Many fields of science begin with a phase of exploration and description, followed by investigations of the processes that account for observed patterns. The science of ecology is no exception, and recent decades have seen a focus on understanding key processes underlying the dynamics of ecological systems. In population ecology, emphasis has shifted from the state variable of population size to the demographic processes responsible for changes in this state variable: birth, death, immigration, and emigration. In evolutionary ecology, some of these same demographic processes, rates of birth and death, are also the determinants of fitness. In animal population ecology, the estimation of state variables and their associated vital rates is especially problematic because of the difficulties in sampling such populations and detecting individual animals. Indeed, early capture–recapture models were developed for the purpose of estimating population size, given the reality that all animals are not caught or detected at any sampling occasion. More recently, capture–recapture models for open populations were developed to draw inferences about survival in the face of these same sampling problems. The focus of this paper is on multi‐state mark–recapture models (MSMR), which first appeared in the 1970s but have undergone substantial development in the last 15 years. These models were developed to deal explicitly with biological variation, in that animals in different “states” (classes defined by location, physiology, behavior, reproductive status, etc.) may have different probabilities of survival and detection. Animal transitions between states are also stochastic and themselves of interest. These general models have proven to be extremely useful and provide a way of thinking about a remarkably wide range of important ecological processes. These methods are now at a stage of refinement and sophistication where they can readily be used by biologists to tackle a wide range of important issues in ecology. In this paper, we draw together information on the state of the art in multistate mark–recapture methods, explaining the models and illustrating their use. We provide a modeling philosophy and a series of general principles on how to conduct analyses. We cover key issues and features, and we anticipate the ways in which we expect the models to develop in the years ahead.
","language":"English","publisher":"Elsevier","doi":"10.1016/S0065-2504(09)00403-6","usgsCitation":"Lebreton, J., Nichols, J., Barker, R., Pradel, R., and Spendelow, J.A., 2009, Modeling individual animal histories with multistate capture–recapture models: Advances in Ecological Research, v. 41, p. 87-173, https://doi.org/10.1016/S0065-2504(09)00403-6.","productDescription":"87 p.","startPage":"87","endPage":"173","ipdsId":"IP-010824","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":330073,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"41","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5809d7c4e4b0f497e78fca77","contributors":{"authors":[{"text":"Lebreton, Jean-Dominique","contributorId":172792,"corporation":false,"usgs":false,"family":"Lebreton","given":"Jean-Dominique","email":"","affiliations":[],"preferred":false,"id":651524,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Nichols, James D. jnichols@usgs.gov","contributorId":139082,"corporation":false,"usgs":true,"family":"Nichols","given":"James D.","email":"jnichols@usgs.gov","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":651525,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Barker, Richard J.","contributorId":6987,"corporation":false,"usgs":true,"family":"Barker","given":"Richard J.","affiliations":[],"preferred":false,"id":651526,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Pradel, Roger","contributorId":176008,"corporation":false,"usgs":false,"family":"Pradel","given":"Roger","email":"","affiliations":[],"preferred":false,"id":651527,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Spendelow, Jeffrey A. 0000-0001-8167-0898 jspendelow@usgs.gov","orcid":"https://orcid.org/0000-0001-8167-0898","contributorId":4355,"corporation":false,"usgs":true,"family":"Spendelow","given":"Jeffrey","email":"jspendelow@usgs.gov","middleInitial":"A.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":true,"id":651528,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70190436,"text":"70190436 - 2009 - Geochemical evolution of a high arsenic, alkaline pit-lake in the Mother Lode Gold District, California","interactions":[],"lastModifiedDate":"2017-08-31T11:17:18","indexId":"70190436","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1472,"text":"Economic Geology","active":true,"publicationSubtype":{"id":10}},"title":"Geochemical evolution of a high arsenic, alkaline pit-lake in the Mother Lode Gold District, California","docAbstract":"The Harvard orebody at the Jamestown gold mine, located along the Melones fault zone in the southern Mother Lode gold district, California, was mined in an open-pit operation from 1987 to 1994. Dewatering during mining produced a hydrologic cone of depression; recovery toward the premining ground-water configuration produced a monomictic pit lake with alkaline Ca-Mg-HCO3-SO4–type pit water, concentrations of As up to 1,200 μg/L, and total dissolved solids (TDS) up to 2,000 mg/L. In this study, pit-wall rocks were mapped and chemically analyzed to provide a context for evaluating observed variability in the composition of the pit-lake waters in relationship to seasonal weather patterns. An integrated hydrogeochemical model of pit-lake evolution based on observations of pit-lake volume, water composition (samples collected between 1998–2000, 2004), and processes occurring on pit walls was developed in three stages using the computer code PHREEQC. Stage 1 takes account of seasonally variable water fluxes from precipitation, evaporation, springs, and ground water, as well as lake stratification and mixing processes. Stage 2 adds CO2fluxes and wall-rock interactions, and stage 3 assesses the predictive capability of the model.
Two major geologic units in fault contact comprise the pit walls. The hanging wall is composed of interlayered slate, metavolcanic and metavolcaniclastic rocks, and schists; the footwall rocks are chlorite-actinolite and talc-tremolite schists generated by metasomatism of greenschist-facies mafic and ultramafic igneous rocks. Alteration in the ore zone provides evidence for mineralizing fluids that introduced CO2, S, and K2O, and redistributed SiO2. Arsenian pyrite associated with the alteration weathers to produce goethite and jarosite on pit walls and in joints, as well as copiapite and hexahydrite efflorescences that accumulate on wall-rock faces during dry California summers. All of these pyrite weathering products incorporate arsenic at concentrations from <100 up to 1,200 ppm. In the pit lake, pH and TDS reach seasonal highs in the summer epilimnion; pH is lowest in the summer hypolimnion. Arsenic and bicarbonate covary in the hypolimnion, rising as stratification proceeds and declining during winter rains. The computational model suggests that water fluxes alone do not account for this seasonal variability. Loss of CO2 to the atmosphere, interaction with pit walls including washoff of efflorescent salts during the first flush and seasonal rainfall, and arsenic sorption appear to contribute to the observed pit-lake characteristics.
