Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (B3 to 8 km per year) and over time. We also estimate 12 host transitions from bison to elk, and 5 from elk to bison. Our results support the notion that free-ranging elk are currently a self-sustaining brucellosis reservoir and the source of livestock infections, and that control measures in bison are unlikely to affect the dynamics of unrelated strains circulating in nearby elk populations.
","language":"English","publisher":"Nature Publishing Group","doi":"10.1038/ncomms11448","usgsCitation":"Kamath, P.L., Foster, J., Drees, K., Luikart, G., Quance, C., Anderson, N.J., Clarke, P.R., Cole, E., Drew, M.L., Edwards, W.H., Rhyan, J.C., Treanor, J.J., Wallen, R.L., White, P.J., Robbe-Austerman, S., and Cross, P.C., 2016, Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock: Nature Communications, v. 7, Article 11448, 10 p., https://doi.org/10.1038/ncomms11448.","productDescription":"Article 11448, 10 p.","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-067034","costCenters":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true},{"id":34983,"text":"Contaminant Biology Program","active":true,"usgs":true}],"links":[{"id":470976,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1038/ncomms11448","text":"Publisher Index Page"},{"id":321439,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"7","publishingServiceCenter":{"id":2,"text":"Denver PSC"},"noUsgsAuthors":false,"publicationDate":"2016-05-11","publicationStatus":"PW","scienceBaseUri":"5740271be4b07e28b65dcfd8","contributors":{"authors":[{"text":"Kamath, Pauline L. pkamath@usgs.gov","contributorId":4517,"corporation":false,"usgs":true,"family":"Kamath","given":"Pauline","email":"pkamath@usgs.gov","middleInitial":"L.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":629890,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Foster, Jeffrey T.","contributorId":8744,"corporation":false,"usgs":true,"family":"Foster","given":"Jeffrey T.","affiliations":[],"preferred":false,"id":629891,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Drees, Kevin P.","contributorId":81759,"corporation":false,"usgs":true,"family":"Drees","given":"Kevin P.","affiliations":[],"preferred":false,"id":629892,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Luikart, Gordon","contributorId":97409,"corporation":false,"usgs":false,"family":"Luikart","given":"Gordon","affiliations":[{"id":6580,"text":"University of Montana, Flathead Lake Biological Station, Polson, Montana 59860, USA","active":true,"usgs":false}],"preferred":false,"id":629893,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Quance, Christine","contributorId":169525,"corporation":false,"usgs":false,"family":"Quance","given":"Christine","email":"","affiliations":[{"id":25553,"text":"USDA-APHIS, National Veterinary Services Laboratory","active":true,"usgs":false}],"preferred":false,"id":629894,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Anderson, Neil J.","contributorId":85870,"corporation":false,"usgs":true,"family":"Anderson","given":"Neil","email":"","middleInitial":"J.","affiliations":[],"preferred":false,"id":629895,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Clarke, P. Ryan","contributorId":169526,"corporation":false,"usgs":false,"family":"Clarke","given":"P.","email":"","middleInitial":"Ryan","affiliations":[{"id":25554,"text":"USDA-APHIS, Veterinary Services","active":true,"usgs":false}],"preferred":false,"id":629896,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Cole, Eric K. 0000-0002-2229-5853","orcid":"https://orcid.org/0000-0002-2229-5853","contributorId":145755,"corporation":false,"usgs":false,"family":"Cole","given":"Eric K.","affiliations":[{"id":16228,"text":"U.S. Fish and Wildlife Service, National Elk Refuge, PO Box 510, Jackson, WY 83001 USA","active":true,"usgs":false}],"preferred":false,"id":629898,"contributorType":{"id":1,"text":"Authors"},"rank":8},{"text":"Drew, Mark L.","contributorId":169527,"corporation":false,"usgs":false,"family":"Drew","given":"Mark","email":"","middleInitial":"L.","affiliations":[{"id":25555,"text":"Idaho Dept. of Fish and Game","active":true,"usgs":false}],"preferred":false,"id":629899,"contributorType":{"id":1,"text":"Authors"},"rank":9},{"text":"Edwards, William H.","contributorId":9144,"corporation":false,"usgs":true,"family":"Edwards","given":"William","email":"","middleInitial":"H.","affiliations":[],"preferred":false,"id":629900,"contributorType":{"id":1,"text":"Authors"},"rank":10},{"text":"Rhyan, Jack C.","contributorId":11185,"corporation":false,"usgs":true,"family":"Rhyan","given":"Jack","email":"","middleInitial":"C.","affiliations":[],"preferred":false,"id":629897,"contributorType":{"id":1,"text":"Authors"},"rank":11},{"text":"Treanor, John J.","contributorId":169528,"corporation":false,"usgs":false,"family":"Treanor","given":"John","email":"","middleInitial":"J.","affiliations":[{"id":5106,"text":"National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190","active":true,"usgs":false}],"preferred":false,"id":629901,"contributorType":{"id":1,"text":"Authors"},"rank":12},{"text":"Wallen, Rick L.","contributorId":169529,"corporation":false,"usgs":false,"family":"Wallen","given":"Rick","email":"","middleInitial":"L.","affiliations":[{"id":5106,"text":"National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190","active":true,"usgs":false}],"preferred":false,"id":629902,"contributorType":{"id":1,"text":"Authors"},"rank":13},{"text":"White, Patrick J.","contributorId":169530,"corporation":false,"usgs":false,"family":"White","given":"Patrick","email":"","middleInitial":"J.","affiliations":[{"id":5106,"text":"National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190","active":true,"usgs":false}],"preferred":false,"id":629903,"contributorType":{"id":1,"text":"Authors"},"rank":14},{"text":"Robbe-Austerman, Suelee","contributorId":169531,"corporation":false,"usgs":false,"family":"Robbe-Austerman","given":"Suelee","email":"","affiliations":[{"id":25553,"text":"USDA-APHIS, National Veterinary Services Laboratory","active":true,"usgs":false}],"preferred":false,"id":629904,"contributorType":{"id":1,"text":"Authors"},"rank":15},{"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":629905,"contributorType":{"id":1,"text":"Authors"},"rank":16}]}} ,{"id":70170968,"text":"ofr20161075 - 2016 - Aquatic Trophic Productivity model: A decision support model for river restoration planning in the Methow River, Washington","interactions":[],"lastModifiedDate":"2017-11-22T15:48:44","indexId":"ofr20161075","displayToPublicDate":"2016-05-19T13:00:00","publicationYear":"2016","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":"2016-1075","title":"Aquatic Trophic Productivity model: A decision support model for river restoration planning in the Methow River, Washington","docAbstract":"The U.S. Geological Survey (USGS) has developed a dynamic food-web simulation model to provide decision support for Bureau of Reclamation (Reclamation) river restoration projects in the Methow River, Washington. This modeling effort was done to contribute to Reasonable and Prudent Alternative actions 56 and 57of the 2014 Federal Columbia River Power System Biological Opinion (FCRPS BO), which calls for exploration of modeling as a means to help evaluate Endangered Species Act (ESA)-listed fish response to river restoration efforts. In the Methow River, these species of concern include Upper Columbia River (UCR) spring Chinook salmon (Oncorhynchus tshawytscha) and UCR summer steelhead (Oncorhynchus mykiss). Additionally, the Independent Scientific Advisory Board (ISAB) for the Columbia River has identified the need for modeling (Independent Scientific Advisory Board, 2011a)—including models that incorporate food-web dynamics (Independent Scientific Advisory Board, 2011b)—to better understand how restoration and management strategies might enhance salmon and steelhead populations.
\nDynamic food-web models, even relatively simple ones, can be valuable tools for exploring responses to river restoration. Although these models have rarely been applied to rivers and streams (but see Mcintire and Colby, 1978; Power and others, 1995), they are commonly used for management decisions in terrestrial and ocean ecosystems (Christensen and Pauly, 1993; Evans and others, 2013). One of the main strengths of these models is that they are rooted in the fundamental laws of thermodynamics (that is, mass balance). Moreover, these models can be easily adapted to different contexts by adding or subtracting different species from the web and by mechanistically linking the dynamics of web members to local environmental conditions, such as water temperature, stream discharge, and channel hydraulics (Power and others, 1995; Doyle, 2006). Alternative management actions can then be evaluated by changing these environmental conditions to simulate potential outcomes following restoration.
\nIn this report, we outline the structure of a stream food-web model constructed to explore how alternative river restoration strategies may affect stream fish populations. We have termed this model the “Aquatic Trophic Productivity model” (ATP). We present the model structure, followed by three case study applications of the model to segments of the Methow River watershed in northern Washington. For two case studies (middle Methow River and lower Twisp River floodplain), we ran a series of simulations to explore how food-web dynamics respond to four distinctly different, but applied, strategies in the Methow River watershed: (1) reconnection of floodplain aquatic habitats, (2) riparian vegetation planting, (3) nutrient augmentation (that is, salmon carcass addition), and (4) enhancement of habitat suitability for fish. For the third case study, we conducted simulations to explore the potential fish and food-web response to habitat improvements conducted in 2012 at the Whitefish Island Side Channel, located in the middle Methow River.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ofr20161075","collaboration":"Prepared in cooperation with the Bureau of Reclamation","usgsCitation":"Benjamin, J.R., and Bellmore, J.R., 2016, Aquatic trophic productivity model: A decision support model for river restoration planning in the Methow River, Washington: U.S. Geological Survey Open-File Report 2016‒1075, 85 p., https://dx.doi.org/10.3133/ofr20161075.","productDescription":"vi, 85 p.","onlineOnly":"Y","additionalOnlineFiles":"N","ipdsId":"IP-071770","costCenters":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"links":[{"id":321408,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/of/2016/1075/coverthb.jpg"},{"id":321409,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/of/2016/1075/ofr20161075.pdf","text":"Report","size":"3.2 MB","linkFileType":{"id":1,"text":"pdf"},"description":"OFR 2016-1075 Report PDF"}],"country":"United States","state":"Washington","otherGeospatial":"Methow River","contact":"Director, Forest and Rangeland Ecosystem Science Center
U.S. Geological Survey
777 NW 9th St., Suite 400
Corvallis, Oregon 97330
http://fresc.usgs.gov/
Climate extremes, such as drought, may have immediate and potentially prolonged effects on carbon cycling. Grasslands store approximately one-third of all terrestrial carbon and may become carbon sources during droughts. However, the magnitude and duration of drought-induced disruptions to the carbon cycle, as well as the mechanisms responsible, remain poorly understood. Over the next century, global climate models predict an increase in two types of drought: chronic but subtle ‘press-droughts’, and shorter term but extreme ‘pulse-droughts’. Much of our current understanding of the ecological impacts of drought comes from experimental rainfall manipulations. These studies have been highly valuable, but are often short term and rarely quantify carbon feedbacks. To address this knowledge gap, we used the Community Land Model 4.0 to examine the individual and interactive effects of pulse- and press-droughts on carbon cycling in a mesic grassland of the US Great Plains. A series of modeling experiments were imposed by varying drought magnitude (precipitation amount) and interannual pattern (press- vs. pulse-droughts) to examine the effects on carbon storage and cycling at annual to century timescales. We present three main findings. First, a single-year pulse-drought had immediate and prolonged effects on carbon storage due to differential sensitivities of ecosystem respiration and gross primary production. Second, short-term pulse-droughts caused greater carbon loss than chronic press-droughts when total precipitation reductions over a 20-year period were equivalent. Third, combining pulse- and press-droughts had intermediate effects on carbon loss compared to the independent drought types, except at high drought levels. Overall, these results suggest that interannual drought pattern may be as important for carbon dynamics as drought magnitude and that extreme droughts may have long-lasting carbon feedbacks in grassland ecosystems.
