Hydrodynamic models are valuable tools for understanding the primary factors influencing daily and peak water levels and for guiding discussions on potential adaptation strategies for managing flood risk in coastal areas. This analysis uses the Delft3D San Francisco Bay-Delta Community Model to simulate water levels and incorporates the effects of a number of adaptation measures in the urban San Francisco Bay estuary, California. In particular, we examine the influence of shoreline hardening, nature-based solutions, and subregional floodgates on regional water levels. The result shows that under present conditions, tidal amplification is responsible for generating a wide distribution of extreme water levels across San Francisco Bay. Tidal amplification is found to decrease under sea level rise, thereby producing a relative damping effect on extremes. A comparison of different shoreline scenarios demonstrates that hard frontal shorelines result in higher tidal amplification, whereas restored (soft) shorelines lower amplification. The current shoreline configuration has both hard and soft characteristics and results in an intermediate tidal response. In some areas, wetland restoration reduces extreme water levels by as much as 20 cm, whereas hard-shoreline addition elevates them by as much as 10 cm for 1.5 m of sea level rise. Furthermore, local floodgates can significantly reduce high water levels without major adverse effects elsewhere in San Francisco Bay. These findings point toward the justification for a range of adaptive measures across political boundaries, weighing hard and soft options in addressing the mounting danger of sea level rise.
","language":"English","publisher":"American Society of Civil Engineers","doi":"10.1061/JWPED5.WWENG-2342","usgsCitation":"Nederhoff, K., Saleh, R., Barnard, P., and Stacey, M.T., 2025, Mitigating flood risks in urban estuaries: Tidal dynamics, shoreline hardening, nature-based solutions, and floodgates in San Francisco Bay: Journal of Waterway, Port, Coastal, and Ocean Engineering, v. 151, no. 6, 04025031, 19 p., https://doi.org/10.1061/JWPED5.WWENG-2342.","productDescription":"04025031, 19 p.","ipdsId":"IP-176674","costCenters":[{"id":520,"text":"Pacific Coastal and Marine Science Center","active":true,"usgs":true}],"links":[{"id":496162,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1061/jwped5.wweng-2342","text":"Publisher Index Page"},{"id":496022,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"California","otherGeospatial":"San Francisco Bay","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -122.71980135286915,\n 38.31126858304765\n ],\n [\n -122.71980135286915,\n 37.4059191605038\n ],\n [\n -121.71348182307679,\n 37.4059191605038\n ],\n [\n -121.71348182307679,\n 38.31126858304765\n ],\n [\n -122.71980135286915,\n 38.31126858304765\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"151","issue":"6","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Nederhoff, Kees 0000-0003-0552-3428","orcid":"https://orcid.org/0000-0003-0552-3428","contributorId":334091,"corporation":false,"usgs":false,"family":"Nederhoff","given":"Kees","affiliations":[{"id":39963,"text":"Deltares-USA","active":true,"usgs":false}],"preferred":true,"id":949331,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Saleh, Rohin","contributorId":265891,"corporation":false,"usgs":false,"family":"Saleh","given":"Rohin","email":"","affiliations":[{"id":54818,"text":"Alameda Flood Control District","active":true,"usgs":false}],"preferred":false,"id":949332,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Barnard, Patrick L. 0000-0003-1414-6476 pbarnard@usgs.gov","orcid":"https://orcid.org/0000-0003-1414-6476","contributorId":147147,"corporation":false,"usgs":true,"family":"Barnard","given":"Patrick L.","email":"pbarnard@usgs.gov","affiliations":[{"id":520,"text":"Pacific Coastal and Marine Science Center","active":true,"usgs":true}],"preferred":true,"id":949333,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Stacey, Mark T.","contributorId":360868,"corporation":false,"usgs":false,"family":"Stacey","given":"Mark","middleInitial":"T.","affiliations":[{"id":6609,"text":"UC Berkeley","active":true,"usgs":false}],"preferred":false,"id":949334,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70273047,"text":"70273047 - 2025 - Invasive predatory fish occupies highest trophic position leading to expansion of isotopic niches in a riverine food web","interactions":[],"lastModifiedDate":"2025-12-12T16:46:35.692791","indexId":"70273047","displayToPublicDate":"2025-09-04T09:39:53","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1465,"text":"Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Invasive predatory fish occupies highest trophic position leading to expansion of isotopic niches in a riverine food web","docAbstract":"Invasive species are drivers of ecological change with the potential to reshape the structure and function of terrestrial and aquatic ecosystems. The invasive flathead catfish (Pylodictis olivaris) is an opportunistic predator that has established a rapidly growing population in the Susquehanna River, Pennsylvania, USA, since they were first detected in 2002. Although the predatory effects of invasive catfishes on native fish communities have been documented, the effects of invasion on riverine food webs are poorly understood. This study quantified the effects of invasive flathead catfish on the trophic position (TP) and isotopic niche of the river's food web by comparing invaded and non-invaded sites. In addition to flathead catfish, the food web components examined included crayfish, minnows, and two ecologically and socioeconomically important fish species: the smallmouth bass (Micropterus dolomieu) and channel catfish (Ictalurus punctatus). We found that flathead catfish occupied the highest TP, with a posterior mean TP of 3.08 (95% credible interval = [2.71, 3.42]), exceeding that of the two resident fish predators, the smallmouth bass and channel catfish. The TP of the resident channel catfish, which occupies a similar ecological niche, declined after flathead catfish invasion. In fact, there was a 0.92 posterior probability that channel catfish TP was lower in invaded sites than at non-invaded sites. Using a Bayesian bivariate ellipses analysis, we found overwhelming evidence of isotopic niche expansion and overlap for all components of the food web in the presence of flathead catfish. These findings support the “trophic disruption hypothesis,” where an introduced species prompts resident species to change diets in an attempt to avoid competition and predation following invasion. Our results indicate that flathead catfish invasion is altering food web structure and energy flow in a large riverine ecosystem and contributes to the breadth of knowledge regarding how ecosystems may respond to the introduction of a large predatory fish species.
","language":"English","publisher":"Ecological Society of America","doi":"10.1002/ecy.70180","usgsCitation":"Hodgson, O.C., Stark, S., Schall, M.K., Smith, G.D., Smalling, K., and Wagner, T., 2025, Invasive predatory fish occupies highest trophic position leading to expansion of isotopic niches in a riverine food web: Ecology, v. 106, no. 9, e70180, 15 p., https://doi.org/10.1002/ecy.70180.","productDescription":"e70180, 15 p.","ipdsId":"IP-172847","costCenters":[{"id":199,"text":"Coop Res Unit Leetown","active":true,"usgs":true}],"links":[{"id":497708,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1002/ecy.70180","text":"Publisher Index Page"},{"id":497484,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Pennsylvania","otherGeospatial":"Susquehanna River, West Branch Susquehanna River","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -77.43310562520305,\n 40.79216536591906\n ],\n [\n -77.43310562520305,\n 39.74998567182175\n ],\n [\n -76.11010271256676,\n 39.74998567182175\n ],\n [\n -76.11010271256676,\n 40.79216536591906\n ],\n [\n -77.43310562520305,\n 40.79216536591906\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"106","issue":"9","noUsgsAuthors":false,"publicationDate":"2025-09-04","publicationStatus":"PW","contributors":{"authors":[{"text":"Hodgson, Olivia C.","contributorId":363985,"corporation":false,"usgs":false,"family":"Hodgson","given":"Olivia","middleInitial":"C.","affiliations":[{"id":6738,"text":"The Pennsylvania State University","active":true,"usgs":false}],"preferred":false,"id":952151,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Stark, Sydney","contributorId":363987,"corporation":false,"usgs":false,"family":"Stark","given":"Sydney","affiliations":[{"id":6738,"text":"The Pennsylvania State University","active":true,"usgs":false}],"preferred":false,"id":952152,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Schall, Megan