","language":"English","publisher":"Society of Economic Geologists","doi":"10.2113/gsecongeo.104.8.1171","usgsCitation":"Savage, K.S., Ashley, R.P., and Bird, D.K., 2009, Geochemical evolution of a high arsenic, alkaline pit-lake in the Mother Lode Gold District, California: Economic Geology, v. 104, no. 8, p. 1171-1211, https://doi.org/10.2113/gsecongeo.104.8.1171.","productDescription":"41 p.","startPage":"1171","endPage":"1211","ipdsId":"IP-012322","costCenters":[{"id":662,"text":"Western Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"links":[{"id":345385,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"California","otherGeospatial":"Mother Lode Gold District","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -120.44079780578613,\n 37.94027155343197\n ],\n [\n -120.43006896972655,\n 37.94027155343197\n ],\n [\n -120.43006896972655,\n 37.94852933714952\n ],\n [\n -120.44079780578613,\n 37.94852933714952\n ],\n [\n -120.44079780578613,\n 37.94027155343197\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"104","issue":"8","publishingServiceCenter":{"id":14,"text":"Menlo Park PSC"},"noUsgsAuthors":false,"publicationDate":"2010-02-12","publicationStatus":"PW","scienceBaseUri":"59a92042e4b07e1a023ccdb0","contributors":{"authors":[{"text":"Savage, Kaye S.","contributorId":196059,"corporation":false,"usgs":false,"family":"Savage","given":"Kaye","email":"","middleInitial":"S.","affiliations":[],"preferred":false,"id":709155,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Ashley, Roger P. ashley@usgs.gov","contributorId":2749,"corporation":false,"usgs":true,"family":"Ashley","given":"Roger","email":"ashley@usgs.gov","middleInitial":"P.","affiliations":[],"preferred":true,"id":709156,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Bird, Dennis K.","contributorId":9339,"corporation":false,"usgs":true,"family":"Bird","given":"Dennis","email":"","middleInitial":"K.","affiliations":[],"preferred":false,"id":709157,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70036372,"text":"70036372 - 2009 - Characterizing canopy biochemistry from imaging spectroscopy and its application to ecosystem studies","interactions":[],"lastModifiedDate":"2012-03-12T17:22:04","indexId":"70036372","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3254,"text":"Remote Sensing of Environment","printIssn":"0034-4257","active":true,"publicationSubtype":{"id":10}},"title":"Characterizing canopy biochemistry from imaging spectroscopy and its application to ecosystem studies","docAbstract":"For two decades, remotely sensed data from imaging spectrometers have been used to estimate non-pigment biochemical constituents of vegetation, including water, nitrogen, cellulose, and lignin. This interest has been motivated by the important role that these substances play in physiological processes such as photosynthesis, their relationships with ecosystem processes such as litter decomposition and nutrient cycling, and their use in identifying key plant species and functional groups. This paper reviews three areas of research to improve the application of imaging spectrometers to quantify non-pigment biochemical constituents of plants. First, we examine recent empirical and modeling studies that have advanced our understanding of leaf and canopy reflectance spectra in relation to plant biochemistry. Next, we present recent examples of how spectroscopic remote sensing methods are applied to characterize vegetation canopies, communities and ecosystems. Third, we highlight the latest developments in using imaging spectrometer data to quantify net primary production (NPP) over large geographic areas. Finally, we discuss the major challenges in quantifying non-pigment biochemical constituents of plant canopies from remotely sensed spectra.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Remote Sensing of Environment","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1016/j.rse.2008.10.018","issn":"00344257","usgsCitation":"Kokaly, R., Asner, G.P., Ollinger, S., Martin, M., and Wessman, C., 2009, Characterizing canopy biochemistry from imaging spectroscopy and its application to ecosystem studies: Remote Sensing of Environment, v. 113, no. SUPPL. 1, https://doi.org/10.1016/j.rse.2008.10.018.","costCenters":[],"links":[{"id":218142,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1016/j.rse.2008.10.018"},{"id":246127,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"113","issue":"SUPPL. 1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059f4efe4b0c8380cd4bfff","contributors":{"authors":[{"text":"Kokaly, R.F. 0000-0003-0276-7101","orcid":"https://orcid.org/0000-0003-0276-7101","contributorId":42381,"corporation":false,"usgs":true,"family":"Kokaly","given":"R.F.","affiliations":[],"preferred":false,"id":455774,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Asner, Gregory P.","contributorId":25393,"corporation":false,"usgs":false,"family":"Asner","given":"Gregory","email":"","middleInitial":"P.","affiliations":[{"id":6986,"text":"Stanford University","active":true,"usgs":false}],"preferred":false,"id":455773,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Ollinger, S.V.","contributorId":107967,"corporation":false,"usgs":true,"family":"Ollinger","given":"S.V.","email":"","affiliations":[],"preferred":false,"id":455777,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Martin, M.E.","contributorId":94097,"corporation":false,"usgs":true,"family":"Martin","given":"M.E.","email":"","affiliations":[],"preferred":false,"id":455776,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Wessman, C.A.","contributorId":48802,"corporation":false,"usgs":true,"family":"Wessman","given":"C.A.","email":"","affiliations":[],"preferred":false,"id":455775,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70032818,"text":"70032818 - 2009 - Characterizing and predicting species distributions across environments and scales: Argentine ant occurrences in the eye of the beholder","interactions":[],"lastModifiedDate":"2012-03-12T17:21:24","indexId":"70032818","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1839,"text":"Global Ecology and Biogeography","active":true,"publicationSubtype":{"id":10}},"title":"Characterizing and predicting species distributions across environments and scales: Argentine ant occurrences in the eye of the beholder","docAbstract":"Aim: Species distribution models (SDMs) or, more specifically, ecological niche models (ENMs) are a useful and rapidly proliferating tool in ecology and global change biology. ENMs attempt to capture associations between a species and its environment and are often used to draw biological inferences, to predict potential occurrences in unoccupied regions and to forecast future distributions under environmental change. The accuracy of ENMs, however, hinges critically on the quality of occurrence data. ENMs often use haphazardly collected data rather than data collected across the full spectrum of existing environmental conditions. Moreover, it remains unclear how processes affecting ENM predictions