","language":"English","publisher":"John Wiley & Sons","doi":"10.1111/gcb.13161","usgsCitation":"Hoover, D.L., and Rogers, B.M., 2016, Not all droughts are created equal: The impacts of interannual drought pattern and magnitude on grassland carbon cycling: Global Change Biology, v. 22, no. 5, p. 1809-1820, https://doi.org/10.1111/gcb.13161.","productDescription":"12 p.","startPage":"1809","endPage":"1820","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-066574","costCenters":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"links":[{"id":321090,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"22","issue":"5","publishingServiceCenter":{"id":14,"text":"Menlo Park PSC"},"noUsgsAuthors":false,"publicationDate":"2016-02-25","publicationStatus":"PW","scienceBaseUri":"5732f81ee4b0dae0d5dc643f","contributors":{"authors":[{"text":"Hoover, David L. dlhoover@usgs.gov","contributorId":5843,"corporation":false,"usgs":true,"family":"Hoover","given":"David","email":"dlhoover@usgs.gov","middleInitial":"L.","affiliations":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"preferred":false,"id":629058,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Rogers, Brendan M.","contributorId":169247,"corporation":false,"usgs":false,"family":"Rogers","given":"Brendan","email":"","middleInitial":"M.","affiliations":[{"id":25456,"text":"Woods Hole Research Center, Falmouth, MA, United States","active":true,"usgs":false}],"preferred":false,"id":629059,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70186267,"text":"70186267 - 2016 - Use of mussel casts from archaeological sites as paleoecological indicators: An example from CA-MRN-254, Marin County, Alta California","interactions":[],"lastModifiedDate":"2017-04-03T12:50:32","indexId":"70186267","displayToPublicDate":"2016-05-09T00:00:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":5361,"text":"California Archaeology","active":true,"publicationSubtype":{"id":10}},"title":"Use of mussel casts from archaeological sites as paleoecological indicators: An example from CA-MRN-254, Marin County, Alta California","docAbstract":"Archaeological investigations at prehistoric site CA-MRN-254 at the Dominican University of California in Marin County, California, revealed evidence of Native American occupation spanning the past 1,800 years. A dominant source of food for the inhabitants in the San Francisco Bay area was the intertidal, quiet-water dwelling blue mussel (Mytilus trossulus), although rare occurrences of the open coast-dwelling California mussel (Mytilus californianus) suggest that this species was also utilized sporadically. On rare occasions, cultural horizons at this site contain abundant sediment-filled casts of the smaller mussel Modiolus sp. These casts were formed soon after death when the shells filled with sediment and were roasted along with living bivalve shellfish for consumption. Thin sections of these mussel casts display sedimentological and microbiological constituents that shed light on the paleoenvironmental conditions when they were alive. Fine-grained sediment and pelletal muds comprising these casts suggest that the mussels were collected in a low energy, inner bay environment. The rare presence of the diatoms Triceratium dubium and Thalassionema nitzschioides indicate more normal marine (35 psu) and possibly warmer conditions than presently exist in San Francisco Bay. Radiocarbon dating of charcoal associated with the mussel casts containing these diatoms correlates with a 600-year period of warming from ca. A.D. 700–1300, known as the Medieval Climatic Anomaly. Results of this mussel cast study demonstrate that they have great potential for providing paleoenvironmental information at this and other archaeological sites.
","language":"English","publisher":"Society for California Archaeology","publisherLocation":"Chico, CA","doi":"10.1080/1947461X.2016.1176367","usgsCitation":"McGann, M., Starratt, S.W., Powell, C.L., and Bieling, D.G., 2016, Use of mussel casts from archaeological sites as paleoecological indicators: An example from CA-MRN-254, Marin County, Alta California: California Archaeology, v. 8, no. 1, p. 63-90, https://doi.org/10.1080/1947461X.2016.1176367.","productDescription":"28 p.","startPage":"63","endPage":"90","ipdsId":"IP-079316","costCenters":[{"id":520,"text":"Pacific Coastal and Marine Science Center","active":true,"usgs":true}],"links":[{"id":339047,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"California","city":"San Rafael","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -122.51884460449217,\n 37.97786403627176\n ],\n [\n -122.51609802246092,\n 37.97786403627176\n ],\n [\n -122.51609802246092,\n 37.979555414681506\n ],\n [\n -122.51884460449217,\n 37.979555414681506\n ],\n [\n -122.51884460449217,\n 37.97786403627176\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"8","issue":"1","publishingServiceCenter":{"id":14,"text":"Menlo Park PSC"},"noUsgsAuthors":false,"publicationDate":"2016-05-09","publicationStatus":"PW","scienceBaseUri":"58e35f7fe4b09da67997ecad","contributors":{"authors":[{"text":"McGann, Mary 0000-0002-3057-2945 mmcgann@usgs.gov","orcid":"https://orcid.org/0000-0002-3057-2945","contributorId":169540,"corporation":false,"usgs":true,"family":"McGann","given":"Mary","email":"mmcgann@usgs.gov","affiliations":[{"id":186,"text":"Coastal and Marine Geology Program","active":true,"usgs":true},{"id":520,"text":"Pacific Coastal and Marine Science Center","active":true,"usgs":true}],"preferred":true,"id":688076,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Starratt, Scott W. 0000-0001-9405-1746 sstarrat@usgs.gov","orcid":"https://orcid.org/0000-0001-9405-1746","contributorId":2891,"corporation":false,"usgs":true,"family":"Starratt","given":"Scott","email":"sstarrat@usgs.gov","middleInitial":"W.","affiliations":[{"id":617,"text":"Volcano Science Center","active":true,"usgs":true},{"id":312,"text":"Geology, Minerals, Energy, and Geophysics Science Center","active":true,"usgs":true}],"preferred":true,"id":688077,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Powell, Charles L. II 0000-0002-1913-555X cpowell@usgs.gov","orcid":"https://orcid.org/0000-0002-1913-555X","contributorId":3243,"corporation":false,"usgs":true,"family":"Powell","given":"Charles","suffix":"II","email":"cpowell@usgs.gov","middleInitial":"L.","affiliations":[{"id":312,"text":"Geology, Minerals, Energy, and Geophysics Science Center","active":true,"usgs":true}],"preferred":false,"id":688078,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Bieling, David G","contributorId":190292,"corporation":false,"usgs":false,"family":"Bieling","given":"David","email":"","middleInitial":"G","affiliations":[],"preferred":false,"id":688079,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70170139,"text":"sir20165046 - 2016 - Simulation of deep ventilation in Crater Lake, Oregon, 1951–2099","interactions":[],"lastModifiedDate":"2021-10-12T17:00:16.258141","indexId":"sir20165046","displayToPublicDate":"2016-05-04T10:00:00","publicationYear":"2016","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":334,"text":"Scientific Investigations Report","code":"SIR","onlineIssn":"2328-0328","printIssn":"2328-031X","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"2016-5046","title":"Simulation of deep ventilation in Crater Lake, Oregon, 1951–2099","docAbstract":"The frequency of deep ventilation events in Crater Lake, a caldera lake in the Oregon Cascade Mountains, was simulated in six future climate scenarios, using a 1-dimensional deep ventilation model (1DDV) that was developed to simulate the ventilation of deep water initiated by reverse stratification and subsequent thermobaric instability. The model was calibrated and validated with lake temperature data collected from 1994 to 2011. Wind and air temperature data from three general circulation models and two representative concentration pathways were used to simulate the change in lake temperature and the frequency of deep ventilation events in possible future climates. The lumped model air2water was used to project lake surface temperature, a required boundary condition for the lake model, based on air temperature in the future climates.
The 1DDV model was used to simulate daily water temperature profiles through 2099. All future climate scenarios projected increased water temperature throughout the water column and a substantive reduction in the frequency of deep ventilation events. The least extreme scenario projected the frequency of deep ventilation events to decrease from about 1 in 2 years in current conditions to about 1 in 3 years by 2100. The most extreme scenario considered projected the frequency of deep ventilation events to be about 1 in 7.7 years by 2100. All scenarios predicted that the temperature of the entire water column will be greater than 4 °C for increasing lengths of time in the future and that the conditions required for thermobaric instability induced mixing will become rare or non-existent.
The disruption of deep ventilation by itself does not provide a complete picture of the potential ecological and water quality consequences of warming climate to Crater Lake. Estimating the effect of warming climate on deep water oxygen depletion and water clarity will require careful modeling studies to combine the physical mixing processes affected by the atmosphere with the multitude of factors affecting the growth of algae and corresponding water clarity.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/sir20165046","collaboration":"Prepared in cooperation with the National Park Service","usgsCitation":"Wood, T.M., Wherry, S.A., Piccolroaz, S., and Girdner, S.F., 2016, Simulation of deep ventilation in Crater Lake, Oregon, 1951–2099: U.S. Geological Survey Scientific Investigations Report 2016–5046, 43 p. https://doi.org/10.3133/sir20165046","productDescription":"vii, 43 p.","onlineOnly":"Y","additionalOnlineFiles":"N","ipdsId":"IP-066051","costCenters":[{"id":518,"text":"Oregon Water Science Center","active":true,"usgs":true}],"links":[{"id":320860,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/sir/2016/5046/sir20165046.pdf","text":"Report","size":"3.2 MB","linkFileType":{"id":1,"text":"pdf"},"description":"OFR 2016-5046 Report PDF"},{"id":320859,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/sir/2016/5046/coverthb.jpg"}],"country":"United States","state":"Oregon","otherGeospatial":"Crater Lake","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -122.18616485595703,\n 42.892567248047285\n ],\n [\n -122.18616485595703,\n 42.986065036562955\n ],\n [\n -122.03922271728514,\n 42.986065036562955\n ],\n [\n -122.03922271728514,\n 42.892567248047285\n ],\n [\n -122.18616485595703,\n 42.892567248047285\n ]\n ]\n ]\n }\n }\n ]\n}","edition":"Version 1.1: February 2020; Version 1.0: October 2016","contact":"Director, Oregon Water Science Center
U.S. Geological Survey
2130 SW 5th Avenue
Portland, Oregon 97201
http://or.water.usgs.gov
Reliably estimating wildlife abundance is fundamental to effective management. Aerial surveys are one of the only spatially robust tools for estimating large mammal populations, but statistical sampling methods are required to address detection biases that affect accuracy and precision of the estimates. Although various methods for correcting aerial survey bias are employed on large mammal species around the world, these have rarely been rigorously validated. Several populations of feral horses (Equus caballus) in the western United States have been intensively studied, resulting in identification of all unique individuals. This provided a rare opportunity to test aerial survey bias correction on populations of known abundance. We hypothesized that a hybrid method combining simultaneous double-observer and sightability bias correction techniques would accurately estimate abundance. We validated this integrated technique on populations of known size and also on a pair of surveys before and after a known number was removed. Our analysis identified several covariates across the surveys that explained and corrected biases in the estimates. All six tests on known populations produced estimates with deviations from the known value ranging from -8.5% to +13.7% and <0.7 standard errors. Precision varied widely, from 6.1% CV to 25.0% CV. In contrast, the pair of surveys conducted around a known management removal produced an estimated change in population between the surveys that was significantly larger than the known reduction. Although the deviation between was only 9.1%, the precision estimate (CV = 1.6%) may have been artificially low. It was apparent that use of a helicopter in those surveys perturbed the horses, introducing detection error and heterogeneity in a manner that could not be corrected by our statistical models. Our results validate the hybrid method, highlight its potentially broad applicability, identify some limitations, and provide insight and guidance for improving survey designs.