K.","contributorId":363989,"corporation":false,"usgs":false,"family":"Schall","given":"Megan","middleInitial":"K.","affiliations":[{"id":6738,"text":"The Pennsylvania State University","active":true,"usgs":false}],"preferred":false,"id":952153,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Smith, Geoffrey D.","contributorId":363991,"corporation":false,"usgs":false,"family":"Smith","given":"Geoffrey","middleInitial":"D.","affiliations":[{"id":36966,"text":"Pennsylvania Fish and Boat Commission","active":true,"usgs":false}],"preferred":false,"id":952154,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Smalling, Kelly L. 0000-0002-1214-4920","orcid":"https://orcid.org/0000-0002-1214-4920","contributorId":221234,"corporation":false,"usgs":true,"family":"Smalling","given":"Kelly","middleInitial":"L.","affiliations":[{"id":470,"text":"New Jersey Water Science Center","active":true,"usgs":true}],"preferred":true,"id":952155,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Wagner, Tyler 0000-0003-1726-016X twagner@usgs.gov","orcid":"https://orcid.org/0000-0003-1726-016X","contributorId":218091,"corporation":false,"usgs":true,"family":"Wagner","given":"Tyler","email":"twagner@usgs.gov","affiliations":[{"id":199,"text":"Coop Res Unit Leetown","active":true,"usgs":true}],"preferred":true,"id":952156,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70271315,"text":"dr1215 - 2025 - Framework developed for geomorphic mapping of Fern Ridge Lake, Oregon, 2023","interactions":[],"lastModifiedDate":"2026-02-03T15:20:52.051701","indexId":"dr1215","displayToPublicDate":"2025-09-04T09:21:48","publicationYear":"2025","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":9318,"text":"Data Report","code":"DR","onlineIssn":"2771-9448","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"1215","displayTitle":"Framework Developed for Geomorphic Mapping of Fern Ridge Lake, Oregon, 2023","title":"Framework developed for geomorphic mapping of Fern Ridge Lake, Oregon, 2023","docAbstract":"The construction and operation of large reservoirs in the Willamette River Basin, Oregon, influences important cultural, biological, and other natural or economic resources in affected river corridors. The present-day landforms and cover within the reservoirs have been shaped by a variety of processes, including the pre-dam valley setting and geomorphic processes related to dam operations. Maps of reservoir geomorphic process domains, landforms, and cover provide a foundation for understanding how erosion and deposition processes in or near the reservoirs may affect cultural resources. Detailed geomorphic mapping of Fern Ridge Lake in 2023 provides a basis for evaluating geomorphic processes and patterns of sediment transfer within the reservoir. These processes are related to geomorphic and hydroclimatic conditions as well as annual lake level fluctuation for seasonal flood-control operations. This geomorphic mapping also provides an inventory of existing landforms from which to evaluate the spatial and temporal geomorphic change over time. Digital maps based on high-resolution digital surface models and orthophotographs acquired during low-pool conditions in 2023 extend over an area of about 30 square kilometers (km) upstream of the Fern Ridge Dam. The mapping framework has 3 main components consisting of several subtypes: 5 process domains, 18 landforms, and 7 cover categories. The overarching classification structure is tied to the process domains, which correspond to dissimilar regions of the reservoir that have distinct landforms and broadly similar suites of geomorphic processes. This document describes the geomorphic mapping framework for the reservoir at Fern Ridge Lake and provides mapping unit descriptions including delineation criteria, hypothesized formation processes inferred from remote-sensing and field observations and the literature, and relevance during drawdown operations.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/dr1215","collaboration":"Prepared in cooperation with the U.S. Army Corps of Engineers","usgsCitation":"Keith, M.K., and Bervid, H.D., 2025, Framework developed for geomorphic mapping of Fern Ridge Lake, Oregon, 2023: U.S. Geological Survey Data Report 1215, 33 p., https://doi.org/10.3133/dr1215.","productDescription":"Report: viii, 33 p.; Data Release","onlineOnly":"Y","ipdsId":"IP-160706","costCenters":[{"id":518,"text":"Oregon Water Science Center","active":true,"usgs":true}],"links":[{"id":496027,"rank":7,"type":{"id":36,"text":"NGMDB Index Page"},"url":"https://ngmdb.usgs.gov/Prodesc/proddesc_118829.htm","linkFileType":{"id":5,"text":"html"}},{"id":495173,"rank":6,"type":{"id":31,"text":"Publication XML"},"url":"https://pubs.usgs.gov/dr/1215/dr1215.XML"},{"id":495168,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/dr/1215/coverthb.jpg"},{"id":495169,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/dr/1215/dr1215.pdf","text":"Report","size":"9.8 MB","linkFileType":{"id":1,"text":"pdf"},"description":"DR 1215"},{"id":495170,"rank":3,"type":{"id":39,"text":"HTML Document"},"url":"https://pubs.usgs.gov/publication/dr1215/full","text":"Report","linkFileType":{"id":5,"text":"html"},"description":"DR 1215"},{"id":495171,"rank":4,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P13MHC5P","text":"USGS data release","description":"USGS data release","linkHelpText":"Geomorphic Mapping of Fern Ridge Lake, Oregon, 2023"},{"id":495172,"rank":5,"type":{"id":34,"text":"Image Folder"},"url":"https://pubs.usgs.gov/dr/1215/images"}],"country":"United States","state":"Oregon","otherGeospatial":"Fern Ridge Lake","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -123.36193413601275,\n 44.13431042059929\n ],\n [\n -123.36193413601275,\n 44.0351205618081\n ],\n [\n -123.23640004823704,\n 44.0351205618081\n ],\n [\n -123.23640004823704,\n 44.13431042059929\n ],\n [\n -123.36193413601275,\n 44.13431042059929\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","contact":"Director, Oregon Water Science Center
U.S. Geological Survey
601 SW 2nd Avenue, Suite 1950
Portland, OR 97204
Invasive species management frameworks, such as the early detection of and rapid response to invasive species, use monitoring programs to detect new species occurrences. Resource managers use environmental DNA (eDNA) as one tool for these monitoring programs. An eDNA detection in a new location may lack perspective for resource managers and researchers because of the rarity of potential invaders and the randomness in their dispersal and detection. An example monitoring program is the eDNA-based sampling approach used by the U.S. Fish and Wildlife Service for bigheaded carps Hypophthalmichthys spp. in the upper Mississippi River and Great Lakes Basins that collects hundreds of water samples per event. The U.S. Fish and Wildlife Service detected a single positive sample for Bighead Carp Hypophthalmichthys nobilis during the spring 2021 sampling event in the Kinnickinnic River within the Milwaukee River Basin, and detected a second single positive sample for bigheaded carps during the fall 2021 sampling event in the Milwaukee River. The U.S. Fish and Wildlife Service did not detect any bigheaded carps in previous years (2015 to 2020) or in either the spring or fall 2022 sampling events. These detections lacked perspective, such as detection numbers for other species. We reanalyzed the 2021 and 2022 samples for four existing species of fish: two fairly common species (Common Carp Cyprinus carpio and Gizzard Shad Dorosoma cepedianum) and two fairly rare species (Burbot Lota lota and Grass Carp Ctenopharyngodon idella). We detected Common Carp during all four sampling events, Gizzard Shad during three of four sampling events, and Burbot and Grass Carp during two of four sampling events. These results demonstrated that current sampling efforts could detect other species, and bigheaded carp eDNA was not common in the Milwaukee River compared to these species. More specifically, this finding indicates bigheaded carp eDNA detections are as rare as, or rarer than, Grass Carp eDNA detections, a recent invader to the basin. Our findings also demonstrated how reanalyzing eDNA samples after positive detections for targeted species can help managers understand the context of the detections and provide perspective for the relative abundance of the targeted species. Additionally, our results highlight the importance of completing long-term eDNA-based monitoring rather than a single sampling or inventory event. These detections may have been missed in a single year or sampling event, whereas a multiyear monitoring program provides an opportunity to observe trends through time.