operate at different spatial scales. The scale (i.e. grain size) of analysis may be dictated more by the sampling regime than by biologically meaningful processes. The aim of our study is to jointly quantify how issues relating to region and scale affect ENM predictions using an economically important and ecologically damaging invasive species, the Argentine ant (Linepithema humile). Location: California, USA. Methods: We analysed the relationship between sampling sufficiency, regional differences in environmental parameter space and cell size of analysis and resampling environmental layers using two independently collected sets of presence/absence data. Differences in variable importance were determined using model averaging and logistic regression. Model accuracy was measured with area under the curve (AUC) and Cohen's kappa. Results: We first demonstrate that insufficient sampling of environmental parameter space can cause large errors in predicted distributions and biological interpretation. Models performed best when they were parametrized with data that sufficiently sampled environmental parameter space. Second, we show that altering the spatial grain of analysis changes the relative importance of different environmental variables. These changes apparently result from how environmental constraints and the sampling distributions of environmental variables change with spatial grain. Conclusions: These findings have clear relevance for biological inference. Taken together, our results illustrate potentially general limitations for ENMs, especially when such models are used to predict species occurrences in novel environments. We offer basic methodological and conceptual guidelines for appropriate sampling and scale matching. ?? 2009 The Authors Journal compilation ?? 2009 Blackwell Publishing.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Global Ecology and Biogeography","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1111/j.1466-8238.2008.00420.x","issn":"14668","usgsCitation":"Menke, S., Holway, D., Fisher, R., and Jetz, W., 2009, Characterizing and predicting species distributions across environments and scales: Argentine ant occurrences in the eye of the beholder: Global Ecology and Biogeography, v. 18, no. 1, p. 50-63, https://doi.org/10.1111/j.1466-8238.2008.00420.x.","startPage":"50","endPage":"63","numberOfPages":"14","costCenters":[],"links":[{"id":213623,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1111/j.1466-8238.2008.00420.x"},{"id":241269,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"18","issue":"1","noUsgsAuthors":false,"publicationDate":"2008-12-09","publicationStatus":"PW","scienceBaseUri":"5059f4efe4b0c8380cd4bff8","contributors":{"authors":[{"text":"Menke, S.B.","contributorId":78938,"corporation":false,"usgs":true,"family":"Menke","given":"S.B.","email":"","affiliations":[],"preferred":false,"id":438055,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Holway, D.A.","contributorId":31581,"corporation":false,"usgs":true,"family":"Holway","given":"D.A.","email":"","affiliations":[],"preferred":false,"id":438053,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Fisher, Robert N. 0000-0002-2956-3240","orcid":"https://orcid.org/0000-0002-2956-3240","contributorId":51675,"corporation":false,"usgs":true,"family":"Fisher","given":"Robert N.","affiliations":[{"id":651,"text":"Western Ecological Research Center","active":true,"usgs":true}],"preferred":true,"id":438054,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Jetz, W.","contributorId":101458,"corporation":false,"usgs":true,"family":"Jetz","given":"W.","affiliations":[],"preferred":false,"id":438056,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70032819,"text":"70032819 - 2009 - Continuing evolution of the Pacific-Juan de Fuca-North America slab window system-A trench-ridge-transform example from the Pacific Rim","interactions":[],"lastModifiedDate":"2013-07-15T09:13:33","indexId":"70032819","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3525,"text":"Tectonophysics","active":true,"publicationSubtype":{"id":10}},"title":"Continuing evolution of the Pacific-Juan de Fuca-North America slab window system-A trench-ridge-transform example from the Pacific Rim","docAbstract":"Many subduction margins that rim the Pacific Ocean contain complex records of Cenozoic slab-window volcanism combined with tectonic disruption of the continental margin. The series of slab windows that opened beneath California and Mexico starting about 28.5 Ma resulted from the death of a series of spreading ridge segments and led to piecewise destruction of a subduction regime. The timing and areal extent of the resultant slab-window volcanism provide constraints on models that depict the subsequent fragmentation and dispersal of the overlying continental margin. The initial Pioneer slab window thermally weakened the overlying western Transverse Ranges and California Borderlands region starting about 28.5 Ma. A second thermal pulse occurred in the same region starting about 19 Ma during growth of the Monterey slab window. This additional heating, combined with the capture of a partially subducted Monterey plate fragment by the Cocos plate, initiated the pulling apart and rotation of the adjacent continental margin. Similarly, the capture of Guadalupe and Magdalena plate fragments by the Pacific plate and initiation of the Guadalupe-Magdalena slab window about 12.5 Ma are coeval with Baja California pulling away from the Mexico continental margin, with the break along the Comondú arc, in crust already thermally weakened by about 10 My of volcanism. In coastal California, distributed crustal extension and subsidence accompanied the new transform plate boundary, and continued until the slab windows cooled and plate motion coalesced along a through-going system of strike-slip faults. The transform boundary continues to evolve, and forward modeling predicts an instability with the current configuration as a result of convergence between the Sierra Nevada and Peninsular Ranges batholiths, starting about 2 My in the future. The instability may be resolved by a shift in the locus of transform motion from the San Andreas fault to the eastern California shear zone, or by breaking off another fragment of the Mojave or southern Sierra Nevada crustal blocks and translating it northward.