A study was conducted in 2014–15 by the U.S. Geological Survey (USGS), in cooperation with the Municipality of Caguas, to determine if changes in the stream sanitary quality during base-flow conditions have occurred since 1997–99, when a similar study was completed by the USGS. Water samples were collected for the current study during two synoptic surveys in 2014 and 2015. Water samples were analyzed for fecal and total coliform bacteria, nitrate plus nitrite as nitrogen, nitrogen and oxygen isotopes of nitrate, and human health and pharmaceutical products. Water sampling occurred at 39 stream locations used during the 1997–99 study by the USGS and at 11 additional sites. A total of 151 stream miles were classified on the basis of fecal and total coliform bacteria results.
The overall spatial pattern of the sanitary quality of surface water during 2014–15 is similar to the pattern observed in 1997–99 in relation to the standards adopted by the Puerto Rico Environmental Quality Board in 1990. Surface water at most of the water-sampling sites exceeded the current standard for fecal coliform of 200 colonies per 100 milliliters adopted by the Puerto Rico Environmental Quality Board in 2010. The poorest sanitary quality was within the urban area of the Municipality of Caguas, particularly in urban stream reaches of Río Caguitas and in rural and suburban reaches bordered by houses in high density that either have inadequate septic tanks or discharge domestic wastewater directly into the stream channels. The best sanitary quality occurred in areas having little or no human development, such as in the wards of San Salvador and Beatriz to the south and southwest of Caguas, respectively. The concentration of nitrate plus nitrite as nitrogen ranged from 0.02 to 9.0 milligrams per liter, and did not exceed the U.S. Environmental Protection Agency drinking-water standard for nitrate as nitrogen of 10 milligrams per liter. The composition of nitrogen and oxygen isotopes of nitrate indicates that the origin of nitrate in the streams is most likely animal and human waste. A baseline was established for the concentrations of selected human health and pharmaceutical products at stations in some of the streams within the Municipality of Caguas. Thirty-eight human health and pharmaceutical products were present at or above the measurement detection level.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/sir20175045","collaboration":"Prepared in cooperation with the Autonomous Municipality of Caguas","usgsCitation":"Rodríguez-Martínez, Jesús, and Guzmán-Ríos, Senén, 2017, Sanitary quality of surface water during base-flow conditions in the Municipality of Caguas, Puerto Rico, 2014–15: A comparison with results from a similar 1997–99 study: U.S. Geological Survey Scientific Investigations Report 2017–5045, 20 p., https://doi.org/10.3133/sir20175045.","productDescription":"Report: vii, 20 p.; Plate: 20.66 x 40.73 inches","onlineOnly":"Y","additionalOnlineFiles":"Y","ipdsId":"IP-068670","costCenters":[{"id":156,"text":"Caribbean Water Science Center","active":true,"usgs":true}],"links":[{"id":342871,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/sir/2017/5045/sir20175045.pdf","text":"Report","size":"6.38 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U.S. Geological Survey
4446 Pet Lane, Suite 108
Lutz, FL 33559
The U.S. Geological Survey (USGS) has completed an assessment of water and proppant requirements and water production associated with the possible future production of undiscovered oil and gas resources in the Three Forks and Bakken Formations (Late Devonian to Early Mississippian) of the Williston Basin Province in Montana and North Dakota. This water and proppant assessment is directly linked to the geology-based assessment of the undiscovered, technically recoverable continuous oil and gas resources that is described in USGS Fact Sheet 2013–3013.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/fs20173044","usgsCitation":"Haines, S.S., Varela, B.A., Hawkins, S.J., Gianoutsos, N.J., Thamke, J.N., Engle, M.A., Tennyson, M.E., Schenk, C.J., Gaswirth, S.B., Marra, K.R., Kinney, S.A., Mercier, T.J., and Martinez, C.D., 2017, Assessment of water and proppant quantities associated with petroleum production from the Bakken and Three Forks Formations, Williston Basin Province, Montana and North Dakota, 2016: U.S. Geological Survey Fact Sheet 2017–3044, 4 p., https://doi.org/10.3133/fs20173044.","productDescription":"4 p.","onlineOnly":"N","ipdsId":"IP-086605","costCenters":[{"id":164,"text":"Central Energy Resources Science Center","active":true,"usgs":true}],"links":[{"id":438293,"rank":6,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P97TXFRB","text":"USGS data release","linkHelpText":"Input forms for 2016 water and proppant assessment of the Bakken and Three Forks Formations, Williston Basin, USA"},{"id":342809,"rank":4,"type":{"id":22,"text":"Related Work"},"url":"https://doi.org/10.3133/ofr20151117","text":"Open-File Report 2015–1117: Methodology for Assessing Quantities of Water and Proppant Injection, and Water Production Associated with Development of Continuous Petroleum Accumulations"},{"id":342810,"rank":5,"type":{"id":22,"text":"Related Work"},"url":"https://pubs.usgs.gov/fs/2013/3013/","text":"Fact Sheet 2013–3013: Assessment of Undiscovered Oil Resources in the Bakken and Three Forks Formations, Williston Basin Province, Montana, North Dakota, and South Dakota, 2013"},{"id":342808,"rank":3,"type":{"id":22,"text":"Related Work"},"url":"https://doi.org/10.3133/fs20143010","text":"Fact Sheet 2014–3010: A Framework for Assessing Water and Proppant Use and Flowback Water Extraction Associated with Development of Continuous Petroleum Resources"},{"id":342807,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/fs/2017/3044/fs20173044.pdf","text":"Report","size":"708 kB","linkFileType":{"id":1,"text":"pdf"},"description":"FS 2017-3044"},{"id":342806,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/fs/2017/3044/coverthb.jpg"}],"country":"United States","state":"Montana, North Dakota","otherGeospatial":"Bakken Formation and Three Forks Formation","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -102.63427734374999,\n 48.980216985374994\n ],\n [\n -106.98486328124999,\n 48.99463598353405\n ],\n [\n -106.787109375,\n 48.356249029540734\n ],\n [\n -106.32568359375,\n 48.004625021133904\n ],\n [\n -105.6884765625,\n 47.85740289465826\n ],\n [\n -104.8974609375,\n 47.54687159892238\n ],\n [\n -104.32617187499999,\n 47.368594345213374\n ],\n [\n -103.73291015625,\n 46.800059446787316\n ],\n [\n -103.24951171875,\n 46.604167162931844\n ],\n [\n -102.72216796875,\n 46.58906908309182\n ],\n [\n -102.48046875,\n 46.89023157359399\n ],\n [\n -101.953125,\n 47.234489635299184\n ],\n [\n -101.84326171875,\n 47.3834738721015\n ],\n [\n -102.63427734374999,\n 48.980216985374994\n ]\n ]\n ]\n }\n }\n ]\n}","contact":"Central Energy Resources Science Center
U.S. Geological Survey
Box 25046, MS-939
Denver, CO 80225-0046
The North American Cordillera is home to a greater diversity of volcanic provinces than any comparably sized region in the world. The interplay between changing plate-margin interactions, tectonic complexity, intra-crustal magma differentiation, and mantle melting have resulted in a wealth of volcanic landscapes. Field trips in this guide book collection (published as USGS Scientific Investigations Report 2017–5022) visit many of these landscapes, including (1) active subduction-related arc volcanoes in the Cascade Range; (2) flood basalts of the Columbia Plateau; (3) bimodal volcanism of the Snake River Plain-Yellowstone volcanic system; (4) some of the world’s largest known ignimbrites from southern Utah, central Colorado, and northern Nevada; (5) extension-related volcanism in the Rio Grande Rift and Basin and Range Province; and (6) the eastern Sierra Nevada featuring Long Valley Caldera and the iconic Bishop Tuff. Some of the field trips focus on volcanic eruptive and emplacement processes, calling attention to the fact that the western United States provides opportunities to examine a wide range of volcanological phenomena at many scales.
The 2017 Scientific Assembly of the International Association of Volcanology and Chemistry of the Earth’s Interior (IAVCEI) in Portland, Oregon, was the impetus to update field guides for many of the volcanoes in the Cascades Arc, as well as publish new guides for numerous volcanic provinces and features of the North American Cordillera. This collection of guidebooks summarizes decades of advances in understanding of magmatic and tectonic processes of volcanic western North America.
These field guides are intended for future generations of scientists and the general public as introductions to these fascinating areas; the hope is that the general public will be enticed toward further exploration and that scientists will pursue further field-based research.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/sir20175022","costCenters":[{"id":617,"text":"Volcano Science Center","active":true,"usgs":true}],"links":[{"id":342832,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/sir/2017/5022/coverthb.jpg"},{"id":342833,"rank":2,"type":{"id":13,"text":"Illustration"},"url":"https://pubs.usgs.gov/sir/2017/5022/sir20175022_map.pdf","text":"Field-trip overview map","size":"5 MB","linkFileType":{"id":1,"text":"pdf"},"description":"SIR 2017-5022"}],"contact":"Volcano Science Center - Menlo Park
U.S. Geological Survey
345 Middlefield Road, MS 910
Menlo Park, CA 94025
Study region
Arkansas River, east of the Rocky Mountains.
Study focus
Cretaceous sedimentary rocks in the western United States generally pose challenges to water quality, often through mobilization of salts and trace metals by irrigation. However, in the Arkansas River Basin of Colorado, patchy exposure of multiple Cretaceous formations has made it difficult to identify which formations are most problematic. This paper examines water quality in surface-water inflows along a 26-km reach of the Arkansas River relative to the presence or absence of the Cretaceous Niobrara Formation within the watershed.