","language":"English","publisher":"Wiley","doi":"10.1002/jwmg.70102","usgsCitation":"Erickson, R.A., DeHaan, P.W., Frohnauer, N.K., Hayer, C., Oettinger, K., Tajjioui, T., Von Ruden, K.M., Willner, H., and Spear, S.F., 2025, Placing environmental DNA monitoring for new detections into perspective: Fishes in the Milwaukee River, Wisconsin: Journal of Wildlife Management, v. 89, e70102, 14 p., https://doi.org/10.1002/jwmg.70102.","productDescription":"e70102, 14 p.","ipdsId":"IP-169285","costCenters":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"links":[{"id":496403,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Wisconsin","otherGeospatial":"Milwaukee River","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -88.85610165027764,\n 43.71442287244696\n ],\n [\n -88.85610165027764,\n 42.70910667171606\n ],\n [\n -87.8504051385311,\n 42.70910667171606\n ],\n [\n -87.8504051385311,\n 43.71442287244696\n ],\n [\n -88.85610165027764,\n 43.71442287244696\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"89","noUsgsAuthors":false,"publicationDate":"2025-09-04","publicationStatus":"PW","contributors":{"authors":[{"text":"Erickson, Richard A. 0000-0003-4649-482X rerickson@usgs.gov","orcid":"https://orcid.org/0000-0003-4649-482X","contributorId":5455,"corporation":false,"usgs":true,"family":"Erickson","given":"Richard","email":"rerickson@usgs.gov","middleInitial":"A.","affiliations":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"preferred":true,"id":949790,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"DeHaan, Patrick W.","contributorId":361996,"corporation":false,"usgs":false,"family":"DeHaan","given":"Patrick","middleInitial":"W.","affiliations":[{"id":84143,"text":"U.S. Fish and Wildlife Service, Whitney Genetics Laboratory","active":true,"usgs":false}],"preferred":false,"id":949791,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Frohnauer, Nicholas K.","contributorId":361997,"corporation":false,"usgs":false,"family":"Frohnauer","given":"Nicholas","middleInitial":"K.","affiliations":[{"id":84141,"text":"U.S. Fish and Wildlife Service, Midwest Regional Office","active":true,"usgs":false}],"preferred":false,"id":949792,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Hayer, Cari-Ann chayer@usgs.gov","contributorId":177628,"corporation":false,"usgs":false,"family":"Hayer","given":"Cari-Ann","email":"chayer@usgs.gov","affiliations":[],"preferred":false,"id":949793,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Oettinger, Keta L.","contributorId":352251,"corporation":false,"usgs":false,"family":"Oettinger","given":"Keta L.","affiliations":[{"id":84142,"text":"Former contractor, Upper Midwest Environmental Sciences Center","active":true,"usgs":false}],"preferred":false,"id":949794,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Tajjioui, Tariq 0000-0002-0113-0451","orcid":"https://orcid.org/0000-0002-0113-0451","contributorId":215091,"corporation":false,"usgs":true,"family":"Tajjioui","given":"Tariq","email":"","affiliations":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"preferred":true,"id":949795,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Von Ruden, Kyle M.","contributorId":361998,"corporation":false,"usgs":false,"family":"Von Ruden","given":"Kyle","middleInitial":"M.","affiliations":[{"id":84143,"text":"U.S. Fish and Wildlife Service, Whitney Genetics Laboratory","active":true,"usgs":false}],"preferred":false,"id":949796,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Willner, Hailey M.","contributorId":352253,"corporation":false,"usgs":false,"family":"Willner","given":"Hailey M.","affiliations":[{"id":84142,"text":"Former contractor, Upper Midwest Environmental Sciences Center","active":true,"usgs":false}],"preferred":false,"id":949797,"contributorType":{"id":1,"text":"Authors"},"rank":8},{"text":"Spear, Stephen Frank 0000-0001-8351-9382","orcid":"https://orcid.org/0000-0001-8351-9382","contributorId":293162,"corporation":false,"usgs":true,"family":"Spear","given":"Stephen","email":"","middleInitial":"Frank","affiliations":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"preferred":true,"id":949798,"contributorType":{"id":1,"text":"Authors"},"rank":9}]}} ,{"id":70271697,"text":"70271697 - 2025 - Post-hatching maternal attendance in wild Burmese Pythons in southern Florida","interactions":[],"lastModifiedDate":"2025-09-19T14:14:34.125355","indexId":"70271697","displayToPublicDate":"2025-09-04T09:09:21","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1899,"text":"Herpetology Notes","active":true,"publicationSubtype":{"id":10}},"title":"Post-hatching maternal attendance in wild Burmese Pythons in southern Florida","docAbstract":"No abstract available.
","language":"English","publisher":"Societas Europaea Herpetologica","usgsCitation":"Guzy, J.C., Sandfoss, M.R., Rentof, J.M., Baird-Lujano, J.E., Aponte Santiago, G., Torres, J.A., McBride, L.M., Metcalf, M., Kissel, A.M., Romagosa, C., Yackel Adams, A.A., Welty, B.L., Miller, M.A., McCollister, M.F., Mazzotti, F.J., and Hart, K., 2025, Post-hatching maternal attendance in wild Burmese Pythons in southern Florida: Herpetology Notes, v. 18, p. 849-856.","productDescription":"8 p.","startPage":"849","endPage":"856","ipdsId":"IP-173241","costCenters":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true},{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"links":[{"id":495783,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":495771,"rank":1,"type":{"id":15,"text":"Index Page"},"url":"https://herpetologynotes.org/index.php/hn/article/view/72"}],"country":"United States","state":"Florida","volume":"18","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Guzy, Jacquelyn C. 0000-0003-2648-398X","orcid":"https://orcid.org/0000-0003-2648-398X","contributorId":288520,"corporation":false,"usgs":true,"family":"Guzy","given":"Jacquelyn","email":"","middleInitial":"C.","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"preferred":true,"id":949047,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Sandfoss, Mark Robert 0000-0002-0162-7265","orcid":"https://orcid.org/0000-0002-0162-7265","contributorId":328884,"corporation":false,"usgs":true,"family":"Sandfoss","given":"Mark","email":"","middleInitial":"Robert","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":true,"id":949048,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Rentof, John-Kaarli M.","contributorId":360930,"corporation":false,"usgs":false,"family":"Rentof","given":"John-Kaarli","middleInitial":"M.","affiliations":[{"id":36221,"text":"University of Florida","active":true,"usgs":false}],"preferred":false,"id":949049,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Baird-Lujano, Judith E.","contributorId":361588,"corporation":false,"usgs":false,"family":"Baird-Lujano","given":"Judith","middleInitial":"E.","affiliations":[{"id":83764,"text":"Cherokee Nation System Solutions, contracted to the U.S. Geological Survey","active":true,"usgs":false}],"preferred":false,"id":949050,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Aponte Santiago, Genesis 0009-0008-3225-8619","orcid":"https://orcid.org/0009-0008-3225-8619","contributorId":361589,"corporation":false,"usgs":true,"family":"Aponte Santiago","given":"Genesis","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research 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A.","contributorId":361594,"corporation":false,"usgs":false,"family":"Miller","given":"Melissa","middleInitial":"A.","affiliations":[{"id":86317,"text":"University of Florida, Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center","active":true,"usgs":false}],"preferred":false,"id":949059,"contributorType":{"id":1,"text":"Authors"},"rank":13},{"text":"McCollister, Matthew F.","contributorId":361595,"corporation":false,"usgs":false,"family":"McCollister","given":"Matthew","middleInitial":"F.","affiliations":[{"id":86318,"text":"National Park Service, Big Cypress National Preserve","active":true,"usgs":false}],"preferred":false,"id":949060,"contributorType":{"id":1,"text":"Authors"},"rank":14},{"text":"Mazzotti, Frank J.","contributorId":361596,"corporation":false,"usgs":false,"family":"Mazzotti","given":"Frank","middleInitial":"J.","affiliations":[{"id":86317,"text":"University of Florida, Department of Wildlife Ecology and Conservation, Fort 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Article"},"seriesTitle":{"id":2508,"text":"Journal of Wildlife Management","active":true,"publicationSubtype":{"id":10}},"title":"Exploring the importance of metapopulation dynamics with population control strategies for invasive silver carp in the upper Mississippi River","docAbstract":"Invasive bigheaded carps (Bighead Carp Hypophthalmichthys nobilis, Silver Carp Hypophthalmichthys molitrix, and their hybrids Hypophthalmichthys spp.) currently infest the Mississippi River Basin. Bigheaded carps can outcompete native species in invaded waters and can also transform the surrounding environment. Currently, resource managers seek to limit the population abundance of bigheaded carps and their range expansion into additional regions of the Upper Mississippi River (UMR) but lack a tool to evaluate different control strategies. Here, we present an application of a Silver Carp spatial population model in the UMR to fill this gap. We used the model to explore how simulated control strategies could affect Silver Carp metapopulation dynamics. More specifically, we assessed and compared the importance of movement deterrents, removal locations, and recruitment areas on Silver Carp population abundances across the UMR. Strategies that included a combination of removal efforts and deterrents resulted in the largest decreases in Silver Carp abundance in the upper pools of the UMR. Furthermore, scenarios that targeted source populations of Silver Carp rather than sink populations resulted in larger decreases in Silver Carp abundance at the invasion front. The effectiveness of these combined simulated strategies also depended on the location of Silver Carp recruitment. Our work suggests that an understanding of Silver Carp metapopulation dynamics may be important for control efforts and could help to inform the management of Silver Carp in the UMR.