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Tectonophysics","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1016/j.tecto.2008.01.018","issn":"00401","usgsCitation":"McCrory, P., Wilson, D., and Stanley, R., 2009, Continuing evolution of the Pacific-Juan de Fuca-North America slab window system-A trench-ridge-transform example from the Pacific Rim: Tectonophysics, v. 464, no. 1-4, p. 30-42, https://doi.org/10.1016/j.tecto.2008.01.018.","startPage":"30","endPage":"42","numberOfPages":"13","costCenters":[],"links":[{"id":213650,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1016/j.tecto.2008.01.018"},{"id":241298,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"464","issue":"1-4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059fa54e4b0c8380cd4da55","contributors":{"authors":[{"text":"McCrory, P.A.","contributorId":96287,"corporation":false,"usgs":true,"family":"McCrory","given":"P.A.","email":"","affiliations":[],"preferred":false,"id":438059,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Wilson, D.S.","contributorId":55216,"corporation":false,"usgs":true,"family":"Wilson","given":"D.S.","email":"","affiliations":[],"preferred":false,"id":438057,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Stanley, R. G. 0000-0001-6192-8783","orcid":"https://orcid.org/0000-0001-6192-8783","contributorId":77123,"corporation":false,"usgs":true,"family":"Stanley","given":"R. G.","affiliations":[],"preferred":false,"id":438058,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70034688,"text":"70034688 - 2009 - Plant toxicity, adaptive herbivory, and plant community dynamics","interactions":[],"lastModifiedDate":"2012-03-12T17:21:42","indexId":"70034688","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1478,"text":"Ecosystems","active":true,"publicationSubtype":{"id":10}},"title":"Plant toxicity, adaptive herbivory, and plant community dynamics","docAbstract":"We model effects of interspecific plant competition, herbivory, and a plant's toxic defenses against herbivores on vegetation dynamics. The model predicts that, when a generalist herbivore feeds in the absence of plant toxins, adaptive foraging generally increases the probability of coexistence of plant species populations, because the herbivore switches more of its effort to whichever plant species is more common and accessible. In contrast, toxin-determined selective herbivory can drive plant succession toward dominance by the more toxic species, as previously documented in boreal forests and prairies. When the toxin concentrations in different plant species are similar, but species have different toxins with nonadditive effects, herbivores tend to diversify foraging efforts to avoid high intakes of any one toxin. This diversification leads the herbivore to focus more feeding on the less common plant species. Thus, uncommon plants may experience depensatory mortality from herbivory, reducing local species diversity. The depensatory effect of herbivory may inhibit the invasion of other plant species that are more palatable or have different toxins. These predictions were tested and confirmed in the Alaskan boreal forest. ?? 2009 Springer Science+Business Media, LLC.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Ecosystems","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1007/s10021-009-9240-x","issn":"14329840","usgsCitation":"Feng, Z., Liu, R., DeAngelis, D., Bryant, L.C., Kielland, K., Stuart, C.F., and Swihart, R., 2009, Plant toxicity, adaptive herbivory, and plant community dynamics: Ecosystems, v. 12, no. 4, p. 534-547, https://doi.org/10.1007/s10021-009-9240-x.","startPage":"534","endPage":"547","numberOfPages":"14","costCenters":[],"links":[{"id":215570,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1007/s10021-009-9240-x"},{"id":243382,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"12","issue":"4","noUsgsAuthors":false,"publicationDate":"2009-03-10","publicationStatus":"PW","scienceBaseUri":"505a7c02e4b0c8380cd79744","contributors":{"authors":[{"text":"Feng, Z.","contributorId":84991,"corporation":false,"usgs":true,"family":"Feng","given":"Z.","email":"","affiliations":[],"preferred":false,"id":447046,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Liu, R.","contributorId":23731,"corporation":false,"usgs":true,"family":"Liu","given":"R.","email":"","affiliations":[],"preferred":false,"id":447042,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"DeAngelis, D.L. 0000-0002-1570-4057","orcid":"https://orcid.org/0000-0002-1570-4057","contributorId":32470,"corporation":false,"usgs":true,"family":"DeAngelis","given":"D.L.","affiliations":[],"preferred":false,"id":447044,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Bryant, Lee C.","contributorId":62045,"corporation":false,"usgs":false,"family":"Bryant","given":"Lee","email":"","middleInitial":"C.","affiliations":[{"id":12698,"text":"Northern Arizona University","active":true,"usgs":false}],"preferred":true,"id":447045,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Kielland, K.","contributorId":98932,"corporation":false,"usgs":true,"family":"Kielland","given":"K.","affiliations":[],"preferred":false,"id":447048,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Stuart, Chapin F.","contributorId":23781,"corporation":false,"usgs":true,"family":"Stuart","given":"Chapin","email":"","middleInitial":"F.","affiliations":[],"preferred":false,"id":447043,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Swihart, R.K.","contributorId":90560,"corporation":false,"usgs":true,"family":"Swihart","given":"R.K.","email":"","affiliations":[],"preferred":false,"id":447047,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ,{"id":70034692,"text":"70034692 - 2009 - Water quality characterization in some birimian aquifers of the Birim Basin, Ghana","interactions":[],"lastModifiedDate":"2012-03-12T17:21:41","indexId":"70034692","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2578,"text":"KSCE Journal of Civil Engineering","active":true,"publicationSubtype":{"id":10}},"title":"Water quality characterization in some birimian aquifers of the Birim Basin, Ghana","docAbstract":"The objective of this study was to determine the main controls on the hydrochemistry of groundwater in the study area. Mass balance modeling was used simultaneously with multivariate R-mode hierarchical cluster analysis to determine the significant sources of variation in the hydrochemistry. Two water types have been revealed in this area: (1) waters influenced more significantly by the weathering of silicate minerals from the underlying geology, and are rich in silica, sodium, calcium, bicarbonate, and magnesium ions, and (2) waters that have been influenced by the effects of fertilizers and other anthropogenic activities in the area. Mineral speciation and silicate mineral stability diagrams generated from the data suggest that montmorillonite, probably derived from the incongruent dissolution of feldspars and micas, is the most stable silicate phase in the groundwater. The apparent incongruent weathering of silicate minerals in the groundwater system has led to the enrichment of sodium, calcium, magnesium and bicarbonate ions as well as silica, leading to the supersaturation of calcite, aragonite, dolomite and quartz. Stability in the montmorillonite field suggests restricted flow conditions whereby groundwater residence time is relatively high, leading to greater contact of groundwater with the rock to enhance weathering. Cation exchange processes have also been determined to play minor roles in the hydrochemistry.