New hydrological insights for the region
Principal component analysis (PCA) shows Niobrara-influenced inflows have distinctive geochemistry, particularly with respect to Na, Mg, SO42−, and Se. Uranium concentrations are also greater in Niobrara-influenced inflows. During the irrigation season, median dissolved solids, Se, and U concentrations in Niobrara-influenced inflows were 83%, 646%, and 55%, respectively, greater than medians where Niobrara Formation surface exposures were absent. During the non-irrigation season, which better reflects geologic influence, the differences were more striking. Median dissolved solids, Se, and U concentrations in Niobrara-influenced inflows were 288%, 863%, and 155%, respectively, greater than median concentrations where the Niobrara Formation was absent. Identification of the Niobrara Formation as a disproportionate source for dissolved solids, Se, and U will allow for more targeted studies and management, particularly where exposures underlie irrigated agriculture.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.ejrh.2017.05.001","usgsCitation":"Bern, C.R., and Stogner, 2017, The Niobrara Formation as a challenge to water quality in the Arkansas River, Colorado, USA: Journal of Hydrology: Regional Studies, v. 12, p. 181-195, https://doi.org/10.1016/j.ejrh.2017.05.001.","productDescription":"15 p.","startPage":"181","endPage":"195","ipdsId":"IP-081119","costCenters":[{"id":191,"text":"Colorado Water Science Center","active":true,"usgs":true}],"links":[{"id":461505,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1016/j.ejrh.2017.05.001","text":"Publisher Index Page"},{"id":342827,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Colorado","otherGeospatial":"Arkansas River","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -105.3369140625,\n 38.33196157898413\n ],\n [\n -104.94964599609374,\n 38.33196157898413\n ],\n [\n -104.94964599609374,\n 38.5213096674994\n ],\n [\n -105.3369140625,\n 38.5213096674994\n ],\n [\n -105.3369140625,\n 38.33196157898413\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"12","publishingServiceCenter":{"id":2,"text":"Denver PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"594e28b1e4b062508e3abe13","contributors":{"authors":[{"text":"Bern, Carleton R. 0000-0002-8980-1781 cbern@usgs.gov","orcid":"https://orcid.org/0000-0002-8980-1781","contributorId":166816,"corporation":false,"usgs":true,"family":"Bern","given":"Carleton","email":"cbern@usgs.gov","middleInitial":"R.","affiliations":[{"id":211,"text":"Crustal Geophysics and Geochemistry Science Center","active":true,"usgs":true},{"id":191,"text":"Colorado Water Science Center","active":true,"usgs":true}],"preferred":false,"id":700374,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Stogner 0000-0002-3185-1452 rstogner@usgs.gov","orcid":"https://orcid.org/0000-0002-3185-1452","contributorId":938,"corporation":false,"usgs":true,"family":"Stogner","email":"rstogner@usgs.gov","affiliations":[{"id":191,"text":"Colorado Water Science Center","active":true,"usgs":true}],"preferred":false,"id":700375,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70188470,"text":"ofr20171070 - 2017 - Juvenile salmonid monitoring in the White Salmon River, Washington, post-Condit Dam removal, 2016","interactions":[],"lastModifiedDate":"2017-06-24T10:59:14","indexId":"ofr20171070","displayToPublicDate":"2017-06-23T00:00:00","publicationYear":"2017","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":"2017-1070","title":"Juvenile salmonid monitoring in the White Salmon River, Washington, post-Condit Dam removal, 2016","docAbstract":"Condit Dam, at river kilometer 5.3 on the White Salmon River, Washington, was breached in 2011 and removed completely in 2012, allowing anadromous salmonids access to habitat that had been blocked for nearly 100 years. A multi-agency workgroup concluded that the preferred salmonid restoration alternative was natural recolonization with monitoring to assess efficacy, followed by a management evaluation 5 years after dam removal. Limited monitoring of salmon and steelhead spawning has occurred since 2011, but no monitoring of juveniles occurred until 2016. During 2016, we operated a rotary screw trap at river kilometer 2.3 (3 kilometers downstream of the former dam site) from late March through May and used backpack electrofishing during summer to assess juvenile salmonid distribution and abundance. The screw trap captured primarily steelhead (Oncorhynchus mykiss; smolts, parr, and fry) and coho salmon (O. kisutch; smolts and fry). We estimated the number of steelhead smolts at 3,851 (standard error = 1,454) and coho smolts at 1,093 (standard error = 412). In this document, we refer to O. mykiss caught at the screw trap as steelhead because they were actively migrating, but because we did not know migratory status of O. mykiss caught in electrofishing surveys, we simply refer to them as O. mykiss or steelhead/rainbow trout. Steelhead and coho smolts tagged with passive integrated transponder tags were subsequently detected downstream at Bonneville Dam on the Columbia River. Few Chinook salmon (O. tshawytscha) fry were captured, possibly as a result of trap location or effects of a December 2015 flood. Sampling in Mill, Buck, and Rattlesnake Creeks (all upstream of the former dam site) showed that juvenile coho were present in Mill and Buck Creeks, suggesting spawning had occurred there. We compared O. mykiss abundance data in sites on Buck and Rattlesnake Creeks to pre-dam removal data. During 2016, age-0 O. mykiss were more abundant in Buck Creek than in 2009 or 2010, though age-1 and older O. mykiss abundance was similar. In Rattlesnake Creek, age-0 O. mykiss abundance during 2016 slightly exceeded the mean abundance from 2001 through 2005, although age-1 and older O. mykiss abundance was lower than from 2001 through 2005. These sampling efforts also provided the opportunity to collect genetic samples to investigate parental and stock origin, although funding to analyze the samples was not part of this grant. Juvenile salmonid sampling efforts during 2016 have shown that natural spawning produced steelhead and coho smolts and that coho were colonizing some tributaries. The 2016 efforts also provided the first post-dam juvenile abundance estimates. We hope to continue monitoring to better understand abundance trends, distribution, and life history patterns of recolonizing salmonids in the White Salmon River to assess efficacy of natural recolonization and to inform management decisions.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ofr20171070","collaboration":"Prepared in cooperation with Mid-Columbia Fisheries Enhancement Group","usgsCitation":"Jezorek, I.G., and Hardiman, J.M., 2017, Juvenile salmonid monitoring in the White Salmon River, Washington, post-Condit Dam removal, 2016: U.S. Geological Survey Open-File Report 2017-1070, 34 p., https://doi.org/10.3133/ofr20171070.","productDescription":"iv, 34 p.","onlineOnly":"Y","ipdsId":"IP-083906","costCenters":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"links":[{"id":342774,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/of/2017/1070/coverthb.jpg"},{"id":342775,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/of/2017/1070/ofr20171070.pdf","text":"Report","size":"1.1 MB","linkFileType":{"id":1,"text":"pdf"},"description":"OFR 2017-1070"}],"country":"United States","state":"Washington","otherGeospatial":"White Salmon River watershed","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -121.75460815429686,\n 45.64428817847555\n ],\n [\n -121.27258300781251,\n 45.64428817847555\n ],\n [\n -121.27258300781251,\n 45.99076013759662\n ],\n [\n -121.75460815429686,\n 45.99076013759662\n ],\n [\n -121.75460815429686,\n 45.64428817847555\n ]\n ]\n ]\n }\n }\n ]\n}","contact":"Director, Western Fisheries Research Center
U.S. Geological Survey
6505 NE 65th Street
Seattle, Washington 98115
Director, New England Water Science Center
U.S. Geological Survey
331 Commerce Way, Suite 2
Pembroke, NH 03275-3718
To identify potential biomarkers of salt stress in a freshwater sentinel species, we examined transcriptional responses of the common mussel Elliptio complanata to controlled sodium chloride (NaCl) exposures. Ribonucleic acid sequencing (RNA-Seq) of mantle tissue identified 481 transcripts differentially expressed in adult mussels exposed to 2 ppt NaCl (1.2 ppt chloride) for 7 d, of which 290 had nonoverlapping intervals. Differentially expressed gene categories included ion and transmembrane transport, oxidoreductase activity, maintenance of protein folding, and amino acid metabolism. The rate-limiting enzyme for synthesis of taurine, an amino acid frequently linked to osmotic stress in aquatic species, was upregulated, as was the transmembrane ion pump sodium/potassium adenosine 5′-triphosphatase. These patterns confirm a primary transcriptional response to the experimental dose, albeit likely overlapping with nonspecific secondary stress responses. Substantial involvement of the heat shock protein 70 chaperone family and the water-transporting aquaporin family was not detected, however, in contrast to some studies in other bivalves. A subset of the most significantly regulated genes was confirmed by quantitative polymerase chain reaction in an independent sample. Cluster analysis showed separation of mussels exposed to 2 ppt NaCl from control mussels in multivariate space, but mussels exposed to 1 ppt NaCl were largely indistinguishable from controls. Transcriptome-scale analysis of salt exposure under laboratory conditions efficiently identified candidate biomarkers for further functional analysis and field validation
","language":"English","publisher":"Society of Environmental Toxicology and Chemistry","doi":"10.1002/etc.3774","usgsCitation":"Robertson, L.S., Galbraith, H.S., Iwanowicz, D.D., Blakeslee, C.J., and Cornman, R.S., 2017, RNA sequencing analysis of transcriptional change in the freshwater mussel Elliptio complanata after environmentally relevant sodium chloride exposure: Environmental Toxicology and Chemistry, v. 36, no. 9, p. 2352-2366, https://doi.org/10.1002/etc.3774.","productDescription":"15 p.","startPage":"2352","endPage":"2366","ipdsId":"IP-062505","costCenters":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"links":[{"id":438294,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/F7P26WCG","text":"USGS data release","linkHelpText":"Experimental analysis of Elliptio complanata transcriptional response to salt stress"},{"id":342788,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"36","issue":"9","publishingServiceCenter":{"id":10,"text":"Baltimore PSC"},"noUsgsAuthors":false,"publicationDate":"2017-02-22","publicationStatus":"PW","scienceBaseUri":"594cd73ce4b062508e3951c1","contributors":{"authors":[{"text":"Robertson, Laura S. lrobertson@usgs.gov","contributorId":193277,"corporation":false,"usgs":false,"family":"Robertson","given":"Laura","email":"lrobertson@usgs.gov","middleInitial":"S.","affiliations":[],"preferred":false,"id":699586,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Galbraith, Heather S. 0000-0003-3704-3517 hgalbraith@usgs.gov","orcid":"https://orcid.org/0000-0003-3704-3517","contributorId":4519,"corporation":false,"usgs":true,"family":"Galbraith","given":"Heather","email":"hgalbraith@usgs.gov","middleInitial":"S.","affiliations":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":true,"id":699587,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Iwanowicz, Deborah D. 0000-0002-9613-8594 diwanowicz@usgs.gov","orcid":"https://orcid.org/0000-0002-9613-8594","contributorId":2253,"corporation":false,"usgs":true,"family":"Iwanowicz","given":"Deborah","email":"diwanowicz@usgs.gov","middleInitial":"D.","affiliations":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":true,"id":699589,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Blakeslee, Carrie J. 0000-0002-0801-5325 cblakeslee@usgs.gov","orcid":"https://orcid.org/0000-0002-0801-5325","contributorId":5462,"corporation":false,"usgs":true,"family":"Blakeslee","given":"Carrie","email":"cblakeslee@usgs.gov","middleInitial":"J.","affiliations":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":true,"id":699588,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Cornman, Robert S. 0000-0001-9511-2192 rcornman@usgs.gov","orcid":"https://orcid.org/0000-0001-9511-2192","contributorId":5356,"corporation":false,"usgs":true,"family":"Cornman","given":"Robert","email":"rcornman@usgs.gov","middleInitial":"S.","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true},{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":true,"id":699585,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70190131,"text":"70190131 - 2017 - Challenges in recovering resources from acid mine drainage","interactions":[],"lastModifiedDate":"2024-01-24T14:15:25.772446","indexId":"70190131","displayToPublicDate":"2017-06-21T00:00:00","publicationYear":"2017","noYear":false,"publicationType":{"id":24,"text":"Conference Paper"},"publicationSubtype":{"id":19,"text":"Conference Paper"},"title":"Challenges in recovering resources from acid mine drainage","docAbstract":"Metal recovery from mine waters and effluents is not a new approach but one that has occurred largely opportunistically over the last four millennia. Due to the need for low-cost resources and increasingly stringent environmental conditions, mine waters are being considered in a fresh light with a designed, deliberate approach to resource recovery often as part of a larger water treatment evaluation. Mine water chemistry is highly dependent on many factors including geology, ore deposit composition and mineralogy, mining methods, climate, site hydrology, and others. Mine waters are typically Ca-Mg-SO4±Al±Fe with a broad range in pH and metal content. The main issue in recovering components of these waters having potential economic value, such as base metals or rare earth elements, is the separation of these from more reactive metals such as Fe and Al. Broad categories of methods for separating and extracting substances from acidic mine drainage are chemical and biological. Chemical methods include solution, physicochemical, and electrochemical technologies. Advances in membrane techniques such as reverse osmosis have been substantial and the technique is both physical and chemical. Biological methods may be further divided into microbiological and macrobiological, but only the former is considered here as a recovery method, as the latter is typically used as a passive form of water treatment.