","language":"English","publisher":"PLOS","doi":"10.1371/journal.pone.0154902","usgsCitation":"Lubow, B., and Ransom, J.I., 2016, Practical bias correction in aerial surveys of large mammals: Validation of hybrid double-observer with sightability method against known abundance of feral horse (Equus caballus) populations: PLoS ONE, v. 11, no. 5, e0154902, 15 p., https://doi.org/10.1371/journal.pone.0154902.","productDescription":"e0154902, 15 p.","ipdsId":"IP-074372","costCenters":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"links":[{"id":471028,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1371/journal.pone.0154902","text":"Publisher Index Page"},{"id":373550,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Colorado, Nevada, Utah, Wyoming","otherGeospatial":"Cedar Mountain Herd Management Area, Little Owyhee Herd Management Area, McCullough Peaks Herd Management Area, Sand Wash Herd Management Area, Snowstorm Mountains Herd Management Area ","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -109.00634765625,\n 44.308126684886126\n ],\n [\n -107.89672851562499,\n 44.308126684886126\n ],\n [\n -107.89672851562499,\n 44.98034238084973\n ],\n [\n -109.00634765625,\n 44.98034238084973\n ],\n [\n -109.00634765625,\n 44.308126684886126\n ]\n ]\n ]\n }\n },\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -108.984375,\n 40.26276066437183\n ],\n [\n -108.017578125,\n 40.26276066437183\n ],\n [\n -108.017578125,\n 40.896905775860006\n ],\n [\n -108.984375,\n 40.896905775860006\n ],\n [\n -108.984375,\n 40.26276066437183\n ]\n ]\n ]\n }\n },\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -113.48876953125,\n 39.9434364619742\n ],\n [\n -112.87353515625,\n 39.9434364619742\n ],\n [\n -112.87353515625,\n 40.6306300839918\n ],\n [\n -113.48876953125,\n 40.6306300839918\n ],\n [\n -113.48876953125,\n 39.9434364619742\n ]\n ]\n ]\n }\n },\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -117.24609374999999,\n 41.393294288784865\n ],\n [\n -116.52099609375,\n 41.393294288784865\n ],\n [\n -116.52099609375,\n 41.95131994679697\n ],\n [\n -117.24609374999999,\n 41.95131994679697\n ],\n [\n -117.24609374999999,\n 41.393294288784865\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"11","issue":"5","publishingServiceCenter":{"id":2,"text":"Denver PSC"},"noUsgsAuthors":false,"publicationDate":"2016-05-03","publicationStatus":"PW","contributors":{"editors":[{"text":"Schoenecker, Kathryn A. 0000-0001-9906-911X","orcid":"https://orcid.org/0000-0001-9906-911X","contributorId":202531,"corporation":false,"usgs":true,"family":"Schoenecker","given":"Kathryn A.","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":true,"id":785658,"contributorType":{"id":2,"text":"Editors"},"rank":1}],"authors":[{"text":"Lubow, Bruce C.","contributorId":131076,"corporation":false,"usgs":false,"family":"Lubow","given":"Bruce C.","affiliations":[{"id":7230,"text":"Natural Resource Ecology Laboratory, Colorado State University","active":true,"usgs":false}],"preferred":false,"id":785656,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Ransom, Jason I.","contributorId":139841,"corporation":false,"usgs":false,"family":"Ransom","given":"Jason","email":"","middleInitial":"I.","affiliations":[{"id":6924,"text":"National Park Service, Upper Columbia Basin Network","active":true,"usgs":false}],"preferred":false,"id":785657,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70170721,"text":"70170721 - 2016 - Timing and composition of continental volcanism at Harrat Hutaymah, western Saudi Arabia","interactions":[],"lastModifiedDate":"2016-05-04T08:38:28","indexId":"70170721","displayToPublicDate":"2016-05-02T11:30:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2499,"text":"Journal of Volcanology and Geothermal Research","active":true,"publicationSubtype":{"id":10}},"title":"Timing and composition of continental volcanism at Harrat Hutaymah, western Saudi Arabia","docAbstract":"Harrat Hutaymah is an alkali basalt volcanic field in north-central Saudi Arabia, at the eastern margin of a large Neogene continental, intraplate magmatic province. Lava flow, tephra and spatter cone compositions in the field include alkali olivine basalts and basanites. These compositions contrast with the predominantly tholeiitic, fissure-fed basalts found along the eastern margin of the Red Sea. The Hutaymah lava flows were erupted through Proterozoic arc-associated plutonic and meta-sedimentary rocks of the Arabian shield, and commonly contain a range of sub-continental lithospheric xenoliths, although the lavas themselves show little indication of crustal contamination. Previous radiometric dating of this volcanic field (a single published K–Ar age; 1.8 Ma) is suspiciously old given the field measurement of normal magnetic polarity only (i.e. Brunhes interval, ≤ 780 Ka). We report new age determinations on 14 lava flows by the 40Ar–39Ar laser step heating method, all younger than ~ 850 Ka, to better constrain the time frame of volcanism, and major, trace and rare earth element compositions to describe the chemical variation of volcanic activity at Harrat Hutaymah. Crystal fractionation was dominated by olivine ± clinopyroxene at a range of upper mantle and crustal pressures. Rapid ascent and eruption of magma is indicated by the array of lower crustal and lithospheric xenoliths observed in lava flows and tephra. Modeling suggests 1–7% melting of an enriched asthenospheric mantle source occurred beneath Harrat Hutaymah under a relatively thick lithospheric cap (60–80 km).
","language":"English","publisher":"Elsevier","doi":"10.1016/j.jvolgeores.2016.01.010","usgsCitation":"Duncan, R.A., Kent, A.J., Thornber, C., Schliedler, T.D., and Al-Amri, A.M., 2016, Timing and composition of continental volcanism at Harrat Hutaymah, western Saudi Arabia: Journal of Volcanology and Geothermal Research, v. 313, p. 1-14, https://doi.org/10.1016/j.jvolgeores.2016.01.010.","productDescription":"14 p.","startPage":"1","endPage":"14","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-070061","costCenters":[{"id":617,"text":"Volcano Science Center","active":true,"usgs":true}],"links":[{"id":471030,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1016/j.jvolgeores.2016.01.010","text":"Publisher Index Page"},{"id":320813,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Saudi Arabia","otherGeospatial":"Harrat Hutaymah","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n 30,\n 1\n ],\n [\n 30,\n 40\n ],\n [\n 55,\n 40\n ],\n [\n 55,\n 1\n ],\n [\n 30,\n 1\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"313","publishingServiceCenter":{"id":14,"text":"Menlo Park PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"57286c1be4b0b13d3917ce12","contributors":{"authors":[{"text":"Duncan, Robert A.","contributorId":167399,"corporation":false,"usgs":false,"family":"Duncan","given":"Robert","email":"","middleInitial":"A.","affiliations":[{"id":6680,"text":"Oregon State University","active":true,"usgs":false}],"preferred":false,"id":628172,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kent, Adam J R","contributorId":168855,"corporation":false,"usgs":false,"family":"Kent","given":"Adam","email":"","middleInitial":"J R","affiliations":[{"id":6680,"text":"Oregon State University","active":true,"usgs":false}],"preferred":false,"id":628173,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Thornber, Carl 0000-0002-6382-4408 cthornber@usgs.gov","orcid":"https://orcid.org/0000-0002-6382-4408","contributorId":167396,"corporation":false,"usgs":true,"family":"Thornber","given":"Carl","email":"cthornber@usgs.gov","affiliations":[{"id":617,"text":"Volcano Science Center","active":true,"usgs":true}],"preferred":true,"id":628171,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Schliedler, Tyler D","contributorId":169027,"corporation":false,"usgs":false,"family":"Schliedler","given":"Tyler","email":"","middleInitial":"D","affiliations":[{"id":6680,"text":"Oregon State University","active":true,"usgs":false}],"preferred":false,"id":628174,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Al-Amri, Abdullah M","contributorId":169028,"corporation":false,"usgs":false,"family":"Al-Amri","given":"Abdullah","email":"","middleInitial":"M","affiliations":[{"id":24707,"text":"King Saud University, Riyahd, KSA","active":true,"usgs":false}],"preferred":false,"id":628175,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70191257,"text":"70191257 - 2016 - Coesite in suevites from the Chesapeake Bay impact structure","interactions":[],"lastModifiedDate":"2017-10-02T13:57:51","indexId":"70191257","displayToPublicDate":"2016-05-01T00:00:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2715,"text":"Meteoritics and Planetary Science","active":true,"publicationSubtype":{"id":10}},"title":"Coesite in suevites from the Chesapeake Bay impact structure","docAbstract":"The occurrence of coesite in suevites from the Chesapeake Bay impact structure is confirmed within a variety of textural domains in situ by Raman spectroscopy for the first time and in mechanically separated grains by X-ray diffraction. Microtextures of coesite identified in situ investigated under transmitted light and by scanning electron microscope reveal coesite as micrometer-sized grains (1–3 μm) within amorphous silica of impact-melt clasts and as submicrometer-sized grains and polycrystalline aggregates within shocked quartz grains. Coesite-bearing quartz grains are present both idiomorphically with original grain margins intact and as highly strained grains that underwent shock-produced plastic deformation. Coesite commonly occurs in plastically deformed quartz grains within domains that appear brown (toasted) in transmitted light and rarely within quartz of spheroidal texture. The coesite likely developed by a mechanism of solid-state transformation from precursor quartz. Raman spectroscopy also showed a series of unidentified peaks associated with shocked quartz grains that likely represent unidentified silica phases, possibly including a moganite-like phase that has not previously been associated with coesite.