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"KSCE Journal of Civil Engineering","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1007/s12205-009-0179-4","issn":"12267988","usgsCitation":"Bruce, B., Yidana, S., Anku, Y., Akabzaa, T., and Asiedu, D., 2009, Water quality characterization in some birimian aquifers of the Birim Basin, Ghana: KSCE Journal of Civil Engineering, v. 13, no. 3, p. 179-187, https://doi.org/10.1007/s12205-009-0179-4.","startPage":"179","endPage":"187","numberOfPages":"9","costCenters":[],"links":[{"id":476443,"rank":10000,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1007/s12205-009-0179-4","text":"Publisher Index Page"},{"id":215631,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1007/s12205-009-0179-4"},{"id":243448,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"13","issue":"3","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505bc88fe4b08c986b32c9c0","contributors":{"authors":[{"text":"Bruce, B.-Y.","contributorId":101477,"corporation":false,"usgs":true,"family":"Bruce","given":"B.-Y.","email":"","affiliations":[],"preferred":false,"id":447063,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Yidana, S.M.","contributorId":59554,"corporation":false,"usgs":true,"family":"Yidana","given":"S.M.","email":"","affiliations":[],"preferred":false,"id":447060,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Anku, Y.","contributorId":96083,"corporation":false,"usgs":true,"family":"Anku","given":"Y.","affiliations":[],"preferred":false,"id":447062,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Akabzaa, T.","contributorId":39580,"corporation":false,"usgs":true,"family":"Akabzaa","given":"T.","email":"","affiliations":[],"preferred":false,"id":447059,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Asiedu, D.","contributorId":76131,"corporation":false,"usgs":true,"family":"Asiedu","given":"D.","affiliations":[],"preferred":false,"id":447061,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70036000,"text":"70036000 - 2009 - Characterization of Santa Catarina (Brazil) coal with respect to human health and environmental concerns","interactions":[],"lastModifiedDate":"2012-03-12T17:21:50","indexId":"70036000","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1538,"text":"Environmental Geochemistry and Health","active":true,"publicationSubtype":{"id":10}},"title":"Characterization of Santa Catarina (Brazil) coal with respect to human health and environmental concerns","docAbstract":"The current paper presents the concentration, distribution, and modes of occurrence of trace elements of 13 coals from south Brazil. The samples were collected in the state of Santa Catarina. Chemical analyses and the high ash yields indicate that all studied coals are rich in mineral matter, with SiO2 and Al2O3 dominating as determined by inductively coupled plasma-atomic emission spectrometry (ICP-AES). Quartz is the main mineral species and is associated with minor levels of feldspars, kaolinite, hematite, and iron-rich carbonates. The contents of trace elements, including As, Pb, Cd, Ni, Cr, Mn, Be, V, U, Zn, Li, Cu, Tl, and Ni, in coals were determined. A comparison of ranges and means of elemental concentrations in Santa Catarina, Brazil, and world coals shows that the ranges of most elements in Santa Catarina coal are very close to the usual worldwide concentration ranges in coal. ?? Springer Science+Business Media B.V. 2008.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Environmental Geochemistry and Health","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1007/s10653-008-9200-y","issn":"02694042","usgsCitation":"Silva, L., Oliveira, M., Boit, K., and Finkelman, R.B., 2009, Characterization of Santa Catarina (Brazil) coal with respect to human health and environmental concerns: Environmental Geochemistry and Health, v. 31, no. 4, p. 475-485, https://doi.org/10.1007/s10653-008-9200-y.","startPage":"475","endPage":"485","numberOfPages":"11","costCenters":[],"links":[{"id":216152,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1007/s10653-008-9200-y"},{"id":244001,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"31","issue":"4","noUsgsAuthors":false,"publicationDate":"2008-08-03","publicationStatus":"PW","scienceBaseUri":"5059f4bce4b0c8380cd4bea1","contributors":{"authors":[{"text":"Silva, L.F.O.","contributorId":23782,"corporation":false,"usgs":true,"family":"Silva","given":"L.F.O.","email":"","affiliations":[],"preferred":false,"id":453546,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Oliveira, M.L.S.","contributorId":63238,"corporation":false,"usgs":true,"family":"Oliveira","given":"M.L.S.","email":"","affiliations":[],"preferred":false,"id":453548,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Boit, K.M.","contributorId":45926,"corporation":false,"usgs":true,"family":"Boit","given":"K.M.","email":"","affiliations":[],"preferred":false,"id":453547,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Finkelman, R. B.","contributorId":20341,"corporation":false,"usgs":true,"family":"Finkelman","given":"R.","email":"","middleInitial":"B.","affiliations":[],"preferred":false,"id":453545,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70035824,"text":"70035824 - 2009 - Spectral distance decay","interactions":[],"lastModifiedDate":"2021-03-09T15:25:14.763781","indexId":"70035824","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3052,"text":"Photogrammetric Engineering and Remote Sensing","active":true,"publicationSubtype":{"id":10}},"title":"Spectral distance decay","docAbstract":"Remotely sensed data represents key information for character-izing and estimating biodiversity. Spectral distance among sites has proven to be a powerful approach for detecting species composition variability. Regression analysis of species similarity versus spectral distance may allow us to quantitatively estimate how beta-diversity in species changes with respect to spectral and ecological variability. In classical regression analysis, the residual sum of squares is minimized for the mean of the dependent variable distribution. However, many ecological datasets are characterized by a high number of zeroes that can add noise to the regression model. Quantile regression can be used to evaluate trend in the upper quantiles rather than a mean trend across the whole distribution of the dependent variable. In this paper, we used ordinary least square (OLS) and quantile regression to estimate the decay of species similarity versus spectral distance. The achieved decay rates were statistically nonzero (p < 0.05) considering both OLS and quantile regression. Nonetheless, OLS regression estimate of mean decay rate was only half the decay rate indicated by the upper quantiles. Moreover, the intercept value, representing the similarity reached when spectral distance approaches zero, was very low compared with the intercepts of upper quantiles, which detected high species similarity when habitats are more similar. In this paper we demonstrated the power of using quantile regressions applied to spectral distance decay in order to reveal species diversity patterns otherwise lost or underestimated by ordinary least square regression.