","language":"English","publisher":"The Wildlife Society","doi":"10.1002/jwmg.70101","usgsCitation":"Frame, K., Sandland, G.J., Labuzzetta, C.J., Loppnow, G.L., Stanton, J.C., Kao, Y., and Erickson, R.A., 2025, Exploring the importance of metapopulation dynamics with population control strategies for invasive silver carp in the upper Mississippi River: Journal of Wildlife Management, v. 89, no. 8, e70101, 19 p., https://doi.org/10.1002/jwmg.70101.","productDescription":"e70101, 19 p.","ipdsId":"IP-169626","costCenters":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"links":[{"id":496591,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Illinois, Iowa, Minnesota, Missouri, Wisconsin","otherGeospatial":"upper Mississippi River","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -92.42515752205935,\n 44.547455467183056\n ],\n [\n -92.42515752205935,\n 39.31069113760515\n ],\n [\n -89.49821279072381,\n 39.31069113760515\n ],\n [\n -89.49821279072381,\n 44.547455467183056\n ],\n [\n -92.42515752205935,\n 44.547455467183056\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"89","issue":"8","noUsgsAuthors":false,"publicationDate":"2025-09-04","publicationStatus":"PW","contributors":{"authors":[{"text":"Frame, Kassidy","contributorId":362254,"corporation":false,"usgs":false,"family":"Frame","given":"Kassidy","affiliations":[{"id":47908,"text":"University of Wisconsin - La Crosse","active":true,"usgs":false}],"preferred":false,"id":950246,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Sandland, Gregory J. 0000-0002-9716-0232","orcid":"https://orcid.org/0000-0002-9716-0232","contributorId":362255,"corporation":false,"usgs":false,"family":"Sandland","given":"Gregory","middleInitial":"J.","affiliations":[{"id":47908,"text":"University of Wisconsin - La Crosse","active":true,"usgs":false}],"preferred":false,"id":950247,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Labuzzetta, Charles J. 0000-0002-6027-0120","orcid":"https://orcid.org/0000-0002-6027-0120","contributorId":332055,"corporation":false,"usgs":true,"family":"Labuzzetta","given":"Charles","email":"","middleInitial":"J.","affiliations":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"preferred":true,"id":950248,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Loppnow, Grace L.","contributorId":362256,"corporation":false,"usgs":false,"family":"Loppnow","given":"Grace","middleInitial":"L.","affiliations":[{"id":86499,"text":"Minnesota Department of Natural Resources, Ecological and Water Resources, Saint Paul, MN","active":true,"usgs":false}],"preferred":false,"id":950249,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Stanton, Jessica C. 0000-0002-6225-3703 jcstanton@usgs.gov","orcid":"https://orcid.org/0000-0002-6225-3703","contributorId":5634,"corporation":false,"usgs":true,"family":"Stanton","given":"Jessica","email":"jcstanton@usgs.gov","middleInitial":"C.","affiliations":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"preferred":true,"id":950250,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Kao, Yu-Chun","contributorId":35626,"corporation":false,"usgs":false,"family":"Kao","given":"Yu-Chun","affiliations":[{"id":6649,"text":"University of Michigan, School of Natural Resources and Environment","active":true,"usgs":false}],"preferred":false,"id":950251,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Erickson, Richard A. 0000-0003-4649-482X rerickson@usgs.gov","orcid":"https://orcid.org/0000-0003-4649-482X","contributorId":5455,"corporation":false,"usgs":true,"family":"Erickson","given":"Richard","email":"rerickson@usgs.gov","middleInitial":"A.","affiliations":[{"id":606,"text":"Upper Midwest Environmental Sciences Center","active":true,"usgs":true}],"preferred":true,"id":950252,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ,{"id":70271493,"text":"70271493 - 2025 - Bioaccumulation and transfer of per- and polyfluoroalkyl substances (PFAS) in a stream and riparian food web contaminated by food processing wastewater","interactions":[],"lastModifiedDate":"2025-09-18T15:00:15.100545","indexId":"70271493","displayToPublicDate":"2025-09-04T07:47:37","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1565,"text":"Environmental Science & Technology","onlineIssn":"1520-5851","printIssn":"0013-936X","active":true,"publicationSubtype":{"id":10}},"title":"Bioaccumulation and transfer of per- and polyfluoroalkyl substances (PFAS) in a stream and riparian food web contaminated by food processing wastewater","docAbstract":"We evaluated the bioaccumulation and transfer of per- and polyfluoroalkyl substances (PFAS) in a stream food web contaminated by a food processing facility. Abiotic (i.e., water, sediment, and foam) and biotic (i.e., algae, aquatic insect larvae and adults, fish, and riparian spiders) matrices were sampled upstream and downstream of the facility’s wastewater outfall. Compared with upstream, PFAS concentrations were 600-fold higher in downstream water (mean ∑40PFAS 3.67 ng mL–1 ± 0.48 (standard error)) and reflected inputs from the outfall, with 6:2 fluorotelomer sulfonate (6:2 FTS) dominating the PFAS profile. Within the aquatic food web, perfluorooctanesulfonate (PFOS) was the most biomagnified, and 6:2 FTS was the most biodiluted. In contrast, insect-mediated transfer of PFAS to riparian spiders showed trophic enrichment of 6:2 FTS and dilution of PFOS. We observed significant positive associations between phospholipid membrane-water partition coefficient (log KMW) and perfluoroalkyl carboxylate (PFCA) chain length on bioaccumulation across most biological matrices, demonstrating that these chemical parameters are predictive of PFAS bioaccumulation potential in the field. Our research reveals important differences in aquatic versus terrestrial exposure for certain PFAS and that biological processes (e.g., trophic interactions and metamorphosis) and chemical properties (e.g., chain length, log KMW, and concentration) control PFAS uptake, bioaccumulation, and transfer in linked freshwater and terrestrial ecosystems.
","language":"English","publisher":"American Chemical Society","doi":"10.1021/acs.est.5c04867","usgsCitation":"Kotalik, C.J., Hubbard, L.E., Perrotta, B.G., Walters, D.M., Kolpin, D., Gray, J.L., Zachritz, A.M., Kraus, J.M., Givens, C.E., Lamberti, G.A., and Kidd, K.A., 2025, Bioaccumulation and transfer of per- and polyfluoroalkyl substances (PFAS) in a stream and riparian food web contaminated by food processing wastewater: Environmental Science & Technology, v. 59, no. 36, p. 19444-19456, https://doi.org/10.1021/acs.est.5c04867.","productDescription":"13 p.","startPage":"19444","endPage":"19456","ipdsId":"IP-178202","costCenters":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"links":[{"id":495710,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"59","issue":"36","noUsgsAuthors":false,"publicationDate":"2025-09-04","publicationStatus":"PW","contributors":{"authors":[{"text":"Kotalik, Christopher James 0000-0001-6739-6036","orcid":"https://orcid.org/0000-0001-6739-6036","contributorId":301847,"corporation":false,"usgs":true,"family":"Kotalik","given":"Christopher","email":"","middleInitial":"James","affiliations":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"preferred":true,"id":948954,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Hubbard, Laura E. 0000-0003-3813-1500 lhubbard@usgs.gov","orcid":"https://orcid.org/0000-0003-3813-1500","contributorId":4221,"corporation":false,"usgs":true,"family":"Hubbard","given":"Laura","email":"lhubbard@usgs.gov","middleInitial":"E.","affiliations":[{"id":37947,"text":"Upper Midwest Water Science Center","active":true,"usgs":true}],"preferred":true,"id":948955,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Perrotta, Brittany G. 0000-0003-2669-3047","orcid":"https://orcid.org/0000-0003-2669-3047","contributorId":301929,"corporation":false,"usgs":true,"family":"Perrotta","given":"Brittany","middleInitial":"G.","affiliations":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"preferred":true,"id":948956,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Walters, David M. 0000-0002-4237-2158","orcid":"https://orcid.org/0000-0002-4237-2158","contributorId":201754,"corporation":false,"usgs":true,"family":"Walters","given":"David","middleInitial":"M.","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":true,"id":948957,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Kolpin, Dana W. 0000-0002-3529-6505","orcid":"https://orcid.org/0000-0002-3529-6505","contributorId":205652,"corporation":false,"usgs":true,"family":"Kolpin","given":"Dana W.","affiliations":[{"id":35680,"text":"Illinois-Iowa-Missouri Water Science Center","active":true,"usgs":true},{"id":351,"text":"Iowa Water Science Center","active":true,"usgs":true},{"id":36532,"text":"Central Midwest Water Science Center","active":true,"usgs":true},{"id":37947,"text":"Upper Midwest Water Science Center","active":true,"usgs":true}],"preferred":true,"id":948958,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Gray, James L. 0000-0002-0807-5635","orcid":"https://orcid.org/0000-0002-0807-5635","contributorId":205658,"corporation":false,"usgs":true,"family":"Gray","given":"James","email":"","middleInitial":"L.","affiliations":[{"id":5046,"text":"Branch of Analytical Serv (NWQL)","active":true,"usgs":true}],"preferred":true,"id":948959,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Zachritz, Alison M.","contributorId":361537,"corporation":false,"usgs":false,"family":"Zachritz","given":"Alison","middleInitial":"M.","affiliations":[{"id":39516,"text":"University of Notre