","language":"English","publisher":"Wiley","doi":"10.1111/maps.12638","usgsCitation":"Jackson, J.C., Horton, J.W., Chou, I., and Belkin, H.E., 2016, Coesite in suevites from the Chesapeake Bay impact structure: Meteoritics and Planetary Science, v. 51, no. 5, p. 946-965, https://doi.org/10.1111/maps.12638.","productDescription":"20 p.","startPage":"946","endPage":"965","ipdsId":"IP-065888","costCenters":[{"id":245,"text":"Eastern Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"links":[{"id":346318,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","otherGeospatial":"Chesapeake Bay","volume":"51","issue":"5","publishingServiceCenter":{"id":9,"text":"Reston PSC"},"noUsgsAuthors":false,"publicationDate":"2016-03-24","publicationStatus":"PW","scienceBaseUri":"59d35028e4b05fe04cc34d62","contributors":{"authors":[{"text":"Jackson, John C. jjackson@usgs.gov","contributorId":2652,"corporation":false,"usgs":true,"family":"Jackson","given":"John","email":"jjackson@usgs.gov","middleInitial":"C.","affiliations":[{"id":245,"text":"Eastern Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":711703,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Horton, J. Wright Jr. 0000-0001-6756-6365 whorton@usgs.gov","orcid":"https://orcid.org/0000-0001-6756-6365","contributorId":173694,"corporation":false,"usgs":true,"family":"Horton","given":"J.","suffix":"Jr.","email":"whorton@usgs.gov","middleInitial":"Wright","affiliations":[{"id":243,"text":"Eastern Geology and Paleoclimate Science Center","active":true,"usgs":true}],"preferred":false,"id":711704,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Chou, I-Ming 0000-0001-5233-6479 imchou@usgs.gov","orcid":"https://orcid.org/0000-0001-5233-6479","contributorId":882,"corporation":false,"usgs":true,"family":"Chou","given":"I-Ming","email":"imchou@usgs.gov","affiliations":[{"id":245,"text":"Eastern Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":711705,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Belkin, Harvey E. 0000-0001-7879-6529 hbelkin@usgs.gov","orcid":"https://orcid.org/0000-0001-7879-6529","contributorId":581,"corporation":false,"usgs":true,"family":"Belkin","given":"Harvey","email":"hbelkin@usgs.gov","middleInitial":"E.","affiliations":[{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":711706,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70186182,"text":"70186182 - 2016 - Demographic outcomes of diverse migration strategies assessed in a metapopulation of tundra swans","interactions":[],"lastModifiedDate":"2017-03-31T10:15:09","indexId":"70186182","displayToPublicDate":"2016-05-01T00:00:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2792,"text":"Movement Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Demographic outcomes of diverse migration strategies assessed in a metapopulation of tundra swans","docAbstract":"Background\nMigration is a prominent aspect of the life history of many avian species, but the demographic consequences of variable migration strategies have only infrequently been investigated, and rarely when using modern technological and analytical methods for assessing survival, movement patterns, and long-term productivity in the context of life history theory. We monitored the fates of 50 satellite-implanted tundra swans (Cygnus columbianus) over 4 years from five disparate breeding areas in Alaska, and used known-fate analyses to estimate monthly survival probability relative to migration distance, breeding area, migratory flyway, breeding status, and age. We specifically tested whether migratory birds face a trade-off, whereby long-distance migrants realize higher survival rates at the cost of lower productivity because of reduced time on breeding areas relative to birds that migrate shorter distances and spend more time on breeding areas.\nResults\nAnnual migration distances varied significantly among breeding areas (1020 to 12720 km), and were strongly negatively correlated with time spent on breeding areas (r = −0.986). Estimates of annual survival probability varied by wintering area (Pacific coast, Alaska Peninsula, and Eastern seaboard) and ranged from 0.79 (95%CI: 0.70–0.88) to 1.0, depending on criteria used to discern mortalities from radio failures. We did not find evidence for a linear relationship between migration distance and survival as swans from the breeding areas with the shortest and longest migration distances had the highest survival probabilities. Survival was lower in the first year post-marking than in subsequent years, but there was not support for seasonal differences in survival. Productivity varied among breeding populations and was generally inversely correlated to survival, but not migration distance or time spent on breeding areas.\nConclusions\nTundra swans conformed to a major tenet of life history theory, as populations with the highest survival generally had the lowest productivity. The lack of a uniform relationship between time spent on breeding areas and productivity, or time spent on wintering areas and survival, indicates that factors other than temporal investment dictate demographic outcomes in this species. The tremendous diversity of migration strategies we identify in Alaskan tundra swans, without clear impacts on survival, underscores the ability of this species to adapt to different environments and climatic regimes.\nKeywords: Cygnus columbianus, Known fate, Life history, Metapopulation, Migration distance, Productivity, Satellite telemetry, Survival, Transmitter effects, Tundra swan","language":"English","publisher":"BioMed Central","doi":"10.1186/s40462-016-0075-8","usgsCitation":"Ely, C.R., and Meixell, B.W., 2016, Demographic outcomes of diverse migration strategies assessed in a metapopulation of tundra swans: Movement Ecology, v. 4, no. 10, HTML document , https://doi.org/10.1186/s40462-016-0075-8.","productDescription":"HTML document ","ipdsId":"IP-065806","costCenters":[{"id":117,"text":"Alaska Science Center Biology WTEB","active":true,"usgs":true}],"links":[{"id":471317,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1186/s40462-016-0075-8","text":"Publisher Index Page"},{"id":338915,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":338873,"type":{"id":15,"text":"Index Page"},"url":"https://dx.doi.org/10.1186/s40462-016-0075-8"}],"volume":"4","issue":"10","publishingServiceCenter":{"id":12,"text":"Tacoma PSC"},"noUsgsAuthors":false,"publicationDate":"2016-05-01","publicationStatus":"PW","scienceBaseUri":"58df6ac1e4b02ff32c6aea39","chorus":{"doi":"10.1186/s40462-016-0075-8","url":"http://dx.doi.org/10.1186/s40462-016-0075-8","publisher":"Springer Nature","authors":"Ely Craig R., Meixell Brandt W.","journalName":"Movement Ecology","publicationDate":"5/1/2016"},"contributors":{"authors":[{"text":"Ely, Craig R. 0000-0003-4262-0892 cely@usgs.gov","orcid":"https://orcid.org/0000-0003-4262-0892","contributorId":3214,"corporation":false,"usgs":true,"family":"Ely","given":"Craig","email":"cely@usgs.gov","middleInitial":"R.","affiliations":[{"id":117,"text":"Alaska Science Center Biology WTEB","active":true,"usgs":true},{"id":651,"text":"Western Ecological Research Center","active":true,"usgs":true}],"preferred":true,"id":687776,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Meixell, Brandt W. 0000-0002-6738-0349 bmeixell@usgs.gov","orcid":"https://orcid.org/0000-0002-6738-0349","contributorId":138716,"corporation":false,"usgs":true,"family":"Meixell","given":"Brandt","email":"bmeixell@usgs.gov","middleInitial":"W.","affiliations":[{"id":117,"text":"Alaska Science Center Biology WTEB","active":true,"usgs":true}],"preferred":true,"id":687777,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70176210,"text":"70176210 - 2016 - Organic petrology and geochemistry of Eocene Suzak bituminous marl, north-central Afghanistan: Depositional environment and source rock potential","interactions":[],"lastModifiedDate":"2016-09-01T16:21:44","indexId":"70176210","displayToPublicDate":"2016-05-01T00:00:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2682,"text":"Marine and Petroleum Geology","active":true,"publicationSubtype":{"id":10}},"title":"Organic petrology and geochemistry of Eocene Suzak bituminous marl, north-central Afghanistan: Depositional environment and source rock potential","docAbstract":"Organic geochemistry and petrology of Eocene Suzak bituminous marl outcrop samples from Madr village in north-central Afghanistan were characterized via an integrated analytical approach to evaluate depositional environment and source rock potential. Multiple proxies suggest the organic-rich (TOC ∼6 wt.%) bituminous marls are ‘immature’ for oil generation (e.g., vitrinite Ro < 0.4%, Tmax < 425 °C, PI ≤ 0.05, C29 ααα S/S + R ≤ 0.12, C29 ββS/ββS+ααR ≤ 0.10, others), yet oil seeps are present at outcrop and live oil and abundant solid bitumen were observed via optical microscopy. Whole rock sulfur content is ∼2.3 wt.% whereas sulfur content is ∼5.0–5.6 wt.% in whole rock extracts with high polar components, consistent with extraction from S-rich Type IIs organic matter which could generate hydrocarbons at low thermal maturity. Low Fe-sulfide mineral abundance and comparison of Pr/Ph ratios between saturate and whole extracts suggest limited Fe concentration resulted in sulfurization of organic matter during early diagenesis. From these observations, we infer that a Type IIs kerogen in ‘immature’ bituminous marl at Madr could be generating high sulfur viscous oil which is seeping from outcrop. However, oil-seep samples were not collected for correlation studies. Aluminum-normalized trace element concentrations indicate enrichment of redox sensitive trace elements Mo, U and V and suggest anoxic-euxinic conditions during sediment deposition. The bulk of organic matter observed via optical microscopy is strongly fluorescent amorphous bituminite grading to lamalginite, possibly representing microbial mat facies. Short chain n-alkanes peak at C14–C16 (n-C17/n-C29 > 1) indicating organic input from marine algae and/or bacterial biomass, and sterane/hopane ratios are low (0.12–0.14). Monoaromatic steroids are dominated by C28clearly indicating a marine setting. High gammacerane index values (∼0.9) are consistent with anoxia stratification and may indicate intermittent saline-hypersaline conditions. Stable C isotope ratios also suggest a marine depositional scenario for the Suzak samples, consistent with the presence of marine foraminifera including abundant planktic globigerinida(?) and rare benthic discocyclina(?) and nummulites(?). Biomarker 2α-methylhopane for photosynthetic cyanobacteria implies shallow photic zone deposition of Madr marls and 3β-methylhopane indicates presence of methanotrophic archaea in the microbial consortium. The data presented herein are consistent with deposition of Suzak bituminous marls in shallow stratified waters of a restricted marine basin associated with the southeastern incipient or proto-Paratethys. Geochemical proxies from Suzak rock extracts (S content, high polar content, C isotopes, normal (αααR) C27–29 steranes, and C29/C30 and C26/C25 hopane ratios) are similar to extant data from Paleogene oils produced to the north in the Afghan-Tajik Basin. This observation may indicate laterally equivalent strata are effective source rocks as suggested by previous workers; however, further work is needed to strengthen oil-source correlations.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.marpetgeo.2016.02.029","usgsCitation":"Hackley, P.C., and Sanfilipo, J., 2016, Organic petrology and geochemistry of Eocene Suzak bituminous marl, north-central Afghanistan: Depositional environment and source rock potential: Marine and Petroleum Geology, v. 73, p. 572-589, https://doi.org/10.1016/j.marpetgeo.2016.02.029.","productDescription":"18 p.","startPage":"572","endPage":"589","ipdsId":"IP-069387","costCenters":[{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true}],"links":[{"id":328205,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"73","publishingServiceCenter":{"id":9,"text":"Reston PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"57c95130e4b0f2f0cec15bfc","contributors":{"authors":[{"text":"Hackley, Paul C. 0000-0002-5957-2551 phackley@usgs.gov","orcid":"https://orcid.org/0000-0002-5957-2551","contributorId":592,"corporation":false,"usgs":true,"family":"Hackley","given":"Paul","email":"phackley@usgs.gov","middleInitial":"C.","affiliations":[{"id":255,"text":"Energy Resources Program","active":true,"usgs":true},{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":647807,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Sanfilipo, John 0000-0002-8739-5628 jsan@usgs.gov","orcid":"https://orcid.org/0000-0002-8739-5628","contributorId":140236,"corporation":false,"usgs":true,"family":"Sanfilipo","given":"John","email":"jsan@usgs.gov","affiliations":[{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":647808,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70173814,"text":"70173814 - 2016 - The structure of genetic diversity in eelgrass (Zostera marina L.) along the North Pacific and Bering Sea coasts of Alaska","interactions":[],"lastModifiedDate":"2018-08-19T10:07:55","indexId":"70173814","displayToPublicDate":"2016-04-22T00:00:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2980,"text":"PLoS ONE","active":true,"publicationSubtype":{"id":10}},"displayTitle":"The structure of genetic diversity in eelgrass (Zostera marina L.) along the North Pacific and Bering Sea coasts of Alaska","title":"The structure of genetic diversity in eelgrass (Zostera marina L.) along the North Pacific and Bering Sea coasts of Alaska","docAbstract":"Eelgrass (Zostera marina) populations occupying coastal waters of Alaska are separated by a peninsula and island archipelago into two Large Marine Ecosystems (LMEs). From populations in both LMEs, we characterize genetic diversity, population structure, and polarity in gene flow using nuclear microsatellite fragment and chloroplast and nuclear sequence data. An inverse relationship between genetic diversity and latitude was observed (heterozygosity: R2 = 0.738, P < 0.001; allelic richness: R2 = 0.327, P = 0.047), as was significant genetic partitioning across most sampling sites (θ = 0.302, P < 0.0001). Variance in allele frequency was significantly partitioned by region only in cases when a population geographically in the Gulf of Alaska LME (Kinzarof Lagoon) was instead included with populations in the Eastern Bering Sea LME (θp = 0.128–0.172; P < 0.003), suggesting gene flow between the two LMEs in this region. Gene flow among locales was rarely symmetrical, with notable exceptions generally following net coastal ocean current direction. Genetic data failed to support recent proposals that multiple Zostera species (i.e. Z. japonica and Z. angustifolia) are codistributed with Z. marina in Alaska. Comparative analyses also failed to support the hypothesis that eelgrass populations in the North Atlantic derived from eelgrass retained in northeastern Pacific Last Glacial Maximum refugia. These data suggest northeastern Pacific populations are derived from populations expanding northward from temperate populations following climate amelioration at the terminus of the last Pleistocene glaciation.
