffs of Shenandoah National Park provide habitat for several rare and endangered plant and animal species, including the federally endangered Shenandoah Salamander (Plethodon shenandoah; Ludwig et al., 1993). The location of the well-known park tour road, Skyline Drive, along the ridgeline provides exceptional access to many outcrops and cliffs throughout the park for a large number of the park?s 1.2 million annual visitors. Consequently, visitor use of cliff areas has led to natural resource impacts, including marked decreases in size and vigor of known rare plant populations. Despite the clear ecological value and potential threats to the natural resources at cliff areas, managers possess little information on visitor use of cliff sites and presently have no formal planning document to guide management. Thus, a park wide study of cliff sites was initiated during the 2005 visitor use season. As part of this research effort, our study used an integrative approach to study recreational use and visitor-caused resource impacts at one of the more heavily visited cliff sites in the park: Little Stony Man Cliffs (LSMC). In particular, this study integrated data from resource impact measurements and visitor use observation to help assess the effects of recreational use on the natural resources of LSMC. Procedures derived from campsite and trail impact studies were used to measure and characterize the amount of visitor-caused resource impacts on LSMC (Marion & Leung, 2001; Marion, 1995). Visitor use observations were conducted on top of LSMC to document and characterize the type and amount of recreational use the cliffs receive and the behaviors of recreationists that may contribute to cliff-top resource impacts. Resource impact measurement data show trampling disturbance present at LSMC, characterized by vegetation loss, exposed soil, and root exposure. Documentation of informal trails, soil erosion, tree damage, and tree stumps provide further indicators of resource damage at LSMC. Results of visitor use observation offer several insights into contributory factors of cliff-top resource damage by showing differences in use and behavior between visitor types. The findings from this study suggest that a management approach characterized by visitor education, some site hardening, and concentration of visitor use on durable surfaces, along with the installation of fixed anchors at the top of popular climbing routes is likely to have the greatest success at balancing visitor enjoyment with resource protection at LSMC.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Journal of Park and Recreation Administration","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"6680_Wood.pdf","usgsCitation":"Wood, K., Lawson, S., and Marion, J., 2006, Assessing recreation impacts to cliffs in Shenandoah National Park: Integrating visitor observation with trail and recreation site measurements: Journal of Park and Recreation Administration, v. 24, no. 4, p. 86-110.","productDescription":"86-110","startPage":"86","endPage":"110","numberOfPages":"25","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":201914,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":269473,"type":{"id":11,"text":"Document"},"url":"https://js.sagamorepub.com/jpra/article/view/1396"}],"volume":"24","issue":"4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4abbe4b07f02db672a48","contributors":{"authors":[{"text":"Wood, K.T.","contributorId":87658,"corporation":false,"usgs":true,"family":"Wood","given":"K.T.","email":"","affiliations":[],"preferred":false,"id":342496,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Lawson, S.R.","contributorId":14083,"corporation":false,"usgs":true,"family":"Lawson","given":"S.R.","email":"","affiliations":[],"preferred":false,"id":342495,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Marion, J. L. 0000-0003-2226-689X","orcid":"https://orcid.org/0000-0003-2226-689X","contributorId":10888,"corporation":false,"usgs":true,"family":"Marion","given":"J. L.","affiliations":[],"preferred":false,"id":342494,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":5224727,"text":"5224727 - 2006 - Multistate survival models and their extensions in Program MARK","interactions":[],"lastModifiedDate":"2012-02-02T00:15:30","indexId":"5224727","displayToPublicDate":"2010-06-16T12:18:31","publicationYear":"2006","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2508,"text":"Journal of Wildlife Management","active":true,"publicationSubtype":{"id":10}},"title":"Multistate survival models and their extensions in Program MARK","docAbstract":"Program MARK provides .100 models for the estimation of population parameters from mark?encounter data. The multistate model of Brownie et al. (1993) and Hestbeck et al. (1991) allows animals to move between states with a probability of transition. The simplest multistate model is an extension of the Cormack?Jolly?Seber (CJS) live recapture model. arameters estimated are state-specific survival rates and encounter probabilities and transition probabilities between states. The multistate model provides a valuable framework to evaluate important ecological questions. For example, estimation of state-specific survival and transition probabilities between the biological states of breeders and nonbreeders allows estimation of the cost of reproduction. Transitions between physical states, such as spatial areas, provide estimates needed for meta-population models. The basic multistate model uses only live recaptures, but 3 extensions are included in MARK. A multistate model with live and dead encounters is available, although the dead encounters are not state specific. Robust-design multistate models are also included in MARK, with both open and closed robust designs. These models assume that animals move between states only between primary sessions of the robust design. For the closed robust design, we can specify 12 different data types for the modeling of encounter probabilities during the primary session, including 6 versions of the closed model likelihood incorporating population size (N) directly in the likelihood, and 6 versions of the Huggins model in which N is estimated as a derived parameter outside the likelihood. One assumption that is generally necessary to estimate state-specific survival rates in the multistate model is that transitions take place immediately before encounter occasions. Otherwise, survival rates over the interval between encounter occasions are a mix of survival rates over multiple states. Advantages of using MARK to estimate the parameters of the various multistate models include flexibility of model specification to include group, time, and individual covariates, estimation of variance components, model averaging of parameter estimates, and Bayesian parameter estimation using Markov chain Monte Carlo procedures on the logit scale.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Journal of Wildlife Management","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"6679_White.pdf","usgsCitation":"White, G.C., Kendall, W., and Barker, R.J., 2006, Multistate survival models and their extensions in Program MARK: Journal of Wildlife Management, v. 70, no. 6, p. 1521-1529.","productDescription":"1521-1529","startPage":"1521","endPage":"1529","numberOfPages":"9","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":202122,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":16810,"rank":200,"type":{"id":11,"text":"Document"},"url":"https://www.bioone.org/perlserv/?request=get-abstract&doi=10.2193%2F0022-541X%282006%2970%5B1521%3AMSMATE%5D2.0.CO%3B2","linkFileType":{"id":5,"text":"html"}}],"volume":"70","issue":"6","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4805e4b07f02db4cf208","contributors":{"authors":[{"text":"White, Gary C.","contributorId":26256,"corporation":false,"usgs":true,"family":"White","given":"Gary","email":"","middleInitial":"C.","affiliations":[],"preferred":false,"id":342491,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kendall, W. L. 0000-0003-0084-9891","orcid":"https://orcid.org/0000-0003-0084-9891","contributorId":32880,"corporation":false,"usgs":true,"family":"Kendall","given":"W. L.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":342492,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Barker, R. J.","contributorId":34222,"corporation":false,"usgs":false,"family":"Barker","given":"R.","email":"","middleInitial":"J.","affiliations":[],"preferred":false,"id":342493,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ]}