Dame","active":true,"usgs":false}],"preferred":false,"id":948960,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Kraus, Johanna M. 0000-0002-9513-4129 jkraus@usgs.gov","orcid":"https://orcid.org/0000-0002-9513-4129","contributorId":4834,"corporation":false,"usgs":true,"family":"Kraus","given":"Johanna","email":"jkraus@usgs.gov","middleInitial":"M.","affiliations":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true},{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":true,"id":948961,"contributorType":{"id":1,"text":"Authors"},"rank":8},{"text":"Givens, Carrie E. 0000-0003-2543-9610","orcid":"https://orcid.org/0000-0003-2543-9610","contributorId":270741,"corporation":false,"usgs":true,"family":"Givens","given":"Carrie","middleInitial":"E.","affiliations":[{"id":37947,"text":"Upper Midwest Water Science 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1879–1979","interactions":[],"lastModifiedDate":"2026-02-03T15:20:01.84239","indexId":"cir1552","displayToPublicDate":"2025-09-03T15:18:39","publicationYear":"2025","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":307,"text":"Circular","code":"CIR","onlineIssn":"2330-5703","printIssn":"1067-084X","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"1552","displayTitle":"The U.S. Geological Survey, the U.S. Department of Defense, and the U.S. Intelligence Community: 100 Years of Mapping and Remote Sensing Collaboration, 1879–1979","title":"The U.S. Geological Survey, the U.S. Department of Defense, and the U.S. Intelligence Community—100 years of mapping and remote sensing collaboration, 1879–1979","docAbstract":"The U.S. Geological Survey (USGS)—a Federal civilian agency—and U.S. military and intelligence agencies collaborate on mapping and remote sensing and have since the establishment of the USGS. The organizations exchange data and information and share technology to further their respective missions in service to the American people. Often referred to as examples of “good government” or “whole of government,” the collaboration avoids costly duplication and maximizes time and effort for the government sectors. Collaboration between these sectors started with the original mapping of the United States and evolved to include remote sensing after the advent of aerial photography and satellite imagery.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/cir1552","isbn":"978-1-4113-4627-7","programNote":"National Land Imaging Program","usgsCitation":"Young, P.M., 2025, The U.S. Geological Survey, the U.S. Department of Defense, and the U.S. Intelligence Community—100 years of mapping and remote sensing collaboration, 1879–1979: U.S. Geological Survey Circular 1552, 64 p., https://doi.org/10.3133/cir1552.","productDescription":"xi, 64 p.","numberOfPages":"64","onlineOnly":"N","ipdsId":"IP-160464","costCenters":[{"id":36171,"text":"National Civil Applications Center","active":true,"usgs":true}],"links":[{"id":495094,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/circ/1552/coverthb.jpg"},{"id":495095,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/circ/1552/cir1552.pdf","text":"Report","size":"42.4 MB","linkFileType":{"id":1,"text":"pdf"},"description":"CIRC 1552"},{"id":495096,"rank":3,"type":{"id":39,"text":"HTML Document"},"url":"https://pubs.usgs.gov/publication/cir1552/full","linkFileType":{"id":5,"text":"html"},"description":"CIRC 1552 HTML"},{"id":495097,"rank":4,"type":{"id":31,"text":"Publication XML"},"url":"https://pubs.usgs.gov/circ/1552/cir1552.XML","description":"CIRC 1552 XML"},{"id":495098,"rank":5,"type":{"id":34,"text":"Image Folder"},"url":"https://pubs.usgs.gov/circ/1552/images"}],"contact":"Director, National Civil Applications Center
U.S. Geological Survey
12201 Sunrise Valley Drive, MS 562
Reston, VA 20192
https://www.usgs.gov/programs/national-land-imaging-program
For over a century, ecologists have used the concept of trophic state (TS) to characterize an aquatic ecosystem's biological productivity. However, multiple TS classification schemes, each relying on a variety of measurable parameters as proxies for productivity, have emerged to meet use-specific needs. Frequently, chlorophyll a, phosphorus, and Secchi depth are used to classify TS based on autotrophic production, whereas phosphorus, dissolved organic carbon, and true color are used to classify TS based on both autotrophic and heterotrophic production. Both classification approaches aim to characterize an ecosystem's function broadly, but with varying degrees of autotrophic and heterotrophic processes considered in those characterizations. Moreover, differing classification schemes can create inconsistent interpretations of ecosystem integrity. For example, the US Clean Water Act focuses exclusively on algal threats to water quality, framed in terms of eutrophication in response to nutrient loading. This usage lacks information about non-algal threats to water quality, such as dystrophication in response to dissolved organic carbon loading. Consequently, the TS classification schemes used to identify eutrophication and dystrophication may refer to ecosystems similarly (e.g., oligotrophic and eutrophic), yet these categories are derived from different proxies. These inconsistencies in TS classification schemes may be compounded when interdisciplinary projects employ varied TS frameworks. Even with these shortcomings, TS can still be used to distill information on complex aquatic ecosystem function into a set of generalizable expectations. The usefulness of distilling complex information into a TS index is substantial such that usage inconsistencies should be explicitly addressed and resolved. To emphasize the consequences of diverging TS classification schemes, we present three case studies for which an improved understanding of the TS concept advances freshwater research, management efforts, and interdisciplinary collaboration. To increase clarity in TS, the aquatic sciences could benefit from including information about the proxy variables, ecosystem type, as well as the spatiotemporal domains used to classify TS. As the field of aquatic sciences expands and climatic irregularity increases, we highlight the importance of re-evaluating fundamental concepts, such as TS, to ensure their compatibility with evolving science.
","language":"English","publisher":"Ecological Society of America","doi":"10.1002/ecs2.70392","usgsCitation":"Meyer, M.F., Kraemer, B.M., Barbosa, C.C., Cuhna, D.G., Dodds, W., Hampton, S.E., Ordóñez, C., Pilla, R.M., Pollard, A., Culpepper, J.A., Fremier, A.K., King, T.V., Ladwig, R., Leech, D.M., Matsuzaki, S.S., Oleksy, I., Topp, S.N., Woolway, R., Brighenti, L.S., Fickas, K.C., Lanouette, B.P., Ren, J., Werther, M., and Yang, X., 2025, Clarifying the trophic state concept to advance macroscale freshwater science and management: Ecosphere, v. 16, no. 9, e70392, 20 p., https://doi.org/10.1002/ecs2.70392.","productDescription":"e70392, 20 p.","ipdsId":"IP-154125","costCenters":[{"id":518,"text":"Oregon Water Science Center","active":true,"usgs":true},{"id":37786,"text":"WMA - Observing Systems Division","active":true,"usgs":true}],"links":[{"id":496941,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1002/ecs2.70392","text":"Publisher Index 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honeycreeper","interactions":[],"lastModifiedDate":"2025-12-29T16:09:57.481763","indexId":"70273270","displayToPublicDate":"2025-09-03T10:05:48","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1467,"text":"Ecology and Evolution","active":true,"publicationSubtype":{"id":10}},"title":"Variation in gene expression across infection status and elevation in a Hawaiian honeycreeper","docAbstract":"Introduced pathogens exert novel selection on hosts, and although many host species have experienced drastic population declines in the absence of adaptation, some hosts have adapted to highly virulent pathogens. For instance, mosquitoes and Plasmodium relictum introduced to the Hawaiian Islands have resulted in extinctions and catastrophic population declines due to avian malaria, particularly in the diverse clade of Hawaiian honeycreepers. However, some species, such as the Hawai'i 'amakihi (Chlorodrepanis virens), can survive infection. Immunity exists in low-elevation populations where mosquitoes are abundant, whereas high-elevation, unexposed populations of 'amakihi display greatly reduced immunity. To explore the basis of adaptation to P. relictum in low-elevation 'amakihi, we sequenced transcriptomes from 24 low-elevation and 15 high-elevation 'amakihi. We tested for differential gene expression between (i) infected and uninfected birds and (ii) low- and high-elevation birds. Infected birds showed significant differences in expression across many transcripts with diverse cellular functions involved in different pathways of immune response; eight of the top 13 transcripts blasted to genes previously implicated in immunity to malaria in 'amakihi, and 11 have been identified in other infectious disease systems. Thirteen transcripts showed a trend of higher expression in high-elevation birds. These transcripts blasted to genes involved in metabolism, blood coagulation, and immune response. Our results provide increasing support for a subset of genes involved in immunity to malaria in 'amakihi and hint at possible antagonistic interactions between response to pathogens and environmental characteristics associated with elevation. Further work clarifying the nature of these interactions could benefit conservation efforts of Hawaiian honeycreepers in upper elevation refugia that are increasingly subject to malaria exposure.