","language":"English","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0152701","usgsCitation":"Talbot, S.L., Sage, G.K., Rearick, J.R., Fowler, M., Muñiz-Salazar, R., Baibak, B., Wyllie-Echeverria, S., Cabello-Pasini, A., and Ward, D.H., 2016, The structure of genetic diversity in eelgrass (Zostera marina L.) along the North Pacific and Bering Sea coasts of Alaska: PLoS ONE, v. 11, no. 4, Article e0152701; 31 p., https://doi.org/10.1371/journal.pone.0152701.","productDescription":"Article e0152701; 31 p.","onlineOnly":"Y","additionalOnlineFiles":"N","ipdsId":"IP-061219","costCenters":[{"id":117,"text":"Alaska Science Center Biology WTEB","active":true,"usgs":true}],"links":[{"id":471053,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1371/journal.pone.0152701","text":"Publisher Index Page"},{"id":438617,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/F7GQ6VTK","text":"USGS data release","linkHelpText":"Eelgrass (Zostera marina) Microsatellite DNA Data; Pacific Coast of North America, 2000-2009"},{"id":323474,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Alaska","otherGeospatial":"Bering Sea, Gulf of Alaska","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -169.013671875,\n 65.25670649344259\n ],\n [\n -179.033203125,\n 62.34960927573045\n ],\n [\n -172.08984375,\n 55.42901345240742\n ],\n [\n -177.01171875,\n 55.07836723201515\n ],\n [\n -184.04296875,\n 57.468589192089325\n ],\n [\n -183.603515625,\n 55.32914440840507\n ],\n [\n -185.361328125,\n 51.17934297928927\n ],\n [\n -178.857421875,\n 48.864714761802794\n ],\n [\n -158.55468749999997,\n 52.5897007687178\n ],\n [\n -132.451171875,\n 50.56928286558243\n ],\n [\n 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mfowler@usgs.gov","orcid":"https://orcid.org/0000-0002-4947-0236","contributorId":200478,"corporation":false,"usgs":false,"family":"Fowler","given":"Megan C.","email":"mfowler@usgs.gov","affiliations":[{"id":117,"text":"Alaska Science Center Biology WTEB","active":true,"usgs":true}],"preferred":false,"id":638488,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Muñiz-Salazar, Raquel","contributorId":171744,"corporation":false,"usgs":false,"family":"Muñiz-Salazar","given":"Raquel","affiliations":[{"id":26937,"text":"Escuela de Ciencias de la Salid, Universidad Autónoma de Baja California","active":true,"usgs":false}],"preferred":false,"id":638489,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Baibak, Bethany","contributorId":171745,"corporation":false,"usgs":false,"family":"Baibak","given":"Bethany","email":"","affiliations":[{"id":7067,"text":"Humboldt State University","active":true,"usgs":false}],"preferred":false,"id":638490,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Wyllie-Echeverria, Sandy","contributorId":24874,"corporation":false,"usgs":true,"family":"Wyllie-Echeverria","given":"Sandy","email":"","affiliations":[],"preferred":false,"id":638491,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Cabello-Pasini, Alehandro","contributorId":171746,"corporation":false,"usgs":false,"family":"Cabello-Pasini","given":"Alehandro","email":"","affiliations":[{"id":26938,"text":"Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California","active":true,"usgs":false}],"preferred":false,"id":638492,"contributorType":{"id":1,"text":"Authors"},"rank":8},{"text":"Ward, David H. 0000-0002-5242-2526 dward@usgs.gov","orcid":"https://orcid.org/0000-0002-5242-2526","contributorId":3247,"corporation":false,"usgs":true,"family":"Ward","given":"David","email":"dward@usgs.gov","middleInitial":"H.","affiliations":[{"id":114,"text":"Alaska Science Center","active":true,"usgs":true},{"id":117,"text":"Alaska Science Center Biology WTEB","active":true,"usgs":true}],"preferred":true,"id":638493,"contributorType":{"id":1,"text":"Authors"},"rank":9}]}} ,{"id":70170241,"text":"70170241 - 2016 - Role of habitat complexity in predator-prey dynamics between an introduced fish and larval Long-toed Salamanders (Ambystoma macrodactylum)","interactions":[],"lastModifiedDate":"2017-11-22T17:35:48","indexId":"70170241","displayToPublicDate":"2016-04-13T15:45:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1176,"text":"Canadian Journal of Zoology","active":true,"publicationSubtype":{"id":10}},"title":"Role of habitat complexity in predator-prey dynamics between an introduced fish and larval Long-toed Salamanders (Ambystoma macrodactylum)","docAbstract":"Predation by nonnative fishes has reduced abundance and increased extinction risk for amphibian populations worldwide. Although rare, fish and palatable amphibians have been observed to coexist where aquatic vegetation and structural complexity provide suitable refugia. We examined whether larval long-toed salamanders (Ambystoma macrodactylum Baird, 1849) increased use of vegetation cover in lakes with trout and whether adding vegetation structure could reduce predation risk and nonconsumptive effects (NCEs), such as reductions in body size and delayed metamorphosis. We compared use of vegetation cover by larval salamanders in lakes with and without trout and conducted a field experiment to investigate the influence of added vegetation structure on salamander body morphology and life history. The probability of catching salamanders in traps in lakes with trout was positively correlated with the proportion of submerged vegetation and surface cover. Growth rates of salamanders in enclosures with trout cues decreased as much as 85% and the probability of metamorphosis decreased by 56%. We did not find evidence that adding vegetation reduced NCEs in experimental enclosures, but salamanders in lakes with trout utilized more highly-vegetated areas which suggests that adding vegetation structure at the scale of the whole lake may facilitate coexistence between salamanders and introduced trout.
","language":"English","publisher":"NRC Research Press","doi":"10.1139/cjz-2015-0160","usgsCitation":"Kenison, E., Litt, A., Pilliod, D.S., and McMahon, T.E., 2016, Role of habitat complexity in predator-prey dynamics between an introduced fish and larval Long-toed Salamanders (Ambystoma macrodactylum): Canadian Journal of Zoology, v. 94, no. 4, p. 243-249, https://doi.org/10.1139/cjz-2015-0160.","productDescription":"7 p.","startPage":"243","endPage":"249","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-067344","costCenters":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"links":[{"id":471074,"rank":0,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"http://www.nrcresearchpress.com/doi/abs/10.1139/cjz-2015-0160","text":"External Repository"},{"id":320031,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"94","issue":"4","publishingServiceCenter":{"id":12,"text":"Tacoma PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"570f5f9de4b0ef3b7ca32967","contributors":{"authors":[{"text":"Kenison, Erin K","contributorId":168578,"corporation":false,"usgs":false,"family":"Kenison","given":"Erin K","affiliations":[{"id":5120,"text":"Montana State University, Department of Mathematical Sciences, Bozeman, MT 59717","active":true,"usgs":false}],"preferred":false,"id":626573,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Litt, Andrea R.","contributorId":22226,"corporation":false,"usgs":true,"family":"Litt","given":"Andrea R.","affiliations":[],"preferred":false,"id":626574,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Pilliod, David S. 0000-0003-4207-3518 dpilliod@usgs.gov","orcid":"https://orcid.org/0000-0003-4207-3518","contributorId":149254,"corporation":false,"usgs":true,"family":"Pilliod","given":"David","email":"dpilliod@usgs.gov","middleInitial":"S.","affiliations":[{"id":289,"text":"Forest and Rangeland Ecosys Science Center","active":true,"usgs":true},{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":626572,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"McMahon, Tom E","contributorId":168579,"corporation":false,"usgs":false,"family":"McMahon","given":"Tom","email":"","middleInitial":"E","affiliations":[{"id":5120,"text":"Montana State University, Department of Mathematical Sciences, Bozeman, MT 59717","active":true,"usgs":false}],"preferred":false,"id":626575,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70170212,"text":"70170212 - 2016 - The Chahnaly low sulfidation epithermal gold deposit, western Makran volcanic arc, southeastern Iran","interactions":[],"lastModifiedDate":"2016-04-13T08:48:49","indexId":"70170212","displayToPublicDate":"2016-04-13T08:00:00","publicationYear":"2016","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":"The Chahnaly low sulfidation epithermal gold deposit, western Makran volcanic arc, southeastern Iran","docAbstract":"The Chahnaly low-sulfidation epithermal Au deposit and nearby Au prospects are located northwest of the intermittently active Bazman stratovolcano on the western end of the Makran volcanic arc, which formed as the result of subduction of the remnant Neo-Tethyan oceanic crust beneath the Lut block. The arc hosts the Siah Jangal epithermal and Kharestan porphyry prospects, near Taftan volcano, as well as the Saindak Cu-Au porphyry deposit and world-class Reko Diq Cu-Au porphyry deposit, near Koh-i-Sultan volcano to the east-northeast in Pakistan. The host rocks for the Chahnaly deposit include early Miocene andesite and andesitic volcaniclastic rocks that are intruded by younger dacitic domes. Unaltered late Miocene dacitic ignimbrites overlie these rocks. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) U-Pb zircon geochronology data yield ages between 21.8 and 9.9 Ma for the acidic-intermediate regional volcanism. The most recent volcanic activity of the Bazman stratovolcano involved extrusion of an olivine basalt during Pliocene to Quaternary times. Interpretation of geochemical data indicate that the volcanic rocks are synsubduction and calc-alkaline to subalkaline. The lack of a significant negative Eu anomaly, a listric-shaped rare earth element pattern, and moderate La/Yb ratios of host suites indicate a high water content of the source magma.
\nGold and electrum are temporally and spatially related to a series of structurally controlled, 030°-trending, subvertical hydrothermal breccias with chalcedony-adularia that cut porphyritic andesite and andesitic volcaniclastic rocks. Gold is associated with pyrite, a siliceous matrix of hydrothermal breccia, and previously formed vein clasts, as well as with iron oxides and hydroxides in oxidized zones. Rare silver minerals include Ag-bearing electrum and naumannite, iodargyrite, an unnamed silver diiodide, and hessite. Hydrothermal alteration is generally well developed surrounding the ore-bearing hydrothermal breccia. The main types of alteration in the area include an inner ~0.5- to 20-m-thick gold-bearing hydrothermal breccia composed of quartz-chalcedonyadularia-illite-pyrite, a ~5- to 50-m-thick zone of quartz, chalcedony, pyrite, illitic phengite, phengite, illitic muscovite, illite, illitic paragonite, paragonite, muscovite, montmorillonite and, rarely, siderite, and a 30- to 70-m outer propylitic zone of Fe-Mg chlorite, calcite, ankerite, dolomite, epidote, palygorskite, and pyrite.
\nThe Chahnaly Au deposit formed during the early stages of magmatism. LA-ICP-MS zircon U-Pb geochronology of host andesite and 40Ar/39Ar dating of two samples of gold-associated adularia show that the ore-stage adularia (19.83 ± 0.10 and 19.2 ± 0.5 Ma) is younger, by as much as 1.5 million years, than the volcanic host rock (20.32 ± 0.4 Ma). Therefore, either hydrothermal activity continued well after volcanism or a second magmatic event rejuvenated hydrothermal activity. This second magmatic event may be related to eruption of porphyritic andesite at ~20.32 ± 0.40 Ma, which is within error of ~19.83 ± 0.10 Ma adularia. The new LA-ICP-MS zircon U-Pb host rock and vein adularia 40Ar/39Ar ages suggest that early Miocene magmatism and mineralization in the Bazman area is of a similar age to that of the Saindak porphyry and Tanjeel porphyry center of the giant Reko Diq deposit. This confirms the existence of early Miocene arc magmatism and mineralization along the Iranian part of the Makran volcanic arc. Ore, alteration mineralogy, and alteration patterns indicate that the Chahnaly deposit is a typical low-sulfidation epithermal Au deposit, located in a poorly explored part of the Makran volcanic arc in Iran.