","language":"English","publisher":"American Society for Photogrammetry and Remote Sensing","doi":"10.14358/pers.75.10.1225","issn":"00991112","usgsCitation":"Rocchinl, D., Nagendra, H., Ghate, R., and Cade, B., 2009, Spectral distance decay: Photogrammetric Engineering and Remote Sensing, v. 75, no. 10, p. 1225-1230, https://doi.org/10.14358/pers.75.10.1225.","productDescription":"6 p.","startPage":"1225","endPage":"1230","numberOfPages":"6","costCenters":[],"links":[{"id":476313,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.14358/pers.75.10.1225","text":"Publisher Index Page"},{"id":384247,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"75","issue":"10","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505b953ce4b08c986b31ae01","contributors":{"authors":[{"text":"Rocchinl, D.","contributorId":40825,"corporation":false,"usgs":true,"family":"Rocchinl","given":"D.","email":"","affiliations":[],"preferred":false,"id":452590,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Nagendra, H.","contributorId":69809,"corporation":false,"usgs":true,"family":"Nagendra","given":"H.","email":"","affiliations":[],"preferred":false,"id":452592,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Ghate, R.","contributorId":12289,"corporation":false,"usgs":true,"family":"Ghate","given":"R.","email":"","affiliations":[],"preferred":false,"id":452589,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Cade, B.S.","contributorId":47315,"corporation":false,"usgs":true,"family":"Cade","given":"B.S.","affiliations":[],"preferred":false,"id":452591,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70179618,"text":"70179618 - 2009 - Do fish benefit from stream restoration in the Catskill Mountains?","interactions":[],"lastModifiedDate":"2017-04-25T16:53:59","indexId":"70179618","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":5049,"text":"Clear Waters","active":true,"publicationSubtype":{"id":10}},"title":"Do fish benefit from stream restoration in the Catskill Mountains?","docAbstract":"Many streams across North America have been modified or restored in order to stabilize channel banks and beds; however, the effects of stream restoration on fish assemblages and stream habitat are seldom monitored, evaluated, or published. Because the impacts on ecosystems are poorly understood, subsequent restoration projects cannot build upon known successes or failures.
","language":"English","usgsCitation":"Baldigo, B.P., and Ernst, A.G., 2009, Do fish benefit from stream restoration in the Catskill Mountains?: Clear Waters, v. 39, no. Summer, p. 54-59.","productDescription":"6 p.","startPage":"54","endPage":"59","ipdsId":"IP-013606","costCenters":[{"id":474,"text":"New York Water Science Center","active":true,"usgs":true}],"links":[{"id":332940,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"New York","otherGeospatial":"Catskill Mountains","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -74.4,\n 42\n ],\n [\n -74.4,\n 42.3167\n ],\n [\n -74,\n 42.3167\n ],\n [\n -74,\n 42\n ],\n [\n -74.4,\n 42\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"39","issue":"Summer","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"58772d9fe4b0315b4c11feef","contributors":{"authors":[{"text":"Baldigo, Barry P. 0000-0002-9862-9119 bbaldigo@usgs.gov","orcid":"https://orcid.org/0000-0002-9862-9119","contributorId":1234,"corporation":false,"usgs":true,"family":"Baldigo","given":"Barry","email":"bbaldigo@usgs.gov","middleInitial":"P.","affiliations":[{"id":474,"text":"New York Water Science Center","active":true,"usgs":true}],"preferred":true,"id":657916,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Ernst, Anne G.","contributorId":149841,"corporation":false,"usgs":false,"family":"Ernst","given":"Anne","email":"","middleInitial":"G.","affiliations":[{"id":17837,"text":"USGS NY Water Science Center","active":true,"usgs":false}],"preferred":false,"id":657917,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70032598,"text":"70032598 - 2009 - Fragmentary evidence of great-earthquake subsidence during holocene emergence, Valdivia estuary, South Central Chile","interactions":[],"lastModifiedDate":"2012-03-12T17:21:21","indexId":"70032598","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1135,"text":"Bulletin of the Seismological Society of America","onlineIssn":"1943-3573","printIssn":"0037-1106","active":true,"publicationSubtype":{"id":10}},"title":"Fragmentary evidence of great-earthquake subsidence during holocene emergence, Valdivia estuary, South Central Chile","docAbstract":"A reconnaissance of Holocene stratigraphy beneath fringing marshes of the Valdivia estuary, where an M 9.5 earthquake caused 1-2 m of regional coseismic subsidence in 1960, shows only fragmentary evidence of prehistoric coseismic subsidence. In most of the 150 hand-driven cores that were examined, a distinct unconformity separates 0.5-1.5 m of late Holocene tidal and floodplain mud, peat, and sand from underlying middle Holocene subtidal mud and sand. At the Las Coloradas site, where stratigraphy is best preserved, two A horizons of marsh and meadow soils abruptly overlain by sand and mud probably record coseismic subsidence shortly followed by tsunamis. The amount of subsidence during the earthquakes proved difficult to reconstruct with a diatom transfer function because of differences between modern and fossil diatom assemblages. Maximum 14C ages on macrofossils from the two A horizons at the Las Coloradas site of 1.7-1.3 ka and 2.7-1.7 ka allow correlation of the younger horizon with either of two of six 14C-dated A horizons buried by tsunami sand or post-tsunami tidal sand 200 km to the south at Maull??n, and with a lake-wide mass wasting event in Lago Puyehue, 100 km to the southeast. Tidal records of prehistoric coseismic subsidence at Valdivia are scarce because of a sea-level fall of 3-8 m over the past 6000 years, erosion of marsh and meadow soils during subsidence-induced flooding of the estuary, and largely complete land-level recovery during cycles of coseismic subsidence and postseismic uplift.