","language":"English","publisher":"Wiley","doi":"10.1002/ece3.72078","usgsCitation":"Cassin-Sackett, L., McClure, K.M., Callicrate, T., Paxton, E.H., and Fleischer, R., 2025, Variation in gene expression across infection status and elevation in a Hawaiian honeycreeper: Ecology and Evolution, v. 15, no. 9, e72078, 20 p., https://doi.org/10.1002/ece3.72078.","productDescription":"e72078, 20 p.","ipdsId":"IP-176601","costCenters":[{"id":521,"text":"Pacific Island Ecosystems Research Center","active":false,"usgs":true}],"links":[{"id":498273,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1002/ece3.72078","text":"Publisher Index Page"},{"id":498147,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Hawaii","otherGeospatial":"Island of Hawaii","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -155.43131657241724,\n 19.902375791429492\n ],\n [\n -155.43131657241724,\n 19.300971730675755\n ],\n [\n -154.7972264794636,\n 19.300971730675755\n ],\n [\n -154.7972264794636,\n 19.902375791429492\n ],\n [\n -155.43131657241724,\n 19.902375791429492\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"15","issue":"9","noUsgsAuthors":false,"publicationDate":"2025-09-03","publicationStatus":"PW","contributors":{"authors":[{"text":"Cassin-Sackett, Loren","contributorId":364635,"corporation":false,"usgs":false,"family":"Cassin-Sackett","given":"Loren","affiliations":[{"id":63963,"text":"University of Louisiana","active":true,"usgs":false}],"preferred":false,"id":952973,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"McClure, Katherine Maria 0000-0001-8595-7677","orcid":"https://orcid.org/0000-0001-8595-7677","contributorId":332279,"corporation":false,"usgs":true,"family":"McClure","given":"Katherine","email":"","middleInitial":"Maria","affiliations":[{"id":521,"text":"Pacific Island Ecosystems Research Center","active":false,"usgs":true}],"preferred":true,"id":952974,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Callicrate, Taylor","contributorId":364636,"corporation":false,"usgs":false,"family":"Callicrate","given":"Taylor","affiliations":[{"id":37784,"text":"Smithsonian Conservation Biology Institute","active":true,"usgs":false}],"preferred":false,"id":952975,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Paxton, Eben H. 0000-0001-5578-7689","orcid":"https://orcid.org/0000-0001-5578-7689","contributorId":19640,"corporation":false,"usgs":true,"family":"Paxton","given":"Eben","email":"","middleInitial":"H.","affiliations":[{"id":5049,"text":"Pacific Islands Ecosys Research Center","active":true,"usgs":true}],"preferred":true,"id":952976,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Fleischer, Robert C.","contributorId":258062,"corporation":false,"usgs":false,"family":"Fleischer","given":"Robert C.","affiliations":[{"id":52221,"text":"Center for Conservation Genomics, Smithsonian Conservation Biology Institute","active":true,"usgs":false}],"preferred":false,"id":952977,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70271988,"text":"70271988 - 2025 - Assessment of natural gas pipeline construction on stream temperature and turbidity in southwestern Virginia, 2017—25","interactions":[{"subject":{"id":70271988,"text":"70271988 - 2025 - Assessment of natural gas pipeline construction on stream temperature and turbidity in southwestern Virginia, 2017—25","indexId":"70271988","publicationYear":"2025","noYear":false,"title":"Assessment of natural gas pipeline construction on stream temperature and turbidity in southwestern Virginia, 2017—25"},"predicate":"SUPERSEDED_BY","object":{"id":70275059,"text":"sir20265011 - 2026 - Assessment of natural gas pipeline construction on stream temperature and turbidity in southwestern Virginia, 2017–25","indexId":"sir20265011","publicationYear":"2026","noYear":false,"title":"Assessment of natural gas pipeline construction on stream temperature and turbidity in southwestern Virginia, 2017–25"},"id":1}],"supersededBy":{"id":70275059,"text":"sir20265011 - 2026 - Assessment of natural gas pipeline construction on stream temperature and turbidity in southwestern Virginia, 2017–25","indexId":"sir20265011","publicationYear":"2026","noYear":false,"title":"Assessment of natural gas pipeline construction on stream temperature and turbidity in southwestern Virginia, 2017–25"},"lastModifiedDate":"2026-04-14T17:23:06.565541","indexId":"70271988","displayToPublicDate":"2025-09-03T09:41:16","publicationYear":"2025","noYear":false,"publicationType":{"id":27,"text":"Preprint"},"publicationSubtype":{"id":32,"text":"Preprint"},"seriesTitle":{"id":18346,"text":"EarthArXiv","active":true,"publicationSubtype":{"id":32}},"title":"Assessment of natural gas pipeline construction on stream temperature and turbidity in southwestern Virginia, 2017—25","docAbstract":"The natural gas pipeline network in the United States is extensive and often intersects streams and other sensitive habitats, yet there are limited case studies utilizing a comparative upstream-downstream approach to evaluate potential short- and long-term effects of pipeline stream crossing construction from pre-construction to post-site restoration. In 2017, the U.S. Geological Survey, in cooperation with the Virginia Department of Environmental Quality (DEQ), deployed real-time continuous stream monitoring stations upstream and downstream of six proposed Mountain Valley Pipeline (MVP) stream crossings in southwestern Virginia. Water temperature and turbidity data collected at the upstream and downstream sites were compared across three periods – before crossing construction, during crossing construction, and after crossing construction – to elucidate potential impacts from the stream crossing construction. Additionally, the monitoring network was utilized to notify regulators of potentially anomalous conditions throughout the entire monitoring period.
Results of this study indicate (1) at all six monitored streams, pipeline stream crossing construction did not affect long-term or short-term upstream-to-downstream water temperature conditions; (2) pipeline stream crossing construction did not affect long-term upstream-to-downstream turbidity conditions in all six monitored streams. Some short-term anomalously elevated turbidity conditions were observed and attributable to pipeline stream crossing construction; however, the duration and magnitude were not sufficient to alter the long-term turbidity regime of the streams in which they were observed; and (3) the application of the monitoring network as a real-time alert system successfully alerted regulators to potentially anomalous conditions.
Traditional remote sensing retrieval models for water quality have historically relied on limited, localized data sets due to the prohibitive costs of extensive field campaigns and logistical challenges of collecting match-up data with satellite overpasses. As a result, these models often lack generalizability across seasons, tides, and sites. Furthermore, small field data sets limit the utility of modern machine learning techniques to advance remote sensing retrieval models. In situ optical sensors deployed in a sensor network to continuously monitor larger water bodies can drastically increase the number of measurements, providing the opportunity to develop new approaches for building robust remote sensing retrieval models by leveraging both remote sensing data and in situ networks as an integrated monitoring system. This study leverages a large “ground-to-space” sensor network that combines an in situ optical sensor network with satellite-based remote sensing to overcome these limitations. Utilizing a large-scale data set from the U.S. Geological Survey's Sacramento—San Joaquin River Delta monitoring network, of dissolved organic matter fluorescence measurements, and remote sensing data from the European Space Agency's Sentinel-2A and -2B satellites, this study implemented a data driven approach for dissolved organic matter models. The data set, consisting of 982 samples collected between 2018 and 2021 was used to train and validate a random forest model (R2 = 0.76, RMSE = 6.1 Quinine Sulfate Equivalents), with demonstrated applicability across diverse site conditions, tidal stages, and seasons. This work provides a scalable solution to address critical challenges in water quality monitoring and offers a replicable framework for global water quality management.
","language":"English","publisher":"American Geophysical Union","doi":"10.1029/2024EA004048","usgsCitation":"Avouris, D., Hestir, E.L., Fleck, J., Hansen, J.A., and Bergamaschi, B.A., 2025, An integrated sensor network and data driven approach to satellite remote sensing of dissolved organic matter: Earth and Space Science, v. 12, no. 12, e2024EA004048, 19 p., https://doi.org/10.1029/2024EA004048.","productDescription":"e2024EA004048, 19 p.","ipdsId":"IP-172592","costCenters":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"links":[{"id":495389,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1029/2024ea004048","text":"Publisher Index Page"},{"id":495247,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Calfornia","otherGeospatial":"Sacramento-San Joaquin River Delta","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -121.34190472520478,\n 37.92367880802452\n ],\n [\n -121.34190472520478,\n 38.5486708617789\n ],\n [\n -121.98676504474714,\n 38.5486708617789\n ],\n [\n -121.98676504474714,\n 37.92367880802452\n ],\n [\n -121.34190472520478,\n 37.92367880802452\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"12","issue":"12","noUsgsAuthors":false,"publicationDate":"2025-09-03","publicationStatus":"PW","contributors":{"authors":[{"text":"Avouris, Dulcinea Marie 0000-0001-5797-3960","orcid":"https://orcid.org/0000-0001-5797-3960","contributorId":335170,"corporation":false,"usgs":true,"family":"Avouris","given":"Dulcinea Marie","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":948141,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Hestir, Erin L","contributorId":361027,"corporation":false,"usgs":false,"family":"Hestir","given":"Erin","middleInitial":"L","affiliations":[{"id":38695,"text":"University of California Merced","active":true,"usgs":false}],"preferred":false,"id":948142,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Fleck, Jacob 0000-0002-3217-3972 jafleck@usgs.gov","orcid":"https://orcid.org/0000-0002-3217-3972","contributorId":168694,"corporation":false,"usgs":true,"family":"Fleck","given":"Jacob","email":"jafleck@usgs.gov","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":948143,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Hansen, Jeffrey A. 0000-0002-2185-1686","orcid":"https://orcid.org/0000-0002-2185-1686","contributorId":205441,"corporation":false,"usgs":true,"family":"Hansen","given":"Jeffrey","email":"","middleInitial":"A.","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":948144,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Bergamaschi, Brian A. 0000-0002-9610-5581 bbergama@usgs.gov","orcid":"https://orcid.org/0000-0002-9610-5581","contributorId":140776,"corporation":false,"usgs":true,"family":"Bergamaschi","given":"Brian","email":"bbergama@usgs.gov","middleInitial":"A.","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":948145,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70271333,"text":"70271333 - 2025 - Impacts of lake elevation decline on spawning habitat of a critical, native forage species","interactions":[],"lastModifiedDate":"2025-12-01T16:30:30.860959","indexId":"70271333","displayToPublicDate":"2025-09-03T08:18:53","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3624,"text":"Transactions of the American Fisheries Society","active":true,"publicationSubtype":{"id":10}},"title":"Impacts of lake elevation decline on spawning habitat of a critical, native forage species","docAbstract":"Objective
Lake elevation decline is a global phenomenon with pronounced effects in arid regions that changes the characteristics of nearshore habitat area available to lacustrine spawners, potentially impacting recruitment and whole-lake food web dynamics. Our objective was to understand the potential effects of lake elevation decline on spawning habitat for the Tui Chub Siphateles bicolor, a lacustrine spawner and critical component of the native food web in Pyramid Lake, Nevada.