","language":"English","publisher":"Society of Economic Geologists","doi":"10.2113/econgeo.111.3.619","usgsCitation":"Sholeh, A., Rastad, E., Huston, D.L., Gemmell, J.B., and Taylor, R.D., 2016, The Chahnaly low sulfidation epithermal gold deposit, western Makran volcanic arc, southeastern Iran: Economic Geology, v. 111, no. 3, p. 619-639, https://doi.org/10.2113/econgeo.111.3.619.","productDescription":"21 p.","startPage":"619","endPage":"639","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-055033","costCenters":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"links":[{"id":320016,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Iran, Pakistan","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n 60.216064453125,\n 27.98470011861268\n ],\n [\n 60.216064453125,\n 29.869228848968312\n ],\n [\n 63.4075927734375,\n 29.869228848968312\n ],\n [\n 63.4075927734375,\n 27.98470011861268\n ],\n [\n 60.216064453125,\n 27.98470011861268\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"111","issue":"3","publishingServiceCenter":{"id":2,"text":"Denver PSC"},"noUsgsAuthors":false,"publicationDate":"2016-04-08","publicationStatus":"PW","scienceBaseUri":"570f5f9de4b0ef3b7ca32970","contributors":{"authors":[{"text":"Sholeh, Ali","contributorId":168565,"corporation":false,"usgs":false,"family":"Sholeh","given":"Ali","email":"","affiliations":[{"id":25338,"text":"Tarbiat Modares University","active":true,"usgs":false}],"preferred":false,"id":626483,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Rastad, Ebrahim","contributorId":119934,"corporation":false,"usgs":true,"family":"Rastad","given":"Ebrahim","email":"","affiliations":[],"preferred":false,"id":626484,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Huston, David L.","contributorId":67139,"corporation":false,"usgs":true,"family":"Huston","given":"David","email":"","middleInitial":"L.","affiliations":[],"preferred":false,"id":626485,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Gemmell, J. Bruce","contributorId":168566,"corporation":false,"usgs":false,"family":"Gemmell","given":"J.","email":"","middleInitial":"Bruce","affiliations":[{"id":16141,"text":"University of Tasmania","active":true,"usgs":false}],"preferred":false,"id":626486,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Taylor, Ryan D. 0000-0002-8845-5290 rtaylor@usgs.gov","orcid":"https://orcid.org/0000-0002-8845-5290","contributorId":3412,"corporation":false,"usgs":true,"family":"Taylor","given":"Ryan","email":"rtaylor@usgs.gov","middleInitial":"D.","affiliations":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":626482,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70170157,"text":"70170157 - 2016 - From \"Duck Factory\" to \"Fish Factory\": Climate induced changes in vertebrate communities of prairie pothole wetlands and small lakes","interactions":[],"lastModifiedDate":"2017-01-03T16:18:55","indexId":"70170157","displayToPublicDate":"2016-04-07T09:45:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3750,"text":"Wetlands","onlineIssn":"1943-6246","printIssn":"0277-5212","active":true,"publicationSubtype":{"id":10}},"title":"From \"Duck Factory\" to \"Fish Factory\": Climate induced changes in vertebrate communities of prairie pothole wetlands and small lakes","docAbstract":"The Prairie Pothole Region’s myriad wetlands and small lakes contribute to its stature as the “duck factory” of North America. The fishless nature of the region’s aquatic habitats, a result of frequent drying, freezing, and high salinity, influences its importance to waterfowl. Recent precipitation increases have resulted in higher water levels and wetland/lake freshening. In 2012–13, we sampled chemical characteristics and vertebrates (fish and salamanders) of 162 Prairie Pothole wetlands and small lakes. We used non-metric multidimensional scaling, principal component analysis, and bootstrapping techniques to reveal relationships. We found fish present in a majority of sites (84 %). Fish responses to water chemistry varied by species. Fathead minnows (Pimephales promelas) and brook sticklebacks (Culaea inconstans) occurred across the broadest range of conditions. Yellow perch (Perca flavescens) occurred in a smaller, chemically defined, subset. Iowa darters (Etheostoma exile) were restricted to the narrowest range of conditions. Tiger salamanders (Ambystoma mavortium) rarely occurred in lakes with fish. We also compared our chemical data to similar data collected in 1966–1976 to explore factors contributing to the expansion of fish into previously fishless sites. Our work contributes to a better understanding of relationships between aquatic biota and climate-induced changes in this ecologically important area.
","language":"English","publisher":"Society of Wetland Scientists","publisherLocation":"McClean, VA","doi":"10.1007/s13157-016-0766-3","usgsCitation":"McLean, K.I., Mushet, D.M., and Stockwell, C., 2016, From \"Duck Factory\" to \"Fish Factory\": Climate induced changes in vertebrate communities of prairie pothole wetlands and small lakes: Wetlands, v. 36, no. s2, p. 407-421, https://doi.org/10.1007/s13157-016-0766-3.","productDescription":"15 p.","startPage":"407","endPage":"421","numberOfPages":"15","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-068956","costCenters":[{"id":480,"text":"Northern Prairie Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":319944,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"North Dakota","county":"Kidder County, Stutsman County","geographicExtents":"{\"type\":\"FeatureCollection\",\"features\":[{\"type\":\"Feature\",\"geometry\":{\"type\":\"Polygon\",\"coordinates\":[[[-100.1129,47.3272],[-100.0347,47.327],[-99.6498,47.3274],[-99.6077,47.3267],[-99.5248,47.3275],[-99.4801,47.3267],[-99.2669,47.3268],[-98.8466,47.327],[-98.8392,47.327],[-98.8232,47.3272],[-98.8152,47.3271],[-98.4991,47.327],[-98.467,47.3266],[-98.4677,47.2402],[-98.4685,46.9788],[-98.4412,46.9789],[-98.4396,46.6296],[-98.7894,46.6294],[-99.0379,46.6309],[-99.1616,46.6317],[-99.4122,46.6316],[-99.4498,46.6319],[-99.912,46.6319],[-100.0799,46.6316],[-100.0794,46.705],[-100.0794,46.7123],[-100.0792,46.7454],[-100.0791,46.7513],[-100.0777,46.9794],[-100.1162,46.98],[-100.1139,47.1567],[-100.1129,47.3272]]]},\"properties\":{\"name\":\"Kidder\",\"state\":\"ND\"}}]}","volume":"36","issue":"s2","publishingServiceCenter":{"id":4,"text":"Rolla PSC"},"noUsgsAuthors":false,"publicationDate":"2016-04-07","publicationStatus":"PW","scienceBaseUri":"570ccab2e4b0ef3b7ca14718","contributors":{"authors":[{"text":"McLean, Kyle I. kmclean@usgs.gov","contributorId":147397,"corporation":false,"usgs":true,"family":"McLean","given":"Kyle","email":"kmclean@usgs.gov","middleInitial":"I.","affiliations":[{"id":480,"text":"Northern Prairie Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":626292,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Mushet, David M. 0000-0002-5910-2744 dmushet@usgs.gov","orcid":"https://orcid.org/0000-0002-5910-2744","contributorId":1299,"corporation":false,"usgs":true,"family":"Mushet","given":"David","email":"dmushet@usgs.gov","middleInitial":"M.","affiliations":[{"id":480,"text":"Northern Prairie Wildlife Research Center","active":true,"usgs":true}],"preferred":true,"id":626291,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Stockwell, Craig A.","contributorId":55257,"corporation":false,"usgs":true,"family":"Stockwell","given":"Craig A.","affiliations":[],"preferred":false,"id":626293,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70169099,"text":"70169099 - 2016 - Movement and survival of an amphibian in relation to sediment and culvert design","interactions":[],"lastModifiedDate":"2016-05-27T08:11:41","indexId":"70169099","displayToPublicDate":"2016-04-02T09:15:00","publicationYear":"2016","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":"Movement and survival of an amphibian in relation to sediment and culvert design","docAbstract":"Habitat disturbance from stream culverts can affect aquatic organisms by increasing sedimentation or forming barriers to movement. Land managers are replacing many culverts to reduce these negative effects, primarily for stream fishes. However, these management actions are likely to have broad implications for many organisms, including amphibians in small streams. To assess the effects of culverts on movement and survival of the Idaho giant salamander (Dicamptodon aterrimus), we used capture-mark-recapture surveys and measured sediment in streams with 2 culvert types (i.e., unimproved culverts, improved culverts) and in streams without culverts (i.e., reference streams). We predicted culverts would increase stream sediment levels, limit movement, and reduce survival of Idaho giant salamanders. We also determined the effect of sediment levels on survival of salamanders because although sediment is often associated with distribution and abundance of stream amphibians, links with vital rates remain unclear. To estimate survival, we used a spatial Cormack–Jolly–Seber (CJS) model that explicitly incorporated information on movement, eliminating bias in apparent survival estimated from traditional (i.e., non-spatial) CJS models caused by permanent emigration beyond the study area. To demonstrate the importance of using spatial data in studies of wildlife populations, we compared estimates from the spatial CJS to estimates of apparent survival from a traditional CJS model. Although high levels of sediment reduced survival of salamanders, culvert type was unrelated to sediment levels or true survival of salamanders. Across all streams, we documented only 15 movement events between study reaches. All movement events were downstream, and they occurred disproportionately in 1 stream, which precluded measuring the effect of culvert design on movement. Although movement was low overall, the variance among streams was high enough to bias estimates of apparent survival compared to true survival. Our results suggest that where sedimentation occurs from roads and culverts, survival of the Idaho giant salamander could be reduced. Though culverts clearly do not completely block downstream movements of Idaho giant salamanders, the degree to which culvert improvements affect movements under roads in comparison to unimproved culverts remains unclear, especially for rare, but potentially important, upstream movements.
","language":"English","publisher":"Wildlife Society","publisherLocation":"Washington, D.C.","doi":"10.1002/jwmg.1056","usgsCitation":"Honeycutt, R., Lowe, W., and Hossack, B.R., 2016, Movement and survival of an amphibian in relation to sediment and culvert design: Journal of Wildlife Management, v. 80, no. 4, p. 761-770, https://doi.org/10.1002/jwmg.1056.","startPage":"761","endPage":"770","numberOfPages":"10","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-065843","costCenters":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"links":[{"id":321812,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Idaho, Montana","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -116.510009765625,\n 45.75219336063106\n ],\n [\n -116.510009765625,\n 48.125767833701666\n ],\n [\n -113.97766113281249,\n 48.125767833701666\n ],\n [\n -113.97766113281249,\n 45.75219336063106\n ],\n [\n -116.510009765625,\n 45.75219336063106\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"80","issue":"4","publishingServiceCenter":{"id":2,"text":"Denver PSC"},"noUsgsAuthors":false,"publicationDate":"2016-04-02","publicationStatus":"PW","scienceBaseUri":"57496fb1e4b07e28b665cc7e","contributors":{"authors":[{"text":"Honeycutt, R.K","contributorId":167621,"corporation":false,"usgs":false,"family":"Honeycutt","given":"R.K","email":"","affiliations":[{"id":24785,"text":"Wildlife Biology Program, University of Montana, 32 Campus","active":true,"usgs":false}],"preferred":false,"id":622926,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Lowe, W.H.","contributorId":91961,"corporation":false,"usgs":true,"family":"Lowe","given":"W.H.","affiliations":[],"preferred":false,"id":622927,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Hossack, Blake R. 0000-0001-7456-9564 blake_hossack@usgs.gov","orcid":"https://orcid.org/0000-0001-7456-9564","contributorId":1177,"corporation":false,"usgs":true,"family":"Hossack","given":"Blake","email":"blake_hossack@usgs.gov","middleInitial":"R.","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true},{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":622925,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70178035,"text":"70178035 - 2016 - Airborne pathogens from dairy manure aerial irrigation and the human health risk","interactions":[],"lastModifiedDate":"2016-12-19T17:44:05","indexId":"70178035","displayToPublicDate":"2016-04-01T00:00:00","publicationYear":"2016","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":3,"text":"Organization Series"},"title":"Airborne pathogens from dairy manure aerial irrigation and the human health risk","docAbstract":"Dairy manure, like the fecal excrement from any domesticated or wild animal, can contain pathogens capable of infecting humans and causing illness or even death. Pathogens in dairy manure can be broadly divided into categories of taxonomy or infectiousness. Dividing by taxonomy there are three pathogen groups in dairy manure: viruses (e.g., bovine rotavirus), bacteria (e.g., Salmonella species), and protozoa (e.g., Cryptosporidium parvum). There are two categories of infectiousness for pathogens found in animals: those that are zoonotic and those that are not. A zoonotic pathogen is one that can infect both human and animal hosts. Some zoonotic pathogens found in dairy manure cause illness in both hosts (e.g., Salmonella) while other zoonotic pathogens, like Escherichia coli O157:H7, (enterohemorrhagic E. coli (EHEC)) cause illness only in humans. As a general rule, the gastrointestinal viruses found in dairy manure are not zoonotic. While there are exceptions (e.g., rare reports of bovine rotavirus infecting children), for the most part the viruses in dairy manure are not a human health concern. The primary concerns are the zoonotic bacteria and protozoa in dairy manure.