","largerWorkType":{"id":4,"text":"Book"},"largerWorkTitle":"Mine water and circular economy","largerWorkSubtype":{"id":12,"text":"Conference publication"},"conferenceTitle":"IMWA 2017","conferenceDate":"June 25-30, 2017","conferenceLocation":"Lappeenranta, Finland","language":"English","publisher":"International Mine Water Association","usgsCitation":"Nordstrom, D.K., Bowell, R.J., Campbell, K.M., and Alpers, C.N., 2017, Challenges in recovering resources from acid mine drainage, in Mine water and circular economy, Lappeenranta, Finland, June 25-30, 2017, p. 1138-1146.","productDescription":"9 p.","startPage":"1138","endPage":"1146","ipdsId":"IP-086476","costCenters":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true},{"id":5044,"text":"National Research Program - Central Branch","active":true,"usgs":true}],"links":[{"id":424860,"rank":2,"type":{"id":15,"text":"Index Page"},"url":"http://www.imwa.de/imwaconferencesandcongresses/proceedings/300-proceedings-2017.html","linkFileType":{"id":5,"text":"html"}},{"id":344788,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"publishingServiceCenter":{"id":2,"text":"Denver PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"59b76ee5e4b08b1644ddfad8","contributors":{"authors":[{"text":"Nordstrom, D. Kirk 0000-0003-3283-5136 dkn@usgs.gov","orcid":"https://orcid.org/0000-0003-3283-5136","contributorId":749,"corporation":false,"usgs":true,"family":"Nordstrom","given":"D.","email":"dkn@usgs.gov","middleInitial":"Kirk","affiliations":[{"id":37277,"text":"WMA - Earth System Processes Division","active":true,"usgs":true},{"id":5044,"text":"National Research Program - Central Branch","active":true,"usgs":true}],"preferred":false,"id":707607,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Bowell, Robert J.","contributorId":150175,"corporation":false,"usgs":false,"family":"Bowell","given":"Robert","email":"","middleInitial":"J.","affiliations":[{"id":17927,"text":"SRK Consulting Ltd.","active":true,"usgs":false}],"preferred":false,"id":707608,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Campbell, Kate M. 0000-0002-8715-5544 kcampbell@usgs.gov","orcid":"https://orcid.org/0000-0002-8715-5544","contributorId":1441,"corporation":false,"usgs":true,"family":"Campbell","given":"Kate","email":"kcampbell@usgs.gov","middleInitial":"M.","affiliations":[{"id":5044,"text":"National Research Program - Central Branch","active":true,"usgs":true}],"preferred":true,"id":707609,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Alpers, Charles N. 0000-0001-6945-7365 cnalpers@usgs.gov","orcid":"https://orcid.org/0000-0001-6945-7365","contributorId":411,"corporation":false,"usgs":true,"family":"Alpers","given":"Charles","email":"cnalpers@usgs.gov","middleInitial":"N.","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":707610,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70188279,"text":"70188279 - 2017 - Widespread occurrence and potential for biodegradation of bioactive contaminants in Congaree National Park, USA","interactions":[],"lastModifiedDate":"2018-09-13T13:51:56","indexId":"70188279","displayToPublicDate":"2017-06-21T00:00:00","publicationYear":"2017","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1571,"text":"Environmental Toxicology and Chemistry","active":true,"publicationSubtype":{"id":10}},"title":"Widespread occurrence and potential for biodegradation of bioactive contaminants in Congaree National Park, USA","docAbstract":"Organic contaminants with designed molecular bioactivity, such as pesticides and pharmaceuticals, originate from human and agricultural sources, occur frequently in surface waters, and threaten the structure and function of aquatic and terrestrial ecosystems. Congaree National Park in South Carolina (USA) is a vulnerable park unit due to its location downstream of multiple urban and agricultural contaminant sources and its hydrologic setting, being composed almost entirely of floodplain and aquatic environments. Seventy-two water and sediment samples were collected from 16 sites in Congaree National Park during 2013 to 2015, and analyzed for 199 and 81 targeted organic contaminants, respectively. More than half of these water and sediment analytes were not detected or potentially had natural sources. Pharmaceutical contaminants were detected (49 total) frequently in water throughout Congaree National Park, with higher detection frequencies and concentrations at Congaree and Wateree River sites, downstream from major urban areas. Forty-seven organic wastewater indicator chemicals were detected in water, and 36 were detected in sediment, of which approximately half are distinctly anthropogenic. Endogenous sterols and hormones, which may originate from humans or wildlife, were detected in water and sediment samples throughout Congaree National Park, but synthetic hormones were detected only once, suggesting a comparatively low risk of adverse impacts. Assessment of the biodegradation potentials of 8 14C-radiolabeled model contaminants indicated poor potentials for some contaminants, particularly under anaerobic sediments conditions.
","language":"English","publisher":"Society of Environmental Toxicology and Chemistry","doi":"10.1002/etc.3873","usgsCitation":"Bradley, P.M., Battaglin, W.A., Clark, J.M., Henning, F., Hladik, M., Iwanowicz, L.R., Journey, C.A., Riley, J.W., and Romanok, K.M., 2017, Widespread occurrence and potential for biodegradation of bioactive contaminants in Congaree National Park, USA: Environmental Toxicology and Chemistry, v. 36, no. 11, p. 3045-3056, https://doi.org/10.1002/etc.3873.","productDescription":"12 p.","startPage":"3045","endPage":"3056","ipdsId":"IP-079959","costCenters":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true},{"id":13634,"text":"South Atlantic Water Science Center","active":true,"usgs":true}],"links":[{"id":342730,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"South Carolina","otherGeospatial":"Congaree National Park","geographicExtents":"{\n \"type\": 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jriley@usgs.gov","orcid":"https://orcid.org/0000-0001-5525-3134","contributorId":3605,"corporation":false,"usgs":true,"family":"Riley","given":"Jeffrey","email":"jriley@usgs.gov","middleInitial":"W.","affiliations":[{"id":13634,"text":"South Atlantic Water Science Center","active":true,"usgs":true},{"id":316,"text":"Georgia Water Science Center","active":true,"usgs":true}],"preferred":true,"id":697067,"contributorType":{"id":1,"text":"Authors"},"rank":8},{"text":"Romanok, Kristin M. 0000-0002-8472-8765 kromanok@usgs.gov","orcid":"https://orcid.org/0000-0002-8472-8765","contributorId":189680,"corporation":false,"usgs":true,"family":"Romanok","given":"Kristin","email":"kromanok@usgs.gov","middleInitial":"M.","affiliations":[{"id":470,"text":"New Jersey Water Science Center","active":true,"usgs":true}],"preferred":true,"id":697068,"contributorType":{"id":1,"text":"Authors"},"rank":9}]}} ,{"id":70186976,"text":"ds1046 - 2017 - The physical characteristics of the sediments on and surrounding Dauphin Island, Alabama","interactions":[],"lastModifiedDate":"2017-06-20T12:58:19","indexId":"ds1046","displayToPublicDate":"2017-06-20T10:30:00","publicationYear":"2017","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":310,"text":"Data Series","code":"DS","onlineIssn":"2327-638X","printIssn":"2327-0271","active":false,"publicationSubtype":{"id":5}},"seriesNumber":"1046","title":"The physical characteristics of the sediments on and surrounding Dauphin Island, Alabama","docAbstract":"Scientists from the U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center collected 303 surface sediment samples from Dauphin Island, Alabama, and the surrounding water bodies in August 2015. These sediments were processed to determine physical characteristics such as organic content, bulk density, and grain-size. The environments where the sediments were collected include high and low salt marshes, washover deposits, dunes, beaches, sheltered bays, and open water. Sampling by the USGS was part of a larger study to assess the feasibility and sustainability of proposed restoration efforts for Dauphin Island, Alabama, and assess the island’s resilience to rising sea level and storm events. The data presented in this publication can be used by modelers to attempt validation of hindcast models and create predictive forecast models for both baseline conditions and storms. This study was funded by the National Fish and Wildlife Foundation, via the Gulf Environmental Benefit Fund.
This report serves as an archive for sedimentological data derived from surface sediments. Downloadable data are available as Excel spreadsheets, JPEG files, and formal Federal Geographic Data Committee metadata.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ds1046","usgsCitation":"Ellis, A.M., Marot, M.E., Smith, C.G., and Wheaton, C.J., 2017, The physical characteristics of the sediments on and surrounding Dauphin Island, Alabama: U.S. Geological Survey Data Series 1046, https://doi.org/10.3133/ds1046.\n\n","productDescription":"HTML document","onlineOnly":"Y","additionalOnlineFiles":"Y","ipdsId":"IP-078883","costCenters":[{"id":574,"text":"St. Petersburg Coastal and Marine Science Center","active":true,"usgs":true}],"links":[{"id":342208,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/ds/1046","text":"Report HTML","linkFileType":{"id":5,"text":"html"},"description":"DS 1046"},{"id":342207,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/ds/1046/coverthb.jpg"}],"country":"United States","state":"Alabama","otherGeospatial":" Dauphin Island","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -88.37127685546875,\n 30.25076353594852\n ],\n [\n -88.34518432617188,\n 30.209234673510014\n ],\n [\n -88.29299926757812,\n 30.20211367909724\n ],\n [\n -88.18450927734375,\n 30.206861065952626\n ],\n [\n -88.08837890625,\n 30.212794977500614\n ],\n [\n -88.04580688476562,\n 30.244831915307145\n ],\n [\n -88.05816650390625,\n 30.278044377800153\n ],\n [\n -88.0609130859375,\n 30.295832146790442\n ],\n [\n -88.08151245117188,\n 30.324285866937423\n ],\n [\n -88.165283203125,\n 30.312431154103745\n ],\n [\n -88.29711914062499,\n 30.292274851024256\n ],\n [\n -88.36715698242186,\n 30.28634573802957\n ],\n [\n -88.37127685546875,\n 30.25076353594852\n ]\n ]\n ]\n }\n }\n ]\n}","contact":"St. Petersburg Coastal and Marine Science Center
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After Hurricane Sandy made landfall along the northeastern Atlantic coast of the United States on October 29, 2012, the U.S. Geological Survey (USGS) carried out scientific investigations to assist with protecting coastal communities and resources from future flooding. The work included development and implementation of the Surge, Wave, and Tide Hydrodynamics (SWaTH) network consisting of more than 900 monitoring stations. The SWaTH network was designed to greatly improve the collection and timely dissemination of information related to storm surge and coastal flooding. The network provides a significant enhancement to USGS data-collection capabilities in the region impacted by Hurricane Sandy and represents a new strategy for observing and monitoring coastal storms, which should result in improved understanding, prediction, and warning of storm-surge impacts and lead to more resilient coastal communities.