Methods
We explored the distribution of ripe Tui Chub in nearshore habitat by associating habitat characteristics to ripe Tui Chub CPUE from a custom gill-net configuration, with data analyzed using generalized linear mixed-effects models. We then explored potential spawning habitat availability at all potential lake elevations using an elevation-explicit model of the basin that we developed based on several bathymetric and geospatial data sets and the knowledge of spawner distribution gained in the first component of the study.
Results
Ripe Tui Chub catch was primarily predicted by temperature, reaching a maximum between 14.2°C and 24.8°C found at less than 15 m of depth in Pyramid Lake throughout the summer spawning period. We estimated that with a contemporary decline in lake elevation of 8 m, Pyramid Lake will host the minimum area of spawning habitat based on morphometry alone at a 40% decrease from a theoretical maximum.
Conclusions
A decrease in lake elevation or an increase in lake temperatures—both of which are probable events based on future climate scenarios and estimates of water extraction upstream of Pyramid Lake—is likely to further restrict Tui Chub spawning habitat area. Our results have important implications for ecological water demand in Pyramid Lake and provide managers with information facilitating a science-based approach to managing the fish community.
","language":"English","publisher":"American Fisheries Society","doi":"10.1093/tafafs/vnaf034","usgsCitation":"Barnes, S., Al-Chokhachy, R., and Budy, P., 2025, Impacts of lake elevation decline on spawning habitat of a critical, native forage species: Transactions of the American Fisheries Society, v. 154, no. 6, p. 640-656, https://doi.org/10.1093/tafafs/vnaf034.","productDescription":"17 p.","startPage":"640","endPage":"656","ipdsId":"IP-161347","costCenters":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"links":[{"id":495220,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Nevada","otherGeospatial":"Pyramid Lake","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -119.72328588180102,\n 40.234157713420586\n ],\n [\n -119.72328588180102,\n 39.842701658708876\n ],\n [\n -119.32079294757592,\n 39.842701658708876\n ],\n [\n -119.32079294757592,\n 40.234157713420586\n ],\n [\n -119.72328588180102,\n 40.234157713420586\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"154","issue":"6","noUsgsAuthors":false,"publicationDate":"2025-09-03","publicationStatus":"PW","contributors":{"authors":[{"text":"Barnes, Sarah","contributorId":360982,"corporation":false,"usgs":false,"family":"Barnes","given":"Sarah","affiliations":[{"id":6682,"text":"Utah State University","active":true,"usgs":false}],"preferred":false,"id":948072,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Al-Chokhachy, Robert 0000-0002-2136-5098","orcid":"https://orcid.org/0000-0002-2136-5098","contributorId":216140,"corporation":false,"usgs":true,"family":"Al-Chokhachy","given":"Robert","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":948073,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Budy, Phaedra E. 0000-0002-9918-1678 pbudy@usgs.gov","orcid":"https://orcid.org/0000-0002-9918-1678","contributorId":140028,"corporation":false,"usgs":true,"family":"Budy","given":"Phaedra","email":"pbudy@usgs.gov","middleInitial":"E.","affiliations":[{"id":438,"text":"National Research Program - Western Branch","active":true,"usgs":true},{"id":200,"text":"Coop Res Unit Seattle","active":true,"usgs":true}],"preferred":true,"id":948074,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70271319,"text":"70271319 - 2025 - Clarifying the trophic state concept to advance macroscale freshwater science and management","interactions":[],"lastModifiedDate":"2025-09-05T14:59:00.832743","indexId":"70271319","displayToPublicDate":"2025-09-03T07:49:56","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1475,"text":"Ecosphere","active":true,"publicationSubtype":{"id":10}},"title":"Clarifying the trophic state concept to advance macroscale freshwater science and management","docAbstract":"For over a century, ecologists have used the concept of trophic state (TS) to characterize an aquatic ecosystem's biological productivity. However, multiple TS classification schemes, each relying on a variety of measurable parameters as proxies for productivity, have emerged to meet use-specific needs. Frequently, chlorophyll a, phosphorus, and Secchi depth are used to classify TS based on autotrophic production, whereas phosphorus, dissolved organic carbon, and true color are used to classify TS based on both autotrophic and heterotrophic production. Both classification approaches aim to characterize an ecosystem's function broadly, but with varying degrees of autotrophic and heterotrophic processes considered in those characterizations. Moreover, differing classification schemes can create inconsistent interpretations of ecosystem integrity. For example, the US Clean Water Act focuses exclusively on algal threats to water quality, framed in terms of eutrophication in response to nutrient loading. This usage lacks information about non-algal threats to water quality, such as dystrophication in response to dissolved organic carbon loading. Consequently, the TS classification schemes used to identify eutrophication and dystrophication may refer to ecosystems similarly (e.g., oligotrophic and eutrophic), yet these categories are derived from different proxies. These inconsistencies in TS classification schemes may be compounded when interdisciplinary projects employ varied TS frameworks. Even with these shortcomings, TS can still be used to distill information on complex aquatic ecosystem function into a set of generalizable expectations. The usefulness of distilling complex information into a TS index is substantial such that usage inconsistencies should be explicitly addressed and resolved. To emphasize the consequences of diverging TS classification schemes, we present three case studies for which an improved understanding of the TS concept advances freshwater research, management efforts, and interdisciplinary collaboration. To increase clarity in TS, the aquatic sciences could benefit from including information about the proxy variables, ecosystem type, as well as the spatiotemporal domains used to classify TS. As the field of aquatic sciences expands and climatic irregularity increases, we highlight the importance of re-evaluating fundamental concepts, such as TS, to ensure their compatibility with evolving science.
","language":"English","publisher":"Ecological Society of America","doi":"10.1002/ecs2.70392","usgsCitation":"Meyer, M.F., Kraemer, B.M., Barbosa, C.C., Cuhna, D.G., Dodds, W., Hampton, S.E., Ordóñez, C., Pilla, R.M., Pollard, A., Culpepper, J.A., Fremier, A.K., King, T.V., Ladwig, R., Leech, D.M., Matsuzaki, S.S., Oleksy, I., Topp, S.N., Woolway, R.I., Brighenti, L.S., Fickas, K., Lanouette, B.P., Ren, J., Werther, M., and Yang, X., 2025, Clarifying the trophic state concept to advance macroscale freshwater science and management: Ecosphere, v. 16, no. 9, e70392, 20 p., https://doi.org/10.1002/ecs2.70392.","productDescription":"e70392, 20 p.","ipdsId":"IP-179274","costCenters":[{"id":518,"text":"Oregon Water Science Center","active":true,"usgs":true}],"links":[{"id":495377,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1002/ecs2.70392","text":"Publisher Index Page"},{"id":495285,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P14KNKHD","text":"USGS data release","linkHelpText":"Clarifying the trophic state concept to advance macroscale freshwater science and management"},{"id":495197,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"16","issue":"9","noUsgsAuthors":false,"publicationDate":"2025-09-03","publicationStatus":"PW","contributors":{"authors":[{"text":"Meyer, Michael Frederick 0000-0002-8034-9434 mmeyer@usgs.gov","orcid":"https://orcid.org/0000-0002-8034-9434","contributorId":304191,"corporation":false,"usgs":true,"family":"Meyer","given":"Michael","email":"mmeyer@usgs.gov","middleInitial":"Frederick","affiliations":[{"id":37786,"text":"WMA - 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In this study, annotation data were transformed into semantic graph triples, mainly for use with the Resource Description Framework (RDF), a type of entity-relationship-attribute data model for graph databases. The transformation of annotation data to semantic graph triples provides complex linguistic meaning with data handling advantages such as reduced data storage needs, improved logical specification of relations between objects, and reusable classes and properties that support logic and inference. A grammar-based framework in graph form supports user questions and queries.
The words defining approximately 334 topographic feature types compiled by the U.S. Geological Survey were tokenized as units of analysis and grouped by part of speech. Their dependency relations were identified for this study using natural language processing libraries. Dependency concepts are used as structured semantic relations among part-of-speech classes. Tokens, units equivalent to words, form instances of classes and were quantified within a tabular output format using PostgreSQL data storage software. Table data were logically aligned as triples following a mapping file and stored with an ontology file using Ontop virtual triplestore software. A grammar ontology schema for the data was synchronized to match queries whose results validated the graph’s structure. The text analysis produced 8 part-of-speech classes of content words for object representations and 4 classes of function words for operational applications. Dependency relations formed 27 ontology properties for topographic subgraph structures. Token occurrences shaped overall ontology salience and formed a lexicon of syntactic terms for subgraph objects and properties. The schema ontology of class and property population shapes formed the lexicon of English terms. SPARQL Protocol and RDF Query Language (SPARQL) was used with the lexicon to conform data to RDF guidelines.