","largerWorkType":{"id":18,"text":"Report"},"largerWorkTitle":"Considerations for the use of manure irrigation practices","language":"English","publisher":"Wisconsin Manure Irrigation Workgroup","collaboration":"Wisconsin Department of Natural Resources","usgsCitation":"Borchardt, M.A., and Burch, T.R., 2016, Airborne pathogens from dairy manure aerial irrigation and the human health risk, C-1-C-24.","productDescription":"C-1-C-24","ipdsId":"IP-069593","costCenters":[{"id":677,"text":"Wisconsin Water Science Center","active":true,"usgs":true}],"links":[{"id":332310,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":330596,"type":{"id":15,"text":"Index Page"},"url":"https://fyi.uwex.edu/manureirrigation/files/2016/04/Manure-Irrigation-Workgroup-Report-2016.pdf"}],"publishingServiceCenter":{"id":6,"text":"Columbus PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"58590009e4b03639a6025e2d","contributors":{"authors":[{"text":"Borchardt, Mark A. 0000-0002-6471-2627","orcid":"https://orcid.org/0000-0002-6471-2627","contributorId":151033,"corporation":false,"usgs":false,"family":"Borchardt","given":"Mark","email":"","middleInitial":"A.","affiliations":[{"id":6684,"text":"USDA Forest Service, Southern Research Station, Aiken, SC","active":true,"usgs":false}],"preferred":false,"id":652579,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Burch, Tucker R tburch@usgs.gov","contributorId":5689,"corporation":false,"usgs":true,"family":"Burch","given":"Tucker","email":"tburch@usgs.gov","middleInitial":"R","affiliations":[{"id":677,"text":"Wisconsin Water Science Center","active":true,"usgs":true}],"preferred":true,"id":652578,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70177907,"text":"70177907 - 2016 - Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus)","interactions":[],"lastModifiedDate":"2016-10-26T12:00:06","indexId":"70177907","displayToPublicDate":"2016-04-01T00:00:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1988,"text":"Infection, Genetics and Evolution","active":true,"publicationSubtype":{"id":10}},"title":"Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus)","docAbstract":"Newcastle disease is caused by virulent forms of avian paramyxovirus of serotype 1 (APMV-1) and has global economic importance. The disease reached panzootic proportions within two decades after first being identified in 1926 in the United Kingdom and Indonesia and still remains endemic in many countries across the world. Here we review information on the host, temporal, and geographic distribution of APMV-1 genetic diversity based on the evolutionary systematics of the complete coding region of the fusion gene. Strains of APMV-1 are phylogenetically separated into two classes (class I and class II) and further classified into genotypes based on genetic differences. Class I viruses are genetically less diverse, generally present in wild waterfowl, and are of low virulence. Class II viruses are genetically and phenotypically more diverse, frequently isolated from poultry with occasional spillovers into wild birds, and exhibit a wider range of virulence. Waterfowl, cormorants, and pigeons are natural reservoirs of all APMV-1 pathotypes, except viscerotropic velogenic viruses for which natural reservoirs have not been identified. Genotypes I and II within class II include isolates of high and low virulence, the latter often being used as vaccines. Viruses of genotypes III and IX that emerged decades ago are now isolated rarely, but may be found in domestic and wild birds in China. Containing only virulent viruses and responsible for the majority of recent outbreaks in poultry and wild birds, viruses from genotypes V, VI, and VII, are highly mobile and have been isolated on different continents. Conversely, virulent viruses of genotypes XI (Madagascar), XIII (mainly Southwest Asia), XVI (North America) and XIV, XVII and XVIII (Africa) appear to have a more limited geographic distribution and have been isolated predominantly from poultry.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.meegid.2016.01.008","usgsCitation":"Dimitrov, K.M., Ramey, A.M., Qiu, X., Bahl, J., and Afonso, C.L., 2016, Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus): Infection, Genetics and Evolution, v. 39, p. 22-34, https://doi.org/10.1016/j.meegid.2016.01.008.","productDescription":"13 p.","startPage":"22","endPage":"34","ipdsId":"IP-069077","costCenters":[{"id":117,"text":"Alaska Science Center Biology WTEB","active":true,"usgs":true}],"links":[{"id":471099,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1016/j.meegid.2016.01.008","text":"Publisher Index Page"},{"id":330406,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"39","publishingServiceCenter":{"id":12,"text":"Tacoma PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5811c0f2e4b0f497e79a5a73","chorus":{"doi":"10.1016/j.meegid.2016.01.008","url":"http://dx.doi.org/10.1016/j.meegid.2016.01.008","publisher":"Elsevier BV","authors":"Dimitrov Kiril M., Ramey Andrew M., Qiu Xueting, Bahl Justin, Afonso Claudio L.","journalName":"Infection, Genetics and Evolution","publicationDate":"4/2016"},"contributors":{"authors":[{"text":"Dimitrov, Kiril M.","contributorId":176311,"corporation":false,"usgs":false,"family":"Dimitrov","given":"Kiril","email":"","middleInitial":"M.","affiliations":[],"preferred":false,"id":652158,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Ramey, Andrew M. 0000-0002-3601-8400 aramey@usgs.gov","orcid":"https://orcid.org/0000-0002-3601-8400","contributorId":1872,"corporation":false,"usgs":true,"family":"Ramey","given":"Andrew","email":"aramey@usgs.gov","middleInitial":"M.","affiliations":[{"id":114,"text":"Alaska Science Center","active":true,"usgs":true},{"id":117,"text":"Alaska Science Center Biology WTEB","active":true,"usgs":true}],"preferred":true,"id":652108,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Qiu, Xueting","contributorId":176312,"corporation":false,"usgs":false,"family":"Qiu","given":"Xueting","email":"","affiliations":[],"preferred":false,"id":652159,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Bahl, Justin","contributorId":171803,"corporation":false,"usgs":false,"family":"Bahl","given":"Justin","affiliations":[{"id":26950,"text":"University of Texas School of Public Health, 1200 Pressler Street, Houston, TX 77030, USA","active":true,"usgs":false}],"preferred":false,"id":652160,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Afonso, Claudio L.","contributorId":171954,"corporation":false,"usgs":false,"family":"Afonso","given":"Claudio","email":"","middleInitial":"L.","affiliations":[],"preferred":false,"id":652161,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70169968,"text":"70169968 - 2016 - DNA and dispersal models highlight constrained connectivity in a migratory marine megavertebrate","interactions":[],"lastModifiedDate":"2017-05-02T14:15:37","indexId":"70169968","displayToPublicDate":"2016-03-31T12:30:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1445,"text":"Ecography","active":true,"publicationSubtype":{"id":10}},"title":"DNA and dispersal models highlight constrained connectivity in a migratory marine megavertebrate","docAbstract":"Population structure and spatial distribution are fundamentally important fields within ecology, evolution, and conservation biology. To investigate pan-Atlantic connectivity of globally endangered green turtles (Chelonia mydas) from two National Parks in Florida, USA, we applied a multidisciplinary approach comparing genetic analysis and ocean circulation modeling. The Everglades (EP) is a juvenile feeding ground, whereas the Dry Tortugas (DT) is used for courtship, breeding, and feeding by adults and juveniles. We sequenced two mitochondrial segments from 138 turtles sampled there from 2006-2015, and simulated oceanic transport to estimate their origins. Genetic and ocean connectivity data revealed northwestern Atlantic rookeries as the major natal sources, while southern and eastern Atlantic contributions were negligible. However, specific rookery estimates differed between genetic and ocean transport models. The combined analyses suggest that post-hatchling drift via ocean currents poorly explains the distribution of neritic juveniles and adults, but juvenile natal homing and population history likely play important roles. DT and EP were genetically similar to feeding grounds along the southern US coast, but highly differentiated from most other Atlantic groups. Despite expanded mitogenomic analysis and correspondingly increased ability to detect genetic variation, no significant differentiation between DT and EP, or among years, sexes or stages was observed. This first genetic analysis of a North Atlantic green turtle courtship area provides rare data supporting local movements and male philopatry. The study highlights the applications of multidisciplinary approaches for ecological research and conservation.
","language":"English","publisher":"Wiley","doi":"10.1111/ecog.02056","usgsCitation":"Naro-Maciel, E., Hart, K.M., Cruciata, R., and Putman, N.F., 2016, DNA and dispersal models highlight constrained connectivity in a migratory marine megavertebrate: Ecography, v. 40, no. 5, p. 586-597, https://doi.org/10.1111/ecog.02056.","productDescription":"12 p.","startPage":"586","endPage":"597","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-068508","costCenters":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"links":[{"id":471111,"rank":0,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"https://doi.org/10.1111/ecog.02056","text":"External Repository"},{"id":319674,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Florida","otherGeospatial":"Dry Tortugas Park, Everglades Park","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -83.1005859375,\n 24.462150693715266\n ],\n [\n -83.1005859375,\n 24.77177232822881\n ],\n [\n -82.6171875,\n 24.77177232822881\n ],\n [\n -82.6171875,\n 24.462150693715266\n ],\n [\n -83.1005859375,\n 24.462150693715266\n ]\n ]\n ]\n }\n },\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -81.09283447265625,\n 25.120419105501256\n ],\n [\n -81.09283447265625,\n 25.564742726875785\n ],\n [\n -80.6341552734375,\n 25.564742726875785\n ],\n [\n -80.6341552734375,\n 25.120419105501256\n ],\n [\n -81.09283447265625,\n 25.120419105501256\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"40","issue":"5","publishingServiceCenter":{"id":8,"text":"Raleigh PSC"},"noUsgsAuthors":false,"publicationDate":"2016-05-23","publicationStatus":"PW","scienceBaseUri":"56fe3c2ce4b075ab2b2aa0aa","contributors":{"authors":[{"text":"Naro-Maciel, Eugenia","contributorId":138902,"corporation":false,"usgs":false,"family":"Naro-Maciel","given":"Eugenia","email":"","affiliations":[{"id":12576,"text":"College of Staten Island, Staten Island, New York","active":true,"usgs":false}],"preferred":false,"id":625738,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Hart, Kristen M. 0000-0002-5257-7974 kristen_hart@usgs.gov","orcid":"https://orcid.org/0000-0002-5257-7974","contributorId":1966,"corporation":false,"usgs":true,"family":"Hart","given":"Kristen","email":"kristen_hart@usgs.gov","middleInitial":"M.","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"preferred":true,"id":625737,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Cruciata, Rossana","contributorId":168380,"corporation":false,"usgs":false,"family":"Cruciata","given":"Rossana","email":"","affiliations":[{"id":25274,"text":"Biology Dept., College of Staten Island, City University of New York","active":true,"usgs":false}],"preferred":false,"id":625739,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Putman, Nathan Freeman","contributorId":145423,"corporation":false,"usgs":false,"family":"Putman","given":"Nathan","email":"","middleInitial":"Freeman","affiliations":[{"id":16119,"text":"National Marine Fisheries Service, Miami, FL","active":true,"usgs":false}],"preferred":false,"id":625740,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70168487,"text":"70168487 - 2016 - Critical elements in sediment-hosted deposits (clastic-dominated Zn-Pb-Ag, Mississippi Valley-type Zn-Pb, sedimentary rock-hosted Stratiform Cu, and carbonate-hosted Polymetallic Deposits): A review: Chapter 12","interactions":[],"lastModifiedDate":"2016-09-01T13:55:26","indexId":"70168487","displayToPublicDate":"2016-03-20T00:00:00","publicationYear":"2016","noYear":false,"publicationType":{"id":5,"text":"Book chapter"},"publicationSubtype":{"id":24,"text":"Book Chapter"},"title":"Critical elements in sediment-hosted deposits (clastic-dominated Zn-Pb-Ag, Mississippi Valley-type Zn-Pb, sedimentary rock-hosted Stratiform Cu, and carbonate-hosted Polymetallic Deposits): A review: Chapter 12","docAbstract":"Some sediment-hosted base metal deposits, specifically the clastic-dominated (CD) Zn-Pb deposits, carbonate-hosted Mississippi Valley-type (MVT) deposits, sedimentary-rock hosted stratiform copper deposits, and carbonate-hosted polymetallic (“Kipushi type”) deposits, are or have been important sources of critical elements including Co, Ga, Ge, and Re. 