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Bulletin of the Seismological Society of America","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1785/0120080103","issn":"00371","usgsCitation":"Nelson, A., Kashima, K., and Bradley, L.A., 2009, Fragmentary evidence of great-earthquake subsidence during holocene emergence, Valdivia estuary, South Central Chile: Bulletin of the Seismological Society of America, v. 99, no. 1, p. 71-86, https://doi.org/10.1785/0120080103.","startPage":"71","endPage":"86","numberOfPages":"16","costCenters":[],"links":[{"id":213948,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1785/0120080103"},{"id":241624,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"99","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505a13b8e4b0c8380cd54763","contributors":{"authors":[{"text":"Nelson, A.R. 0000-0001-7117-7098","orcid":"https://orcid.org/0000-0001-7117-7098","contributorId":55078,"corporation":false,"usgs":true,"family":"Nelson","given":"A.R.","affiliations":[],"preferred":false,"id":436995,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kashima, K.","contributorId":76474,"corporation":false,"usgs":true,"family":"Kashima","given":"K.","email":"","affiliations":[],"preferred":false,"id":436996,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Bradley, L. A.","contributorId":35738,"corporation":false,"usgs":true,"family":"Bradley","given":"L.","email":"","middleInitial":"A.","affiliations":[],"preferred":false,"id":436994,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70035821,"text":"70035821 - 2009 - Sources of land-derived runoff to a coral reef-fringed embayment identified using geochemical tracers in nearshore sediment traps","interactions":[],"lastModifiedDate":"2017-11-05T09:13:21","indexId":"70035821","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1587,"text":"Estuarine, Coastal and Shelf Science","active":true,"publicationSubtype":{"id":10}},"title":"Sources of land-derived runoff to a coral reef-fringed embayment identified using geochemical tracers in nearshore sediment traps","docAbstract":"Geochemical tracers, including Ba, Co, Th, 7Be, 137Cs and 210Pb, and magnetic properties were used to characterize terrestrial runoff collected in nearshore time-series sediment traps in Hanalei Bay, Kauai, during flood and dry conditions in summer 2006, and to fingerprint possible runoff sources in the lower watershed. In combination, the tracers indicate that runoff during a flood in August could have come from cultivated taro fields bordering the lower reach of the river. Land-based runoff associated with summer floods may have a greater impact on coral reef communities in Hanalei Bay than in winter because sediment persists for several months. During dry periods, sediment carried by the Hanalei River appears to have been mobilized primarily by undercutting of low 7Be, low 137Cs riverbanks composed of soil weathered from tholeiitic basalt with low Ba and Co concentrations. Following a moderate rainfall event in September, high 7Be sediment carried by the Hanalei River was probably mobilized by overland flow in the upper watershed. Ba-desorption in low-salinity coastal water limited its use to a qualitative runoff tracer in nearshore sediment. 210Pb had limited usefulness as a terrestrial tracer in the nearshore due to a large dissolved oceanic source and scavenging onto resuspended bottom sediment. 210Pb-scavenging does, however, illustrate the role resuspension could play in the accumulation of particle-reactive contaminants in nearshore sediment. Co and 137Cs were not affected by desorption or geochemical scavenging and showed the greatest potential as quantitative sediment provenance indicators in material collected in nearshore sediment traps.","language":"English","publisher":"Elsevier","doi":"10.1016/j.ecss.2009.09.014","issn":"02727714","usgsCitation":"Takesue, R.K., Bothner, M., and Reynolds, R.L., 2009, Sources of land-derived runoff to a coral reef-fringed embayment identified using geochemical tracers in nearshore sediment traps: Estuarine, Coastal and Shelf Science, v. 85, no. 3, p. 459-471, https://doi.org/10.1016/j.ecss.2009.09.014.","startPage":"459","endPage":"471","numberOfPages":"13","costCenters":[],"links":[{"id":476247,"rank":1,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"https://hdl.handle.net/1912/3091","text":"External Repository"},{"id":243956,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"85","issue":"3","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505b937ee4b08c986b31a4fe","contributors":{"authors":[{"text":"Takesue, Renee K. 0000-0003-1205-0825 rtakesue@usgs.gov","orcid":"https://orcid.org/0000-0003-1205-0825","contributorId":2159,"corporation":false,"usgs":true,"family":"Takesue","given":"Renee","email":"rtakesue@usgs.gov","middleInitial":"K.","affiliations":[{"id":520,"text":"Pacific Coastal and Marine Science Center","active":true,"usgs":true}],"preferred":true,"id":452575,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Bothner, Michael H. mbothner@usgs.gov","contributorId":139855,"corporation":false,"usgs":true,"family":"Bothner","given":"Michael H.","email":"mbothner@usgs.gov","affiliations":[{"id":678,"text":"Woods Hole Coastal and Marine Science Center","active":true,"usgs":true}],"preferred":false,"id":452576,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Reynolds, Richard L. 0000-0002-4572-2942 rreynolds@usgs.gov","orcid":"https://orcid.org/0000-0002-4572-2942","contributorId":441,"corporation":false,"usgs":true,"family":"Reynolds","given":"Richard","email":"rreynolds@usgs.gov","middleInitial":"L.","affiliations":[{"id":271,"text":"Federal Center","active":false,"usgs":true}],"preferred":true,"id":452577,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70035820,"text":"70035820 - 2009 - A one-dimensional heat-transport model for conduit flow in karst aquifers","interactions":[],"lastModifiedDate":"2012-03-12T17:21:49","indexId":"70035820","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2342,"text":"Journal of Hydrology","active":true,"publicationSubtype":{"id":10}},"title":"A one-dimensional heat-transport model for conduit flow in karst aquifers","docAbstract":"A one-dimensional heat-transport model for conduit flow in karst aquifers is presented as an alternative to two or three-dimensional distributed-parameter models, which are data intensive and require knowledge of conduit locations. This model can be applied for cases where water temperature in a well or spring receives all or part