As innovative as it is, SWaTH evolved from previous USGS efforts to collect storm-surge data needed by others to improve storm-surge modeling, warning, and mitigation. This report discusses the development and implementation of the SWaTH network, and some of the regional stories associated with the landfall of Hurricane Sandy, as well as some previous events that informed the SWaTH development effort. Additional discussions on the mechanics of inundation and how the USGS is working with partners to help protect coastal communities from future storm impacts are also included.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/cir1431","isbn":"ISBN 978-1-4113-4149-4","usgsCitation":"Verdi, R.J., Lotspeich, R.R., Robbins, J.C., Busciolano, R.J., Mullaney, J.R., Massey, A.J., Banks, W.S., Roland, M.A., Jenter, H.L., Peppler, M.C., Suro, T.P., Schubert, C.E., and Nardi, M.R., 2017, The surge, wave, and tide hydrodynamics (SWaTH) network of the U.S. Geological Survey—Past and future implementation of storm-response monitoring, data collection, and data delivery: U.S. Geological Survey Circular 1431, 35 p., https://dx.doi.org/10.3133/cir1431.","productDescription":"iv, 35 p. 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Groundwater quality in the 112-square-mile Bear Valley and Lake Arrowhead Watershed (BEAR) study unit was investigated as part of the Priority Basin Project (PBP) of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The study unit comprises two study areas (Bear Valley and Lake Arrowhead Watershed) in southern California in San Bernardino County. The GAMA-PBP is conducted by the California State Water Resources Control Board (SWRCB) in cooperation with the U.S. Geological Survey (USGS) and the Lawrence Livermore National Laboratory.
The GAMA BEAR study was designed to provide a spatially balanced, robust assessment of the quality of untreated (raw) groundwater from the primary aquifer systems in the two study areas of the BEAR study unit. The assessment is based on water-quality collected by the USGS from 38 sites (27 grid and 11 understanding) during 2010 and on water-quality data from the SWRCB-Division of Drinking Water (DDW) database. The primary aquifer system is defined by springs and the perforation intervals of wells listed in the SWRCB-DDW water-quality database for the BEAR study unit.
This study included two types of assessments: (1) a status assessment, which characterized the status of the quality of the groundwater resource as of 2010 by using data from samples analyzed for volatile organic compounds, pesticides, and naturally present inorganic constituents, such as major ions and trace elements, and (2) an understanding assessment, which evaluated the natural and human factors potentially affecting the groundwater quality. The assessments were intended to characterize the quality of groundwater resources in the primary aquifer system of the BEAR study unit, not the treated drinking water delivered to consumers. Bear Valley study area and the Lake Arrowhead Watershed study area were also compared statistically on the basis of water-quality results and factors potentially affecting the groundwater quality.
Relative concentrations (RCs), which are sample concentration of a particular constituent divided by its associated health- or aesthetic-based benchmark concentrations, were used for evaluating the groundwater quality for those constituents that have Federal or California regulatory or non-regulatory benchmarks for drinking-water quality. An RC greater than 1.0 indicates a concentration greater than a benchmark. Organic (volatile organic compounds and pesticides) and special-interest (perchlorate) constituent RCs were classified as “high” (RC greater than 1.0), “moderate” (RC less than or equal to 1.0 and greater than 0.1), or “low” (RC less than or equal to 0.1). For inorganic (radioactive, trace element, major ion, and nutrient) constituents, the boundary between low and moderate RCs was set at 0.5.
Aquifer-scale proportion was used as the primary metric in the status assessment for evaluating groundwater quality at the study-unit scale or for its component areas. High aquifer-scale proportion was defined as the percentage of the area of the primary aquifer system with a RC greater than 1.0 for a particular constituent or class of constituents; the percentage is based on area rather than volume. Moderate and low aquifer-scale proportions were defined as the percentage of the primary aquifer system with moderate and low RCs, respectively. A spatially weighted statistical approach was used to evaluate aquifer-scale proportions for individual constituents and classes of constituents.
The status assessment for the Bear Valley study area found that inorganic constituents with health-based benchmarks were detected at high RCs in 9.0 percent of the primary aquifer system and at moderate RCs in 13 percent. The high RCs of inorganic constituents primarily reflected high aquifer-scale proportions of fluoride (in 5.4 percent of the primary aquifer system) and arsenic (3.6 percent). The RCs of organic constituents with health-based benchmarks were high in 1.0 percent of the primary aquifer system, moderate in 8.1 percent, and low in 70 percent. Organic constituents were detected in 79 percent of the primary aquifer system. Two groups of organic constituents and two individual organic constituents were detected at frequencies greater than 10 percent of samples from the USGS grid sites: trihalomethanes (THMs), solvents, methyl tert-butyl ether (MTBE), and simazine. The special-interest constituent perchlorate was detected in 93 percent of the primary aquifer system; it was detected at moderate RCs in 7.1 percent and at low RCs in 86 percent.
The status assessment in the Lake Arrowhead Watershed study area showed that inorganic constituents with human-health benchmarks were detected at high RCs in 25 percent of the primary aquifer system and at moderate RCs in 41 percent. The high aquifer-scale proportion of inorganic constituents primarily reflected high aquifer-scale proportions of radon‑222 (in 62 percent of the primary aquifer system) and uranium (26 percent). RCs of organic constituents with health-based benchmarks were moderate in 7.7 percent of the primary aquifer system and low in 46 percent. Organic constituents were detected in 54 percent of the primary aquifer system. The only organic constituents that were detected at frequencies greater than 10 percent of samples from the USGS grid sites were THMs. Perchlorate was detected in 62 percent of the primary aquifer system at uniformly low RCs.
The second component of this study, the understanding assessment, identified the natural and human factors that could have affected the groundwater quality in the BEAR study unit by evaluating statistical correlations between water-quality constituents and potential explanatory factors. The potential explanatory factors evaluated were land use (including density of septic tanks and leaking or formerly leaking underground fuel tanks), site type, aquifer lithology, well construction (well depth and depth to the top-of-perforated interval), elevation, aridity index, groundwater-age distribution, and oxidation-reduction condition (including pH and dissolved oxygen concentration). Results of the statistical evaluations were used to explain the distribution of constituents in groundwater of the BEAR study unit.
In the Bear Valley study area, high and moderate RCs of fluoride were found in sites known to be influenced by hydrothermic conditions or that had high concentrations of fluoride historically. The high RC of arsenic can likely be attributed to desorption of arsenic from aquifer sediments saturated in old groundwater with high pH under reducing conditions. The THMs were detected more frequently at USGS grid sites that were wells, part of a large urban water system, and surrounded by urban land use. Solvents, MTBE, and simazine were all detected more frequently at USGS grid sites that were wells with a greater urban percentage of surrounding land use and that accessed older groundwater than other USGS grid sites. Comparison between the observed and predicted detection frequencies of perchlorate at USGS grid sites indicated that anthropogenic sources could have contributed to low levels of perchlorate in the groundwater of the Bear Valley study area.
In the Lake Arrowhead Watershed study area, high and moderate RCs of radon-222 and uranium can be attributed to older groundwater from the granitic fractured-rock primary aquifer system. Low RCs of THMs were detected at USGS grid sites that were wells and part of small water systems. The similarities between the observed and predicted detection frequencies of perchlorate in samples from USGS grid sites indicated that the source and distribution of perchlorate were most likely attributable to precipitation (rain and snow), with minimal, if any, contribution from anthropogenic sources.
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California GAMA
U.S. Geological Survey
6000 J Street, Placer Hall
Sacramento, California 95819
Groundwater provides more than 40 percent of California’s drinking water. To protect this vital resource, the State of California created the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The Priority Basin Project of the GAMA Program provides a comprehensive assessment of the State’s groundwater quality and increases public access to groundwater-quality information. The Bear Valley and Lake Arrowhead Watershed study areas in southern California compose one of the study units being evaluated.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/fs20173037","collaboration":"Prepared in cooperation with the California State Water Resources Control Board","usgsCitation":"Mathany, T.M., Burton, C.A., and Fram, M.S., 2017, Groundwater Quality in the Bear Valley and Lake Arrowhead Watershed, California: U.S. Geological Survey Fact Sheet 2017–3037, 4 p., https://doi.org/10.3133/fs20173037.","productDescription":"4 p.","ipdsId":"IP-071724","costCenters":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"links":[{"id":342680,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/fs/2017/3037/fs20173037.pdf","text":"Report","size":"1.6 MB","linkFileType":{"id":1,"text":"pdf"},"description":"FS 2017-3037"},{"id":342681,"rank":3,"type":{"id":22,"text":"Related Work"},"url":"https://doi.org/10.3133/sir20175043","text":"Scientific Investigations Report 2017-5043"},{"id":342679,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/fs/2017/3037/coverthb.jpg"}],"country":"United States","state":"California","otherGeospatial":"Bear Valley and Lake Arrowhead Watershed study unit","geographicExtents":"{ \"type\": \"FeatureCollection\", \"features\": [ { \"type\": \"Feature\", \"properties\": {}, \"geometry\": { \"type\": \"Polygon\", \"coordinates\": [ [ [ -116.98001861572266, 34.24245948736849 ], [ -116.96250915527344, 34.237350707417534 ], [ -116.95632934570312, 34.23564771187119 ], [ -116.94774627685547, 34.235363875931114 ], [ -116.93950653076172, 34.23564771187119 ], [ -116.91856384277342, 34.23195777001729 ], [ -116.9161605834961, 34.23479620118046 ], [ -116.91753387451172, 34.23820219227295 ], [ -116.91650390625, 34.240756595166985 ], [ -116.91169738769531, 34.239621314560885 ], [ -116.9110107421875, 34.237634536659534 ], [ -116.9058609008789, 34.237350707417534 ], [ -116.89453125, 34.23451236236987 ], [ 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California GAMA
U.S. Geological Survey
6000 J Street, Placer Hall
Sacramento, California 95819
Lithium-cesium-tantalum (LCT) pegmatites comprise a compositionally defined subset of granitic pegmatites. The major minerals are quartz, potassium feldspar, albite, and muscovite; typical accessory minerals include biotite, garnet, tourmaline, and apatite. The principal lithium ore minerals are spodumene, petalite, and lepidolite; cesium mostly comes from pollucite; and tantalum mostly comes from columbite-tantalite. Tin ore as cassiterite and beryllium ore as beryl also occur in LCT pegmatites, as do a number of gemstones and high-value museum specimens of rare minerals. Individual crystals in LCT pegmatites can be enormous: the largest spodumene was 14 meters long, the largest beryl was 18 meters long, and the largest potassium feldspar was 49 meters long.
Lithium-cesium-tantalum pegmatites account for about one-fourth of the world’s lithium production, most of the tantalum production, and all of the cesium production. Giant deposits include Tanco in Canada, Greenbushes in Australia, and Bikita in Zimbabwe. The largest lithium pegmatite in the United States, at King’s Mountain, North Carolina, is no longer being mined although large reserves of lithium remain. Depending on size and attitude of the pegmatite, a variety of mining techniques are used, including artisanal surface mining, open-pit surface mining, small underground workings, and large underground operations using room-and-pillar design. In favorable circumstances, what would otherwise be gangue minerals (quartz, potassium feldspar, albite, and muscovite) can be mined along with lithium and (or) tantalum as coproducts.