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gpederson@usgs.gov","orcid":"https://orcid.org/0000-0002-6014-1425","contributorId":3106,"corporation":false,"usgs":true,"family":"Pederson","given":"Gregory","email":"gpederson@usgs.gov","middleInitial":"T.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":622704,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70169028,"text":"70169028 - 2016 - Paleozoic magmatism and porphyry Cu-mineralization in an evolving tectonic setting in the North Qilian Orogenic Belt, NW China","interactions":[],"lastModifiedDate":"2016-03-11T09:22:50","indexId":"70169028","displayToPublicDate":"2016-03-11T10:15:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2184,"text":"Journal of Asian Earth Sciences","active":true,"publicationSubtype":{"id":10}},"title":"Paleozoic magmatism and porphyry Cu-mineralization in an evolving tectonic setting in the North Qilian Orogenic Belt, NW China","docAbstract":"The NWW-striking North Qilian Orogenic Belt records the Paleozoic accretion–collision processes in NW China, and hosts Paleozoic Cu–Pb–Zn mineralization that was temporally and spatially related to the closure of the Paleo Qilian-Qinling Ocean. The Wangdian Cu deposit is located in the eastern part of the North Qilian Orogenic Belt, NW China. Copper mineralization is spatially associated with an altered early Paleozoic porphyritic granodiorite, which intruded tonalites and volcaniclastic rocks. Alteration zones surrounding the mineralization progress outward from a potassic to a feldspar-destructive phyllic assemblage. Mineralization consists mainly of quartz-sulfide stockworks and disseminated sulfides, with ore minerals chalcopyrite, pyrite, molybdenite, and minor galena and sphalerite. Gangue minerals include quartz, orthoclase, biotite, sericite, and K-feldspar. Zircon LA-ICPMS U–Pb dating of the ore-bearing porphyritic granodiorite yielded a mean 206Pb/238U age of 444.6 ± 7.8 Ma, with a group of inherited zircons yielding a mean U–Pb age of 485 ± 12 Ma, consistent with the emplacement age (485.3 ± 6.2 Ma) of the barren precursor tonalite. Rhenium and osmium analyses of molybdenite grains returned model ages of 442.9 ± 6.8 Ma and 443.3 ± 6.2 Ma, indicating mineralization was coeval with the emplacement of the host porphyritic granodiorite. Rhenium concentrations in molybdenite (208.9–213.2 ppm) suggest a mantle Re source. The tonalities are medium-K calc-alkaline. They are characterized by enrichment of light rare-earth elements (LREEs) and large-ion lithophile elements (LILEs), depletion of heavy rare-earth elements (HREEs) and high-field-strength elements (HFSEs), and minor negative Eu anomalies. They have εHf(t) values in the range of +3.6 to +11.1, with two-stage Hf model ages of 0.67–1.13 Ga, suggesting that the ca. 485 Ma barren tonalites were products of arc magmatism incorporating melts from the mantle wedge and the lithosphere. In contrast, the 40-m.y.-younger ore-bearing porphyritic granodiorite is sub-alkaline and peraluminous. They are enriched in LREEs and LILEs, depleted in HFSEs, and show weak negative Eu anomalies. They displayεHf(t) values of captured or inherited zircons in the range of +8.5 to +10.0, and younger two-stage Hf model ages of 0.78 Ga and 0.86 Ga, similar to those of ca. 485 Ma tonalite. The ca. 445 Ma zircons have εHf(t) values of −2.1 to +9.9, with two-stage Hf model ages of 0.75–1.27 Ga. Moreover, they have relatively high oxygen fugacity than that of the precursor barren tonalite. The ca. 445 Ma magmas at Wangdian thus formed in a subduction setting, and incorporated melts from the subduction-modified lithosphere that had previously been enriched by additions of chalcophile and siderophile element-rich materials by the earlier magmatism and metasomatism during the Paleo Qilian-Qinling Ocean subduction event.
","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Journal of Asian Earth Sciences","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","publisher":"Elsevier","publisherLocation":"Amsterdam","doi":"10.1016/j.jseaes.2016.02.007","collaboration":"Kunfeng Qiu; Jun Deng; Liqiang Yang; Ryan D Taylor; Kairui Song, Yaohui Song; Quanzhong Li; Richard J Goldfarb","usgsCitation":"Qiu, K., Deng, J., Taylor, R.D., Song, K., Song, Y., Li, Q., and Goldfarb, R.J., 2016, Paleozoic magmatism and porphyry Cu-mineralization in an evolving tectonic setting in the North Qilian Orogenic Belt, NW China: Journal of Asian Earth Sciences, v. 122, p. 20-40, https://doi.org/10.1016/j.jseaes.2016.02.007.","productDescription":"21 p.","startPage":"20","endPage":"40","numberOfPages":"21","onlineOnly":"N","additionalOnlineFiles":"N","ipdsId":"IP-063294","costCenters":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"links":[{"id":318811,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"China","otherGeospatial":"North Qilian Orogenic Belt","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n 89.56054687499999,\n 31.203404950917395\n ],\n [\n 89.56054687499999,\n 41.37680856570233\n ],\n [\n 112.412109375,\n 41.37680856570233\n ],\n [\n 112.412109375,\n 31.203404950917395\n ],\n [\n 89.56054687499999,\n 31.203404950917395\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"122","publishingServiceCenter":{"id":2,"text":"Denver PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"56e3ec2be4b0f59b85d42df1","contributors":{"authors":[{"text":"Qiu, Kun-Feng","contributorId":167527,"corporation":false,"usgs":false,"family":"Qiu","given":"Kun-Feng","email":"","affiliations":[{"id":24737,"text":"China University of Geosciences, Beijing","active":true,"usgs":false}],"preferred":false,"id":622593,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Deng, Jun","contributorId":167528,"corporation":false,"usgs":false,"family":"Deng","given":"Jun","email":"","affiliations":[{"id":24737,"text":"China University of Geosciences, Beijing","active":true,"usgs":false}],"preferred":false,"id":622594,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Taylor, Ryan D. 0000-0002-8845-5290 rtaylor@usgs.gov","orcid":"https://orcid.org/0000-0002-8845-5290","contributorId":3412,"corporation":false,"usgs":true,"family":"Taylor","given":"Ryan","email":"rtaylor@usgs.gov","middleInitial":"D.","affiliations":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":622592,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Song, Kai-Rui","contributorId":167530,"corporation":false,"usgs":false,"family":"Song","given":"Kai-Rui","email":"","affiliations":[{"id":24737,"text":"China University of Geosciences, Beijing","active":true,"usgs":false}],"preferred":false,"id":622596,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Song, Yao-Hui","contributorId":167531,"corporation":false,"usgs":false,"family":"Song","given":"Yao-Hui","affiliations":[{"id":24737,"text":"China University of Geosciences, Beijing","active":true,"usgs":false}],"preferred":false,"id":622597,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Li, Quan-Zhong","contributorId":167532,"corporation":false,"usgs":false,"family":"Li","given":"Quan-Zhong","email":"","affiliations":[{"id":24738,"text":"Hefei University of Technology","active":true,"usgs":false}],"preferred":false,"id":622598,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Goldfarb, Richard J. goldfarb@usgs.gov","contributorId":1205,"corporation":false,"usgs":true,"family":"Goldfarb","given":"Richard","email":"goldfarb@usgs.gov","middleInitial":"J.","affiliations":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":false,"id":622599,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ,{"id":70169085,"text":"70169085 - 2016 - Ecology, distribution, and predictive occurrence modeling of Palmers chipmunk (Tamias palmeri): a high-elevation small mammal endemic to the Spring Mountains in southern Nevada, USA","interactions":[],"lastModifiedDate":"2016-12-16T11:08:53","indexId":"70169085","displayToPublicDate":"2016-03-10T14:30:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2373,"text":"Journal of Mammalogy","onlineIssn":"1545-1542","printIssn":"0022-2372","active":true,"publicationSubtype":{"id":10}},"title":"Ecology, distribution, and predictive occurrence modeling of Palmers chipmunk (Tamias palmeri): a high-elevation small mammal endemic to the Spring Mountains in southern Nevada, USA","docAbstract":"Although montane sky islands surrounded by desert scrub and shrub steppe comprise a large part of the biological diversity of the Basin and Range Province of southwestern North America, comprehensive ecological and population demographic studies for high-elevation small mammals within these areas are rare. Here, we examine the ecology and population parameters of the Palmer’s chipmunk (Tamias palmeri) in the Spring Mountains of southern Nevada, and present a predictive GIS-based distribution and probability of occurrence model at both home range and geographic spatial scales. Logistic regression analyses and Akaike Information Criterion model selection found variables of forest type, slope, and distance to water sources as predictive of chipmunk occurrence at the geographic scale. At the home range scale, increasing population density, decreasing overstory canopy cover, and decreasing understory canopy cover contributed to increased survival rates.
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2016 - Application of lime (CaCO3) to promote forest recovery from severe acidification increases potential for earthworm invasion","interactions":[],"lastModifiedDate":"2016-08-17T11:06:43","indexId":"70169001","displayToPublicDate":"2016-03-10T10:15:00","publicationYear":"2016","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1687,"text":"Forest Ecology and Management","active":true,"publicationSubtype":{"id":10}},"title":"Application of lime (CaCO3) to promote forest recovery from severe acidification increases potential for earthworm invasion","docAbstract":"The application of lime (calcium carbonate) may be a cost-effective strategy to promote forest ecosystem recovery from acid impairment, under contemporary low levels of acidic deposition. However, liming acidified soils may create more suitable habitat for invasive earthworms that cause significant damage to forest floor communities and may disrupt ecosystem processes. We investigated the potential effects of liming in acidified soils where earthworms are rare in conjunction with a whole-ecosystem liming experiment in the chronically acidified forests of the western Adirondacks (USA). Using a microcosm experiment that replicated the whole-ecosystem treatment, we evaluated effects of soil liming on Lumbricus terrestris survivorship and biomass growth. We found that a moderate lime application (raising pH from 3.1 to 3.7) dramatically increased survival and biomass of L. terrestris, likely via increases in soil pH and associated reductions in inorganic aluminum, a known toxin. Very few L. terrestris individuals survived in unlimed soils, whereas earthworms in limed soils survived, grew, and rapidly consumed leaf litter. We supplemented this experiment with field surveys of extant earthworm communities along a gradient of soil pH in Adirondack hardwood forests, ranging from severely acidified (pH < 3) to well-buffered (pH > 5). In the field, no earthworms were observed where soil pH < 3.6. Abundance and species richness of earthworms was greatest in areas where soil pH > 4.4 and human dispersal vectors, including proximity to roads and public fishing access, were most prevalent. Overall our results suggest that moderate lime additions can be sufficient to increase earthworm invasion risk where dispersal vectors are present.
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However, there is little empirical evidence that observed competition – colonization tradeoffs are strong enough to maintain diversity in natural systems. This is due in part to a mismatch between theoretical assumptions and biological reality in some systems. We tested whether a competition – colonization tradeoff explains how a diverse trematode guild coexists in California horn snail populations, a system that meets the requisite criteria for the tradeoff to promote coexistence. A field experiment showed that subordinate trematode species tended to have higher colonization rates than dominant species. This tradeoff promoted coexistence in parameterized models but did not fully explain trematode diversity and abundance, suggesting a role of additional diversity maintenance mechanisms. Spatial heterogeneity is an alternative way to promote coexistence if it isolates competing species. We used scale transition theory to expand the competition – colonization tradeoff model to include spatial variation. The parameterized model showed that spatial variation in trematode prevalence did not isolate most species sufficiently to explain the overall high diversity, but could benefit some rare species. Together, the results suggest that several mechanisms combine to maintain diversity, even when a competition – colonization tradeoff occurs.
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