of its water from a phreatic conduit. Heat transport in the conduit is simulated by using a physically-based heat-transport equation that accounts for inflow of diffuse flow from smaller openings and fissures in the surrounding aquifer during periods of low recharge. Additional diffuse flow that is within the zone of influence of the well or spring but has not interacted with the conduit is accounted for with a binary mixing equation to proportion these different water sources. The estimation of this proportion through inverse modeling is useful for the assessment of contaminant vulnerability and well-head or spring protection. The model was applied to 7 months of continuous temperature data for a sinking stream that recharges a conduit and a pumped well open to the Madison aquifer in western South Dakota. The simulated conduit-flow fraction to the well ranged from 2% to 31% of total flow, and simulated conduit velocity ranged from 44 to 353 m/d.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Journal of Hydrology","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1016/j.jhydrol.2009.09.024","issn":"00221694","usgsCitation":"Long, A., and Gilcrease, P., 2009, A one-dimensional heat-transport model for conduit flow in karst aquifers: Journal of Hydrology, v. 378, no. 3-4, p. 230-239, https://doi.org/10.1016/j.jhydrol.2009.09.024.","startPage":"230","endPage":"239","numberOfPages":"10","costCenters":[],"links":[{"id":243955,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":216109,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1016/j.jhydrol.2009.09.024"}],"volume":"378","issue":"3-4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059e4cae4b0c8380cd4692b","contributors":{"authors":[{"text":"Long, Andrew J.","contributorId":80023,"corporation":false,"usgs":false,"family":"Long","given":"Andrew J.","affiliations":[],"preferred":false,"id":452574,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Gilcrease, P.C.","contributorId":58116,"corporation":false,"usgs":true,"family":"Gilcrease","given":"P.C.","email":"","affiliations":[],"preferred":false,"id":452573,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70032458,"text":"70032458 - 2009 - Turbulent stresses and secondary currents in a tidal-forced channel with significant curvature and asymmetric bed forms","interactions":[],"lastModifiedDate":"2020-09-10T17:29:25.087434","indexId":"70032458","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2338,"text":"Journal of Hydraulic Engineering","active":true,"publicationSubtype":{"id":10}},"title":"Turbulent stresses and secondary currents in a tidal-forced channel with significant curvature and asymmetric bed forms","docAbstract":"Acoustic Doppler current profilers are deployed to measure both the mean flow and turbulent properties in a channel with significant curvature. Direct measurements of the Reynolds stress show a significant asymmetry over the tidal cycle where stresses are enhanced during the flood tide and less prominent over the ebb tide. This asymmetry is corroborated by logarithmic fits using
Loads and yields of suspended sediment and carbonate were measured and modeled at three locations on the Yukon, Tanana, and Porcupine Rivers in Alaska during water years 2001–2005 (1 October 2000 to 30 September 2005). Annual export of suspended sediment and carbonate upstream from the Yukon Delta averaged 68 Mt a−1 and 387 Gg a−1, respectively, with 50% of the suspended sediment load originating in the Tanana River Basin and 88% of the carbonate load originating in the White River Basin. About half the annual suspended sediment export occurred during spring, and half occurred during summer‐autumn, with very little export in winter. On average, a minimum of 11 Mt a−1 of suspended sediment is deposited in floodplains between Eagle, Alaska, and Pilot Station, Alaska, on an annual basis, mostly in the Yukon Flats. There is about a 27% loss in the carbonate load between Eagle and Yukon River near Stevens Village, with an additional loss of about 29% between Stevens Village and Pilot Station, owing to a combination of deposition and dissolution. Comparison of current and historical suspended sediment loads for Tanana River suggests a possible link between suspended sediment yield and the Pacific decadal oscillation.
","language":"English","publisher":"American Geophysical Union","doi":"10.1029/2008WR007546","usgsCitation":"Dornblaser, M.M., and Striegl, R.G., 2009, Suspended sediment and carbonate transport in the Yukon River Basin, Alaska: Fluxes and potential future responses to climate change: Water Resources Research, v. 45, no. 6, Article W06411; 12 p., https://doi.org/10.1029/2008WR007546.","productDescription":"Article W06411; 12 p.","costCenters":[],"links":[{"id":476402,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1029/2008wr007546","text":"Publisher Index Page"},{"id":243701,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"45","issue":"6","noUsgsAuthors":false,"publicationDate":"2009-06-11","publicationStatus":"PW","scienceBaseUri":"505ba300e4b08c986b31faee","contributors":{"authors":[{"text":"Dornblaser, Mark M. 0000-0002-6298-3757 mmdornbl@usgs.gov","orcid":"https://orcid.org/0000-0002-6298-3757","contributorId":1636,"corporation":false,"usgs":true,"family":"Dornblaser","given":"Mark","email":"mmdornbl@usgs.gov","middleInitial":"M.","affiliations":[{"id":37277,"text":"WMA - Earth System Processes Division","active":true,"usgs":true},{"id":5044,"text":"National Research Program - Central Branch","active":true,"usgs":true}],"preferred":true,"id":447146,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Striegl, Robert G. 0000-0002-8251-4659 rstriegl@usgs.gov","orcid":"https://orcid.org/0000-0002-8251-4659","contributorId":1630,"corporation":false,"usgs":true,"family":"Striegl","given":"Robert","email":"rstriegl@usgs.gov","middleInitial":"G.","affiliations":[{"id":36183,"text":"Hydro-Ecological Interactions Branch","active":true,"usgs":true},{"id":5044,"text":"National Research Program - Central Branch","active":true,"usgs":true},{"id":200,"text":"Coop Res Unit Seattle","active":true,"usgs":true},{"id":37277,"text":"WMA - Earth System Processes Division","active":true,"usgs":true}],"preferred":false,"id":447147,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ]}