Most LCT pegmatites are hosted in metamorphosed supracrustal rocks in the upper greenschist to lower amphibolite facies. Lithium-cesium-tantalum pegmatite intrusions generally are emplaced late during orogeny, with emplacement being controlled by pre-existing structures. Typically, they crop out near evolved, peraluminous granites and leucogranites from which they are inferred to be derived by fractional crystallization. In cases where a parental granite pluton is not exposed, one is inferred to lie at depth. Lithium-cesium-tantalum LCT pegmatite melts are enriched in fluxing components including H2O, F, P, and B, which depress the solidus temperature, lower the density, and increase rates of ionic diffusion. This, in turn, enables pegmatites to form thin dikes and massive crystals despite having a felsic composition and temperatures that are significantly lower than ordinary granitic melts. Lithium-cesium-tantalum pegmatites crystallized at remarkably low temperatures (about 350–550 °C) in a remarkably short time (days to years).
Lithium-cesium-tantalum pegmatites form in orogenic hinterlands as products of plate convergence. Most formed during collisional orogeny (for example, Kings Mountain district, North Carolina). Specific causes of LCT pegmatite-related magmatism could include: ordinary arc processes; over thickening of continental crust during collision or subduction; slab breakoff during or after collision; slab delamination before, during, or after collision; and late collisional extensional collapse and consequent decompression melting. Lithium-cesium-tantalum pegmatite deposits are present in all continents including Antarctica and in rocks spanning 3 billion years of Earth history. The global age distribution of LCT pegmatites is similar to those of common pegmatites, orogenic granites, and detrital zircons. Peak times of LCT pegmatite genesis at about 2640, 1800, 960, 485, and 310 Ma (million years before present) correspond to times of collisional orogeny and supercontinent assembly. Between these pulses were long intervals when few or no LCT pegmatites formed. These minima overlap with supercontinent tenures at ca. 2450–2225, 1625–1000, 875–725, and 250–200 Ma.
Exploration and assessment for LCT pegmatites are guided by a number of observations. In frontier areas where exploration has been minimal at best, the key first-order criteria are an orogenic hinterland setting, appropriate regional metamorphic grades, and the presence of evolved granites and common granitic pegmatites. New LCT pegmatites are most likely to be found near known deposits. Pegmatites tend to show a regional mineralogical and geochemical zoning pattern with respect to the inferred parental granite, with the greatest enrichment in the more distal pegmatites. Mineral-chemical trends in common pegmatites that can point toward an evolved LCT pegmatite include: increasing rubidium in potassium feldspar, increasing lithium in white mica, increasing manganese in garnet, and increasing tantalum and manganese in columbite-tantalite. Most LCT pegmatite bodies show a distinctive internal zonation featuring four zones: border, wall, intermediate (where lithium, cesium, and tantalum are generally concentrated), and core. This zonation is expressed both in cross section and map view; thus, what may appear to be a common pegmatite may instead be the edge of a mineralized body.
Neither lithium-cesium-tantalum pegmatites nor their parental granites are likely to cause serious environmental concerns. Soils and country rock surrounding a LCT pegmatite, as well as waste from mining operations, may be enriched in characteristic elements relative to global average soil and bedrock values. These elements may include lithium, cesium, tantalum, beryllium, boron, fluorine, phosphorus, manganese, gallium, rubidium, niobium, tin, and hafnium. Among this suite of elements, however, the only ones that might present a concern for environmental health are beryllium and fluorine, which are included in the U.S. Environmental Protection Agency drinking-water regulations with maximum contaminant levels of 4 micrograms per liter and 4 milligrams per liter, respectively.
","largerWorkType":{"id":18,"text":"Report"},"largerWorkTitle":"Mineral deposit model for resource assessment (Scientific Investigations Report 2010-5070)","largerWorkSubtype":{"id":5,"text":"USGS Numbered Series"},"language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/sir20105070O","usgsCitation":"Bradley, D.C., McCauley, A.D., and Stillings, L.M., 2017, Mineral-deposit model for lithium-cesium-tantalum pegmatites: U.S. Geological Survey Scientific Investigations Report 2010–5070–O, 48 p., https://doi.org/10.3133/sir20105070O.","productDescription":"v, 48 p.","numberOfPages":"58","onlineOnly":"Y","ipdsId":"IP-055446","costCenters":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"links":[{"id":342538,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/sir/2010/5070/o/sir20105070o.pdf","text":"Report","size":"3.80 MB","linkFileType":{"id":1,"text":"pdf"},"description":"SIR 2010–5070–O"},{"id":342537,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/sir/2010/5070/o/coverthb.jpg"}],"contact":"Director, Central Mineral and Environmental Resources Science Center
U.S. Geological Survey
Box 25046, MS–973
Denver, CO 80225
We studied how drought and an associated stressor, wildfire, influenced stream flow permanence and thermal regimes in a Great Basin stream network. We quantified these responses by collecting information with a spatially extensive network of data loggers. To understand the effects of wildfire specifically, we used data from 4 additional sites that were installed prior to a 2012 fire that burned nearly the entire watershed. Within the sampled network 73 reaches were classified as perennial, yet only 51 contained surface water during logger installation in 2014. Among the sites with pre-fire temperature data, we observed 2–4 °C increases in maximum daily stream temperature relative to an unburned control in the month following the fire; effects (elevated up to 6.6 °C) appeared to persist for at least one year. When observed August mean temperatures in 2015 (the peak of regionally severe drought) were compared to those predicted by a regional stream temperature model, we observed deviations of −2.1°-3.5°. The model under-predicted and over-predicted August mean by > 1 °C in 54% and 10% of sites, respectively, and deviance from predicted was negatively associated with elevation. Combined drought and post-fire conditions appeared to greatly restrict thermally-suitable habitat for Lahontan cutthroat trout (Oncorhynchus clarkii henshawi).
","language":"English","publisher":"Elsevier","doi":"10.1016/j.jaridenv.2017.05.008","usgsCitation":"Schultz, L., Heck, M., Hockman-Wert, D., Allai, T., Wenger, S., Cook, and Dunham, J.B., 2017, Spatial and temporal variability in the effects of wildfire and drought on thermal habitat for a desert trout: Journal of Arid Environments, v. 145, p. 60-68, https://doi.org/10.1016/j.jaridenv.2017.05.008.","productDescription":"9 p.","startPage":"60","endPage":"68","ipdsId":"IP-083354","costCenters":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"links":[{"id":438296,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/F7BR8QFV","text":"USGS data release","linkHelpText":"Stream temperature data from Willow-Whitehorse and Little Blitzen watersheds, southeast Oregon, 2011-2015"},{"id":342751,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Oregon","otherGeospatial":"Willow-Whitehorse Watershed","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -118.62213134765626,\n 42.04521345501039\n ],\n [\n -117.14447021484375,\n 42.04521345501039\n ],\n [\n -117.14447021484375,\n 43.113014204188914\n ],\n [\n -118.62213134765626,\n 43.113014204188914\n ],\n [\n -118.62213134765626,\n 42.04521345501039\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"145","publishingServiceCenter":{"id":12,"text":"Tacoma PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"594cd73fe4b062508e3951d8","contributors":{"authors":[{"text":"Schultz, Luke 0000-0002-6751-4626 lschultz@usgs.gov","orcid":"https://orcid.org/0000-0002-6751-4626","contributorId":193171,"corporation":false,"usgs":true,"family":"Schultz","given":"Luke","email":"lschultz@usgs.gov","affiliations":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true},{"id":289,"text":"Forest and Rangeland Ecosys Science Center","active":true,"usgs":true}],"preferred":true,"id":698993,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Heck, Michael 0000-0001-8858-7325 mheck@usgs.gov","orcid":"https://orcid.org/0000-0001-8858-7325","contributorId":4796,"corporation":false,"usgs":true,"family":"Heck","given":"Michael","email":"mheck@usgs.gov","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":698994,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Hockman-Wert, David 0000-0003-2436-6237 dhockman-wert@usgs.gov","orcid":"https://orcid.org/0000-0003-2436-6237","contributorId":3891,"corporation":false,"usgs":true,"family":"Hockman-Wert","given":"David","email":"dhockman-wert@usgs.gov","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":698995,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Allai, T","contributorId":193172,"corporation":false,"usgs":false,"family":"Allai","given":"T","affiliations":[],"preferred":false,"id":698996,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Wenger, Seth J.","contributorId":177838,"corporation":false,"usgs":false,"family":"Wenger","given":"Seth J.","affiliations":[],"preferred":false,"id":698997,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Cook","contributorId":193173,"corporation":false,"usgs":false,"family":"Cook","email":"","affiliations":[],"preferred":false,"id":698998,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Dunham, Jason B. 0000-0002-6268-0633 jdunham@usgs.gov","orcid":"https://orcid.org/0000-0002-6268-0633","contributorId":147808,"corporation":false,"usgs":true,"family":"Dunham","given":"Jason","email":"jdunham@usgs.gov","middleInitial":"B.","affiliations":[{"id":289,"text":"Forest and Rangeland Ecosys Science Center","active":true,"usgs":true},{"id":365,"text":"Leetown Science Center","active":true,"usgs":true},{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":698992,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ,{"id":70186812,"text":"sir20175028 - 2017 - Geophysics- and geochemistry-based assessment of the geochemical characteristics and groundwater-flow system of the U.S. part of the Mesilla Basin/Conejos-Médanos aquifer system in Doña Ana County, New Mexico, and El Paso County, Texas, 2010–12","interactions":[],"lastModifiedDate":"2017-06-23T10:09:56","indexId":"sir20175028","displayToPublicDate":"2017-06-16T00:00:00","publicationYear":"2017","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":"2017-5028","title":"Geophysics- and geochemistry-based assessment of the geochemical characteristics and groundwater-flow system of the U.S. part of the Mesilla Basin/Conejos-Médanos aquifer system in Doña Ana County, New Mexico, and El Paso County, Texas, 2010–12","docAbstract":"One of the largest rechargeable groundwater systems by total available volume in the Rio Grande/Río Bravo Basin (hereinafter referred to as the “Rio Grande”) region of the United States and Mexico, the Mesilla Basin/Conejos-Médanos aquifer system, supplies water for irrigation as well as for cities of El Paso, Texas; Las Cruces, New Mexico; and Ciudad Juárez, Chihuahua, Mexico. The U.S. Geological Survey in cooperation with the Bureau of Reclamation assessed the groundwater resources in the Mesilla Basin and surrounding areas in Doña Ana County, N. Mex., and El Paso County, Tex., by using a combination of geophysical and geochemical methods. The study area consists of approximately 1,400 square miles in Doña Ana County, N. Mex., and 100 square miles in El Paso County, Tex. The Mesilla Basin composes most of the study area and can be divided into three parts: the Mesilla Valley, the West Mesa, and the East Bench. The Mesilla Valley is the part of the Mesilla Basin that was incised by the Rio Grande between Selden Canyon to the north and by a narrow valley (about 4 miles wide) to the southeast near El Paso, Tex., named the Paso del Norte, which is sometimes referred to in the literature as the “El Paso Narrows.”
Previously published geophysical data for the study area were compiled and these data were augmented by collecting additional geophysical and geochemical data. Geophysical resistivity measurements from previously published helicopter frequency domain electromagnetic data, previously published direct-current resistivity soundings, and newly collected (2012) time-domain electromagnetic soundings were used in the study to detect spatial changes in the electrical properties of the subsurface, which reflect changes that occur within the hydrogeology. The geochemistry of the groundwater system was evaluated by analyzing groundwater samples collected in November 2010 for physicochemical properties, major ions, trace elements, nutrients, pesticides (reported but not used in the assessment), and environmental tracers. The data obtained from these samples (with the exception of the pesticide data) were used to gain insights into processes controlling the groundwater movement through the groundwater system in the study area. Results from the geophysical and geochemical assessments facilitated the interpretation of the geochemical characteristics of the groundwater sources and geochemical groups within the groundwater system.
The groundwater-flow system in the study area consists primarily of the Mesilla Basin aquifer system, which can be divided into four hydrogeologic units by using an informal classification scheme based on basin-fill stratigraphy and sedimentology with an emphasis on aquifer characteristics. The four hydrogeologic units are (1) the Rio Grande alluvium, which is the shallow aquifer of the Mesilla Basin within the confines of the Mesilla Valley, and the three hydrogeologic units that compose the Santa Fe Group: (2) the lower part of the Santa Fe Group, which is the least productive zone, (3) the middle part of the Santa Fe Group, which is the primary water-bearing hydrogeologic unit in the basin and is generally saturated, and (4) the upper part of the Santa Fe Group, which is the most productive water-bearing unit within the Santa Fe Group but is only partially saturated in the north and largely unsaturated in the south and western parts of the Mesilla Basin.
The helicopter frequency domain electromagnetic survey results indicated that approximately half of the resistivity values were less than 10 ohm-meters at depths of 50 and 100 feet with a transition where the resistivity values changed from relatively high values (greater than 20 ohm-meters) to relatively low resistivity values (less than 10 ohm-meters) near Vado, New Mexico. Slightly more than 25 percent of the gridded resistivity values from the three-dimensional grid of the combined inverse modeling results of the direct-current resistivity and time-domain electromagnetic soundings were equal to or less than 10 ohm-meters with large regions of low resistivity becoming apparent in the southernmost part of the study area near the Paso Del Norte where these low resistivity features are spatially the widest at or below the top of the bedrock. These low resistivity values might represent clayey deposits, sediments composed largely of sand and gravel saturated with saline water, or both. Historical dissolved-solids-concentration data within the surface geophysical subset area of the study area were compiled and compared to the inverse modeling results of the combined direct-current resistivity and time-domain soundings; this comparison was done to strengthen the interpretation made from the combined inverse modeling results that the low resistivity features were representative of sand and gravel deposits saturated with saline water and not clayey deposits.
Water-level altitudes within the Rio Grande alluvium generally decreased from north to south, with a west to east decrease in water-level altitudes near Las Cruces, New Mexico, as a result of groundwater pumping. Groundwater flow within the Santa Fe Group is more complex than the groundwater flow within the Rio Grande alluvium because of the larger lateral and vertical extent of the Santa Fe Group compared to the Rio Grande alluvium. Groundwater from the Organ Mountains flows directly south towards the Paso del Norte. Groundwater from the Robledo Mountains, the Rough and Ready Hills, and the Sleeping Lady Hills generally flows to the southeast. Groundwater flowing near the north end of the midbasin uplift generally continues east towards the Rio Grande and then flows south on the east side of the midbasin uplift. Groundwater flowing near the west side of the midbasin uplift generally continues south parallel to the faults that make up the midbasin uplift and then flows east towards the Paso del Norte when it reaches the south end of the midbasin uplift. Groundwater from the Aden Hills and the East and West Potrillo Mountains flows to the south end of the midbasin uplift and then continues east towards the Paso del Norte. Throughout most of the Mesilla Valley, the vertical hydraulic gradient was downward because the water-level altitude in the Rio Grande alluvium was higher than it was in the Santa Fe Group, but in some areas (typically in the middle and southern parts of the Mesilla Valley), the vertical hydraulic gradient was substantially reduced or even reversed to an upward hydraulic gradient.
The geochemistry data indicate that there was a complex system of multiple geochemical endmembers and mixing between these endmembers with recharge to the Rio Grande alluvium and Santa Fe Group composed mostly of seepage from the Rio Grande, inflows from deeper or neighboring water systems, and mountain-front recharge. Five distinct geochemical groups were identified in the Mesilla Basin study area: (1) ancestral Rio Grande (pre-Pleistocene) geochemical group, (2) modern Rio Grande (Pleistocene to present) geochemical group, (3) mountain-front geochemical group, (4) deep groundwater upwelling geochemical group, and (5) unknown freshwater geochemical group. The ancestral Rio Grande groundwater was water that recharged into the system as seepage losses from the ancestral Rio Grande; this groundwater generally flows from north to south-southeast towards the Paso del Norte. Groundwater on the west side of the midbasin uplift generally flows south until it reaches the southern part of the study area; from the southern part of the study area, the groundwater flows east towards the Paso del Norte. Groundwater on the east side of the midbasin uplift flows south-southeast towards the Paso del Norte where it mixes with groundwater from the modern Rio Grande, uplifted areas in the west, and the deep saline source. The water type of the modern Rio Grande geochemical group ranged from calcium-sulfate water type in the northern part of the study area to sodium-chloride-sulfate water type in the southern part of the study area; from north to south there was a substantial increase in specific conductance, strontium-87/strontium-86 ratio, potassium, and the trace metals of iron and lithium, changing the water chemistry such that it became similar to the water chemistry of the deep groundwater upwelling geochemical group. From age-dating results, water in the modern Rio Grande geochemical group was recharged to the Rio Grande alluvium within the past 10 years. The mountain-front geochemical group was generally old water (apparent age was greater than 10,000 carbon-14 years before present) that was somewhat mineralized and has relatively high concentrations of fluoride and silica, which might indicate longer exposure to volcanic and siliciclastic rocks or aluminosilicate minerals. There were five different locations of recharge determined from the groundwater geochemistry within the mountain-front geochemical group, all having a slightly different geochemical signature: (1) the Rough and Ready Hills, Robledo Mountains, and the Sleeping Lady Hills, (2) the Doña Ana Mountains, (3) the Aden Hills and West Potrillo Mountains, (4) the East Potrillo Mountains, and (5) the Sierra Juárez in Mexico. The groundwater from the Rough and Ready Hills, Robledo Mountains, the Sleeping Lady Hills, and the Doña Ana Mountains generally flows toward the Rio Grande and eventually mixes together and with the modern Rio Grande groundwater. The groundwater originating from the Aden Hills and East and West Potrillo Mountains generally flows east to southeast at a slow rate and eventually mixes and continues east, where it mixes with groundwater from the ancestral Rio Grande geochemical group and with the groundwater from the Sierra Juárez. The groundwater from the Sierra Juárez flows north and then east towards the Paso del Norte where it mixes with groundwater from the uplifted areas in the west, ancestral and modern Rio Grande groundwater, and the upwelling groundwater from a deep saline source. The deep groundwater upwelling geochemical group had the highest concentrations of bicarbonate, potassium, silica, aluminum, iron, and lithium within the study area, indicating that it had been in contact with carbonate and siliciclastic rocks for a much longer period of time and at higher temperatures compared to the other geochemical groups, and was most likely ancient marine groundwater originating from the Paleozoic and Cretaceous carbonate rocks which was upwelling into the Mesilla Basin aquifer system in the southeastern part of the study area through the extensive fault systems. Direct-current resistivity and time-domain electromagnetic soundings support the interpretation of ancient marine groundwater upwelling into the Mesilla Basin aquifer system, as do the analytical results from wells, and the helicopter frequency domain electromagnetic data collected along the Rio Grande. The hydrogen-2/hydrogen-1 ratio and oxygen-18/oxygen-16 ratio isotopic results for samples in the unknown freshwater geochemical group did not plot on the Rio Grande evaporation line, indicating this group did not have a Rio Grande signature (that is, there was no isotopic evidence of a component of Rio Grande water) and it also had the lowest mineralized content of any geochemical group in the study area.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/sir20175028","collaboration":"Prepared in cooperation with the Bureau of Reclamation","usgsCitation":"Teeple, A.P., 2017, Geophysics- and geochemistry-based assessment of the geochemical characteristics and groundwater-flow system of the U.S. part of the Mesilla Basin/Conejos-Médanos aquifer system in Doña Ana County, New Mexico, and El Paso County, Texas, 2010–12: U.S. Geological Survey Scientific Investigations Report 2017–5028, 183 p., https://doi.org/10.3133/sir20175028.","productDescription":"Report: x, 183 p.; 2 Figures; Project Sites, Read Me","onlineOnly":"Y","additionalOnlineFiles":"Y","ipdsId":"IP-070474","costCenters":[{"id":583,"text":"Texas Water Science Center","active":true,"usgs":true}],"links":[{"id":438297,"rank":8,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/F7PV6HJ3","text":"USGS data release","linkHelpText":"Time-Domain Electromagnetic Data Used in the Assessment of the U.S. Part of the Mesilla Basin/Conejos-Mdanos Aquifer System in Doa Ana County, New Mexico, and El Paso County, Texas"},{"id":342582,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/sir/2017/5028/sir20175028.pdf","text":"Report","size":"16.6 MB","linkFileType":{"id":1,"text":"pdf"},"description":"SIR 2017–5028"},{"id":342585,"rank":5,"type":{"id":20,"text":"Read Me"},"url":"https://pubs.usgs.gov/sir/2017/5028/sir20175028_readme_figures14_17.pdf","size":"890 kB","linkFileType":{"id":1,"text":"pdf"},"description":"SIR 2017–5028 Read Me"},{"id":342586,"rank":6,"type":{"id":18,"text":"Project Site"},"url":"https://water.usgs.gov/ogw/","text":"Office of Groundwater"},{"id":342587,"rank":7,"type":{"id":18,"text":"Project Site"},"url":"https://www.usgs.gov/science/mission-areas/water/national-water-quality-program?qt-programs_l2_landing_page=0#qt-programs_l2_landing_page","text":"National Water-Quality Assessment Program"},{"id":342581,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/sir/2017/5028/coverthb.jpg"},{"id":342584,"rank":4,"type":{"id":29,"text":"Figure"},"url":"https://pubs.usgs.gov/sir/2017/5028/sir20175028_figure17.pdf","text":"Figure 17","size":"23.1 MB","linkFileType":{"id":1,"text":"pdf"},"description":"SIR 2017–5028 Figure 17"},{"id":342583,"rank":3,"type":{"id":29,"text":"Figure"},"url":"https://pubs.usgs.gov/sir/2017/5028/sir20175028_figure14.pdf","text":"Figure 14","size":"22.3 MB","linkFileType":{"id":1,"text":"pdf"},"description":"SIR 2017–5028 Figure 14"}],"country":"United States","state":"New Mexico, Texas","county":"Doña Ana County, El Paso County","otherGeospatial":"Mesilla Basin/Conejos-Médanos Aquifer System","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -107.25,\n 31.65\n ],\n [\n -106.375,\n 31.65\n ],\n [\n -106.375,\n 32.625\n ],\n [\n -107.25,\n 32.625\n ],\n [\n -107.25,\n 31.65\n ]\n ]\n ]\n }\n }\n ]\n}","contact":"Director, Texas Water Science Center
U.S. Geological Survey
1505 Ferguson Lane
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This study presents an extensive database on groundwater conditions in and around Devils Postpile National Monument. The database contains chemical analyses of springs and the monument water-supply well, including major-ion chemistry, trace element chemistry, and the first information on a list of organic compounds known as emerging contaminants. Diurnal, seasonal, and annual variations in groundwater discharge and chemistry are evaluated from data collected at five main monitoring sites, where streams carry the aggregate flow from entire groups of springs. These springs drain the Mammoth Mountain area and, during the fall months, contribute a significant fraction of the San Joaquin River flow within the monument. The period of this study, from fall 2012 to fall 2015, includes some of the driest years on record, though the seasonal variability observed in 2013 might have been near normal. The spring-fed streams generally flowed at rates well below those observed during a sequence of wet years in the late 1990s. However, persistence of flow and reasonably stable water chemistry through the recent dry years are indicative of a sizeable groundwater system that should provide a reliable resource during similar droughts in the future. Only a few emerging contaminants were detected at trace levels below 1 microgram per liter (μg/L), suggesting that local human visitation is not degrading groundwater quality. No indication of salt from the ski area on the north side of Mammoth Mountain could be found in any of the groundwaters. Chemical data instead show that natural mineral water, such as that discharged from local soda springs, is the main source of anomalous chloride in the monument supply well and in the San Joaquin River. The results of the study are used to develop a set of recommendations for future monitoring to enable detection of deleterious impacts to groundwater quality and quantity
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/sir20175048","usgsCitation":"Evans, W.C., and Bergfeld, D., 2017, Groundwater resources of the Devils Postpile National Monument—Current conditions and future vulnerabilities: U.S. Geological Survey Scientific Investigations Report 2017–5048, 31 p., https://doi.org/10.3133/sir20175048.","productDescription":"Report: v, 31 p.; Table","startPage":"1","endPage":"31","numberOfPages":"40","onlineOnly":"Y","ipdsId":"IP-079650","costCenters":[{"id":438,"text":"National Research Program - Western Branch","active":true,"usgs":true}],"links":[{"id":342512,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/sir/2017/5048/coverthb.jpg"},{"id":342513,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/sir/2017/5048/sir20175048.pdf","text":"Report","size":"10 MB","linkFileType":{"id":1,"text":"pdf"},"description":"SIR 2017-5048"},{"id":342514,"rank":3,"type":{"id":27,"text":"Table"},"url":"https://pubs.usgs.gov/sir/2017/5048/sir20175048_table 2.xlsx","text":"Table 2","size":"62 KB","linkFileType":{"id":3,"text":"xlsx"},"description":"SIR 2017-5048"}],"country":"United States","state":"California","otherGeospatial":"Devils Postpile National Park","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -120.41015624999999,\n 37.86618078529668\n ],\n [\n -120.1409912109375,\n 37.56635122499224\n ],\n [\n -119.5806884765625,\n 37.208456662000195\n ],\n [\n -119.4049072265625,\n 37.020098201368114\n ],\n [\n -119.13574218749999,\n 36.59788913307022\n ],\n [\n -119.05883789062501,\n 36.39033486213649\n ],\n [\n -118.97644042968749,\n 36.363798554158635\n ],\n [\n -118.74572753906249,\n 36.37264499608118\n ],\n [\n -118.63037109375,\n 36.36822190085111\n ],\n [\n -118.54248046874999,\n 36.36822190085111\n ],\n [\n -118.3612060546875,\n 36.37706783983682\n ],\n [\n -118.1304931640625,\n 36.42570252039198\n ],\n [\n -117.9876708984375,\n 36.50963615733049\n ],\n [\n -117.75146484375,\n 36.54936246839778\n ],\n [\n -117.586669921875,\n 36.474306755095235\n ],\n [\n -117.2735595703125,\n 36.421282443649496\n ],\n [\n -117.29553222656249,\n 36.84006462037767\n ],\n [\n -117.53173828125,\n 37.08585785263673\n ],\n [\n -117.71301269531249,\n 37.31775185163688\n ],\n [\n -117.93273925781249,\n 37.53150992479082\n ],\n [\n -118.23486328125,\n 37.8271414168374\n ],\n [\n -118.487548828125,\n 38.05674222065296\n ],\n [\n -118.597412109375,\n 38.302869955150044\n ],\n [\n -118.751220703125,\n 38.47939467327645\n ],\n [\n -118.89404296875,\n 38.47509432050245\n ],\n [\n -118.98193359375,\n 38.46649284538942\n ],\n [\n -119.24560546875001,\n 38.453588708941375\n ],\n [\n -119.8553466796875,\n 38.44498466889473\n ],\n [\n -120.16845703125,\n 38.41055825094609\n ],\n [\n -120.5914306640625,\n 38.302869955150044\n ],\n [\n -120.640869140625,\n 38.19502155795575\n ],\n [\n -120.574951171875,\n 38.06106741381201\n ],\n [\n -120.41015624999999,\n 37.86618078529668\n ]\n ]\n ]\n }\n }\n ]\n}","contact":"NRP staff
National Research Program
U.S. Geological Survey
345 Middlefield Road, MS-435
Menlo Park, CA 94025
Coral barium to calcium (Ba/Ca) ratios have been used to reconstruct records of upwelling, river and groundwater discharge, and sediment and dust input to the coastal ocean. However, this proxy has not yet been explicitly tested to determine if Ba inclusion in the coral skeleton is directly proportional to seawater Ba concentration and to further determine how additional factors such as temperature and calcification rate control coral Ba/Ca ratios. We measured the inclusion of Ba within aquaria reared juvenile corals (Favia fragum) at three temperatures (∼27.7, 24.6 and 22.5 °C) and three seawater Ba concentrations (73, 230 and 450 nmol kg−1). Coral polyps were settled on tiles conditioned with encrusting coralline algae, which complicated chemical analysis of the coral skeletal material grown during the aquaria experiments. We utilized Sr/Ca ratios of encrusting coralline algae (as low as 3.4 mmol mol−1) to correct coral Ba/Ca for this contamination, which was determined to be 26 ± 11% using a two end member mixing model. Notably, there was a large range in Ba/Ca across all treatments, however, we found that Ba inclusion was linear across the full concentration range. The temperature sensitivity of the distribution coefficient is within the range of previously reported values. Finally, calcification rate, which displayed large variability, was not correlated to the distribution coefficient. The observed temperature dependence predicts a change in coral Ba/Ca ratios of 1.1 μmol mol−1 from 20 to 28 °C for typical coastal ocean Ba concentrations of 50 nmol kg−1. Given the linear uptake of Ba by corals observed in this study, coral proxy records that demonstrate peaks of 10–25 μmol mol−1 would require coastal seawater Ba of between 60 and 145 nmol kg−1. Further validation of the coral Ba/Ca proxy requires evaluation of changes in seawater chemistry associated with the environmental perturbation recorded by the coral as well as verification of these results for Porites species, which are widely used in paleo reconstructions.
","language":"English","publisher":"Geochemical Society","doi":"10.1016/j.gca.2017.04.006","usgsCitation":"Gonneea Eagle, M., Cohen, A.L., DeCarlo, T.M., and Charette, M.A., 2017, Relationship between water and aragonite barium concentrations in aquaria reared juvenile corals: Geochimica et Cosmochimica Acta, v. 209, p. 123-134, https://doi.org/10.1016/j.gca.2017.04.006.","productDescription":"12 p.","startPage":"123","endPage":"134","ipdsId":"IP-079452","costCenters":[{"id":678,"text":"Woods Hole Coastal and Marine Science Center","active":true,"usgs":true}],"links":[{"id":469749,"rank":0,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"https://hdl.handle.net/1912/9163","text":"External Repository"},{"id":342424,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"209","publishingServiceCenter":{"id":11,"text":"Pembroke PSC"},"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5965b1c8e4b0d1f9f05b37b0","contributors":{"authors":[{"text":"Gonneea Eagle, Meagan 0000-0001-5072-2755 mgonneea@usgs.gov","orcid":"https://orcid.org/0000-0001-5072-2755","contributorId":174590,"corporation":false,"usgs":true,"family":"Gonneea Eagle","given":"Meagan","email":"mgonneea@usgs.gov","affiliations":[{"id":678,"text":"Woods Hole Coastal and Marine Science Center","active":true,"usgs":true}],"preferred":true,"id":697917,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Cohen, Anne L.","contributorId":190716,"corporation":false,"usgs":false,"family":"Cohen","given":"Anne","email":"","middleInitial":"L.","affiliations":[],"preferred":false,"id":697918,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"DeCarlo, Thomas M.","contributorId":190720,"corporation":false,"usgs":false,"family":"DeCarlo","given":"Thomas","email":"","middleInitial":"M.","affiliations":[],"preferred":false,"id":697919,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Charette, Matthew A.","contributorId":92355,"corporation":false,"usgs":true,"family":"Charette","given":"Matthew","email":"","middleInitial":"A.","affiliations":[],"preferred":false,"id":697920,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70188568,"text":"70188568 - 2017 - Climate change may restrict dryland forest regeneration in the 21st century","interactions":[],"lastModifiedDate":"2017-06-15T13:40:23","indexId":"70188568","displayToPublicDate":"2017-06-15T00:00:00","publicationYear":"2017","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1465,"text":"Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Climate change may restrict dryland forest regeneration in the 21st century","docAbstract":"The persistence and geographic expansion of dryland forests in the 21st century will be influenced by how climate change supports the demographic processes associated with tree regeneration. Yet, the way that climate change may alter regeneration is unclear. We developed a quantitative framework that estimates forest regeneration potential (RP) as a function of key environmental conditions for ponderosa pine, a key dryland forest species. We integrated meteorological data and climate projections for 47 ponderosa pine forest sites across the western United States, and evaluated RP using an ecosystem water balance model. Our primary goal was to contrast conditions supporting regeneration among historical, mid-21st century and late-21st century time frames. Future climatic conditions supported 50% higher RP in 2020–2059 relative to 1910–2014. As temperatures increased more substantially in 2060–2099, seedling survival decreased, RP declined by 50%, and the frequency of years with very low RP increased from 25% to 58%. Thus, climate change may initially support higher RP and increase the likelihood of successful regeneration events, yet will ultimately reduce average RP and the frequency of years with moderate climate support of regeneration. Our results suggest that climate change alone may begin to restrict the persistence and expansion of dryland forests by limiting seedling survival in the late 21st century.
","language":"English","publisher":"Ecological Society of America","doi":"10.1002/ecy.1791","usgsCitation":"Petrie, M., Bradford, J.B., Hubbard, R., Lauenroth, W., Andrews, C.M., and Schlaepfer, D., 2017, Climate change may restrict dryland forest regeneration in the 21st century: Ecology, v. 98, no. 6, p. 1548-1559, https://doi.org/10.1002/ecy.1791.","productDescription":"12 p.","startPage":"1548","endPage":"1559","ipdsId":"IP-081499","costCenters":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"links":[{"id":342558,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -128.408203125,\n 26.27371402440643\n ],\n [\n -96.328125,\n 26.27371402440643\n ],\n [\n -96.328125,\n 51.12421275782688\n ],\n [\n -128.408203125,\n 51.12421275782688\n ],\n [\n -128.408203125,\n 26.27371402440643\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"98","issue":"6","publishingServiceCenter":{"id":14,"text":"Menlo Park PSC"},"noUsgsAuthors":false,"publicationDate":"2017-05-30","publicationStatus":"PW","scienceBaseUri":"59439c91e4b062508e31a97e","contributors":{"authors":[{"text":"Petrie, M.D.","contributorId":192983,"corporation":false,"usgs":false,"family":"Petrie","given":"M.D.","email":"","affiliations":[],"preferred":false,"id":698374,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Bradford, John B. 0000-0001-9257-6303 jbradford@usgs.gov","orcid":"https://orcid.org/0000-0001-9257-6303","contributorId":611,"corporation":false,"usgs":true,"family":"Bradford","given":"John","email":"jbradford@usgs.gov","middleInitial":"B.","affiliations":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"preferred":true,"id":698373,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Hubbard, R.M.","contributorId":167015,"corporation":false,"usgs":false,"family":"Hubbard","given":"R.M.","email":"","affiliations":[{"id":24595,"text":"USDA Forest Service, Fort Collins CO","active":true,"usgs":false}],"preferred":false,"id":698375,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Lauenroth, W.K.","contributorId":192984,"corporation":false,"usgs":false,"family":"Lauenroth","given":"W.K.","email":"","affiliations":[],"preferred":false,"id":698376,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Andrews, Caitlin M. 0000-0003-4593-1071 candrews@usgs.gov","orcid":"https://orcid.org/0000-0003-4593-1071","contributorId":192985,"corporation":false,"usgs":true,"family":"Andrews","given":"Caitlin","email":"candrews@usgs.gov","middleInitial":"M.","affiliations":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"preferred":true,"id":698377,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Schlaepfer, D.R.","contributorId":140421,"corporation":false,"usgs":false,"family":"Schlaepfer","given":"D.R.","email":"","affiliations":[{"id":13488,"text":"Dept. of Botany, University of Wyoming, 1000 E. UNIVersity Avenue, Laramie, WY 82070","active":true,"usgs":false}],"preferred":false,"id":698378,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70188351,"text":"ofr20171069 - 2017 - Inter-annual variability in apparent relative production, survival, and growth of juvenile Lost River and shortnose suckers in Upper Klamath Lake, Oregon, 2001–15","interactions":[],"lastModifiedDate":"2017-06-16T08:26:47","indexId":"ofr20171069","displayToPublicDate":"2017-06-15T00:00:00","publicationYear":"2017","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":"2017-1069","title":"Inter-annual variability in apparent relative production, survival, and growth of juvenile Lost River and shortnose suckers in Upper Klamath Lake, Oregon, 2001–15","docAbstract":"Populations of the once abundant Lost River (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris) of the Upper Klamath Basin, decreased so substantially throughout the 20th century that they were listed under the Endangered Species Act in 1988. Major landscape alterations, deterioration of water quality, and competition with and predation by exotic species are listed as primary causes of the decreases in populations. Upper Klamath Lake populations are decreasing because fish lost due to adult mortality, which is relatively low for adult Lost River suckers and variable for adult shortnose suckers, are not replaced by new young adult suckers recruiting into known adult spawning aggregations. Catch-at-age and size data indicate that most adult suckers presently in Upper Klamath Lake spawning populations were hatched around 1991. While, a lack of egg production and emigration of young fish (especially larvae) may contribute, catch-at-length and age data indicate high mortality during the first summer or winter of life may be the primary limitation to the recruitment of young adults. The causes of juvenile sucker mortality are unknown.
We compiled and analyzed catch, length, age, and species data on juvenile suckers from Upper Klamath Lake from eight prior studies conducted from 2001 to 2015 to examine annual variation in apparent production, survival, and growth of young suckers. We used a combination of qualitative assessments, general linear models, and linear regression to make inferences about annual differences in juvenile sucker dynamics. The intent of this exercise is to provide information that can be compared to annual variability in environmental conditions with the hopes of understanding what drives juvenile sucker population dynamics.
Age-0 Lost River suckers generally grew faster than age-0 shortnose suckers, but the difference in growth rates between the two species varied among years. This unsynchronized annual variation in daily growth may be an indication that environmental conditions are affecting growth rates of these species in different ways.
The combined evidence outlined in this report and in Simon and others (2012) indicates that years of relatively high age-0 sucker production occurred in the late 1990s through at least 2000, in 2006, and in 2011. Our analysis of annual age-0 sucker catch per unit effort (CPUE), which accounted for zero inflated data and annual variation in sampling gears and locations, indicated that 2006 had the greatest apparent relative production of age-0 suckers ≥ 45 mm standard length (SL) during the time period examined. Midsummer trap net effort by the U.S. Geological Survey (USGS) was too sparse to examine age-0 sucker CPUE from 2011 to 2013. Relatively frequent catches of age-1 suckers in 2001, 2007, and 2012 corroborated relatively high CPUE for age-0 suckers during 1999–2000, 2006, and 2011, as reported by USGS or Simon and others (2012).
There were several indications in the data that juvenile sucker survival is low from at least midsummer of the first year of life through mid-September of the second year of life. Our estimated index of relative apparent age-0 sucker late-summer survival, which accounted for zero inflated data and variations in sampling gears and locations, was higher in 2009 than in 2004. Our index of apparent age-0 sucker mortality for all other years from 2001 to 2015 was similar among years. Seventy-five percent of age-1 suckers were captured prior to July 17 each year. In 2007, the one year with substantial age-1 sucker summertime catches, the proportion of nets to capture age-1 suckers decreased from July to mid-September. Maximum annual age-2+ sucker CPUE was 0.02 fish per net, 10,000 times less than the maximum annual age-0 sucker CPUE.
Analysis of species data indicated that juvenile Lost River suckers may have greater apparent mortality than shortnose suckers. Lost River suckers made up a smaller proportion of age-0 suckers captured in July each year than would be expected, based on the abundance of adult Lost River suckers relative to shortnose suckers, and higher Lost River than shortnose sucker fecundity. The proportion of age-0 suckers captured that were Lost River suckers decreased from July to September in several years. Only 14 percent of age-1 or older juvenile suckers identified to species over the 15-year time period were Lost River suckers.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ofr20171069","collaboration":"Prepared in cooperation with the Bureau of Reclamation","usgsCitation":"Burdick, S.M., and Martin, B.A., 2017, Inter-annual variability in apparent relative production, survival, and growth of juvenile Lost River and shortnose suckers in Upper Klamath Lake, Oregon, 2001–15: U.S. Geological Survey Open-File Report 2017–1069, 55 p., https://doi.org/10.3133/ofr20171069.","productDescription":"Report: vi, 55 p.; Data Release","onlineOnly":"Y","ipdsId":"IP-082248","costCenters":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"links":[{"id":342516,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/of/2017/1069/ofr20171069.pdf","text":"Report","size":"3.8 MB","linkFileType":{"id":1,"text":"pdf"},"description":"OFR 2017-1069"},{"id":342517,"rank":3,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/F7ZC812F","text":"USGS data release","description":"USGS data release","linkHelpText":"Data for trap net captured juvenile Lost River and shortnose suckers from Upper Klamath Lake, Oregon"},{"id":342515,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/of/2017/1069/coverthb.jpg"}],"country":"United States","state":"Oregon","otherGeospatial":"Upper Klamath Lake","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -122.14,\n 42.20\n ],\n [\n -121.7,\n 42.20\n ],\n [\n -121.7,\n 42.64\n ],\n [\n -122.14,\n 42.64\n ],\n [\n -122.14,\n 42.20\n ]\n ]\n ]\n }\n }\n ]\n}","contact":"Director, Western Fisheries Research Center
U.S. Geological Survey
6505 NE 65th Street
Seattle, Washington 98115
INTRODUCTION
Changes in the size and proportion of limbs and other structures have played a key role in the evolution of species. One common class of limb modification is recurrent wing reduction and loss of flight in birds. Indeed, Darwin used the occurrence of flightless birds as an argument in favor of his theory of natural selection. Loss of flight has evolved repeatedly and is found among 26 families of birds in 17 different orders. Despite the frequency of these modifications, we have a limited understanding of their underpinnings at the genetic and molecular levels.
RATIONALE
To better understand the evolution of changes in limb size, we studied a classic case of recent loss of flight in the Galapagos cormorant (Phalacrocorax harrisi). Cormorants are large water birds that live in coastal areas or near lakes, and P. harrisi is the only flightless cormorant among approximately 40 extant species. The entire population is distributed along the coastlines of Isabela and Fernandina islands in the Galapagos archipelago. P. harrisi has a pair of short wings, which are smaller than those of any other cormorant. The extreme reduction of the wings and pectoral skeleton observed in P. harrisi is an attractive model for studying the evolution of loss of flight because it occurred very recently; phylogenetic evidence suggests that P. harrisi diverged from its flighted relatives within the past 2 million years. We developed a comparative and predictive genomics approach that uses the genome sequences of P. harrisi and its flighted relatives to find candidate genetic variants that likely contributed to the evolution of loss of flight.
RESULTS
We sequenced and de novo assembled the whole genomes of P. harrisi and three closely related flighted cormorant species. We identified thousands of coding variants exclusive to P. harrisi and classified them according to their probability of altering protein function based on conservation. Variants most likely to alter protein function were significantly enriched in genes mutated in human skeletal ciliopathies, including Ofd1, Evc, Wdr34, and Ift122. We carried out experiments in Caenorhabditis elegans to confirm that a missense variant present in the Galapagos cormorant IFT122 protein is sufficient to affect ciliary function. The primary cilium is essential for Hedgehog (Hh) signaling in vertebrates, and individuals affected by ciliopathies have small limbs and ribcages, mirroring the phenotype of P. harrisi. We also identified a 4–amino acid deletion in the regulatory domain of Cux1, a highly conserved transcription factor that has been experimentally shown to regulate limb growth in chicken. The four missing amino acids are perfectly conserved in all birds and mammals sequenced to date. We tested the consequences of this deletion in a chondrogenic cell line and showed that it impairs the ability of CUX1 to transcriptionally up-regulate cilia-related genes (some of which contain function-altering variants in P. harrisi) and to promote chondrogenic differentiation. Finally, we show that positive selection may have played a role in the fixation of the variants associated with loss of flight in P. harrisi.
CONCLUSION
Our results indicate that the combined effect of variants in genes necessary for the correct transcriptional regulation and function of the primary cilium likely contributed to the evolution of highly reduced wings and other skeletal adaptations associated with loss of flight in P. harrisi. Our approach may be generally useful for identification of variants underlying evolutionary novelty from genomes of closely related species.