This study confirms the hypothesis that although linguistic logic varies from description logic, its approximation applies to ontology design. Property and query use case patterns extracted from the analysis support queries concerning complex topographic relations and patterns normally embedded within text definitions. The method used in this study could be applied to text forms in other domains, such as survey notes.
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U.S. Geological Survey
Box 25046, Mail Stop 510
Denver, Colorado 80225-0046
Symbiodiniaceae-associated microbiota strongly influence cnidarian symbioses. We systematically reduced the bacterial and fungal communities associated with Symbiodiniaceae to study potential effects on the cnidarian holobiont Exaiptasia diaphana (Aiptasia). Clonal anemones were inoculated with xenic Breviolum minutum (SSB01) and microbiome-manipulated cultures after antibacterial or antifungal treatment. The asexual reproduction of pedal laceration allowed for three generations of clonal aposymbiotic Aiptasia to be utilised in this study, from the initial adult generation (G0), to the first (G1), and second (G2) generation. We inoculated small and large G1 Aiptasia with SSB01 algae and monitored onset of symbiosis, rate of algal proliferation, and holobiont characteristics. Sequencing the 16S and 18S rRNA gene regions identified significant differences in the bacterial and fungal communities of the G0 and G1 generations, alongside differences between the size classes of small and large G1 anemones. The microbiome of larger G1 individuals was distinct to the smaller G1 anemones, suggesting a microbiome maturation process. Control Breviolum minutum cultures exhibited a significantly greater proliferation rate in large G1 anemones when compared to antibacterial or antifungal treated cultures, whereas the opposite trend was documented in the small G1 anemones. Although no differences were observed between algal photochemical parameters, or the growth and polyp activity of G1 juveniles, we observed a significant influence in the production of G2 clones between treatments. Overall, we provide strong ecological implications of manipulating Symbiodiniaceae microbiome, not for the algae themselves, but for the maturation of the host Aiptasia, as well as for the cnidarian holobiont over multiple generations.
","language":"English","publisher":"Oxford Academic","doi":"10.1093/ismejo/wraf189","usgsCitation":"Mccauley, M., Montesanto, F., Bedgood, S.A., Miner, C., Plichon, K., Weis, V.M., and Loesgen, S., 2025, Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host: The ISME Journal, v. 19, no. 1, wraf189, 14 p., https://doi.org/10.1093/ismejo/wraf189.","productDescription":"wraf189, 14 p.","ipdsId":"IP-180949","costCenters":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"links":[{"id":497741,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1093/ismejo/wraf189","text":"Publisher Index Page"},{"id":497644,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"19","issue":"1","noUsgsAuthors":false,"publicationDate":"2025-09-02","publicationStatus":"PW","contributors":{"authors":[{"text":"Mccauley, Mark 0000-0001-5347-6860","orcid":"https://orcid.org/0000-0001-5347-6860","contributorId":357083,"corporation":false,"usgs":true,"family":"Mccauley","given":"Mark","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"preferred":true,"id":952549,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Montesanto, Federica","contributorId":364337,"corporation":false,"usgs":false,"family":"Montesanto","given":"Federica","affiliations":[{"id":86810,"text":"Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA","active":true,"usgs":false}],"preferred":false,"id":952550,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Bedgood, Samuel A.","contributorId":364338,"corporation":false,"usgs":false,"family":"Bedgood","given":"Samuel","middleInitial":"A.","affiliations":[{"id":86811,"text":"Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA","active":true,"usgs":false}],"preferred":false,"id":952551,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Miner, Cody","contributorId":364339,"corporation":false,"usgs":false,"family":"Miner","given":"Cody","affiliations":[{"id":86810,"text":"Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA","active":true,"usgs":false}],"preferred":false,"id":952552,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Plichon, Keyla","contributorId":364340,"corporation":false,"usgs":false,"family":"Plichon","given":"Keyla","affiliations":[{"id":86811,"text":"Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA","active":true,"usgs":false}],"preferred":false,"id":952553,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Weis, Virginia M.","contributorId":364341,"corporation":false,"usgs":false,"family":"Weis","given":"Virginia","middleInitial":"M.","affiliations":[{"id":86811,"text":"Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA","active":true,"usgs":false}],"preferred":false,"id":952554,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Loesgen, Sandra","contributorId":364342,"corporation":false,"usgs":false,"family":"Loesgen","given":"Sandra","affiliations":[{"id":86810,"text":"Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA","active":true,"usgs":false}],"preferred":false,"id":952555,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ,{"id":70271701,"text":"70271701 - 2025 - Satellite tracking reveals heavy use of local MPAs by green turtles (Chelonia mydas) nesting in southeast Florida, USA","interactions":[],"lastModifiedDate":"2025-09-19T14:49:14.117443","indexId":"70271701","displayToPublicDate":"2025-09-02T09:44:34","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2660,"text":"Marine Biology","active":true,"publicationSubtype":{"id":10}},"displayTitle":"Satellite tracking reveals heavy use of local MPAs by green turtles (Chelonia mydas) nesting in southeast Florida, USA","title":"Satellite tracking reveals heavy use of local MPAs by green turtles (Chelonia mydas) nesting in southeast Florida, USA","docAbstract":"Florida hosts a regionally important nesting aggregation of green turtles (Chelonia mydas) in the North Atlantic, yet internesting and post-nesting movements for this rookery remain poorly understood. Here, we used satellite telemetry to track 23 green turtles nesting on southeast Florida beaches from 2017 to 2021 to investigate their spatial ecology and use of marine protected areas (MPAs) during internesting, migration, and foraging. Marine protected areas are widely used in marine conservation and can be powerful tools for managing species and protecting biodiversity. During internesting, turtles used nearshore, unprotected coastal waters adjacent to the study site. After the nesting season, turtles migrated 24.1 to 203.5 km to previously identified foraging grounds, including areas within Biscayne National Park and Florida Keys National Marine Sanctuary, as well as a high-use but unprotected area off Cape Sable, Florida. Throughout the internesting and foraging periods, turtles exhibited little spatial overlap of core-use areas, suggesting limited space-use sharing even in high-density regions. This study provides the first satellite telemetry dataset for green turtles from southeast Florida and reveals their strong reliance on a relatively small MPA network along southwest Florida. Our findings underscore how these MPAs can support conservation efforts for Florida’s overall green turtle nesting population, while further emphasizing the potential benefits of expanded protections in key areas to safeguard regionally important green turtle habitat.
","language":"English","publisher":"Springer Nature","doi":"10.1007/s00227-025-04694-5","usgsCitation":"Goodwin, G.D., Hart, K., Evans, A.C., and Burkholder, D.A., 2025, Satellite tracking reveals heavy use of local MPAs by green turtles (Chelonia mydas) nesting in southeast Florida, USA: Marine Biology, v. 172, no. 10, 153, 13 p., https://doi.org/10.1007/s00227-025-04694-5.","productDescription":"153, 13 p.","ipdsId":"IP-173964","costCenters":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"links":[{"id":495795,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Florida","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -83,\n 26.5\n ],\n [\n -83,\n 24\n ],\n [\n -80,\n 24\n ],\n [\n -80,\n 26.5\n ],\n [\n -83,\n 26.5\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"172","issue":"10","noUsgsAuthors":false,"publicationDate":"2025-09-02","publicationStatus":"PW","contributors":{"authors":[{"text":"Goodwin, Glenn D.","contributorId":361599,"corporation":false,"usgs":false,"family":"Goodwin","given":"Glenn","middleInitial":"D.","affiliations":[{"id":81512,"text":"Halmos College of Arts and Sciences, Nova Southeastern University","active":true,"usgs":false}],"preferred":false,"id":949064,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Hart, Kristen 0000-0002-5257-7974","orcid":"https://orcid.org/0000-0002-5257-7974","contributorId":222407,"corporation":false,"usgs":true,"family":"Hart","given":"Kristen","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"preferred":true,"id":949065,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Evans, Abby C.","contributorId":361600,"corporation":false,"usgs":false,"family":"Evans","given":"Abby","middleInitial":"C.","affiliations":[{"id":81512,"text":"Halmos College of Arts and Sciences, Nova Southeastern University","active":true,"usgs":false}],"preferred":false,"id":949066,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Burkholder, Derek A. 0000-0001-6315-6932","orcid":"https://orcid.org/0000-0001-6315-6932","contributorId":289783,"corporation":false,"usgs":false,"family":"Burkholder","given":"Derek","email":"","middleInitial":"A.","affiliations":[{"id":62249,"text":"Halmos College of Natural Sciences and Oceanography, Department of Marine and Environmental Science, Nova Southeastern University","active":true,"usgs":false}],"preferred":false,"id":949067,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70273218,"text":"70273218 - 2025 - A scientific vision and roadmap for earthquake rupture forecast developments, a USGS perspective","interactions":[],"lastModifiedDate":"2025-12-22T15:16:05.64178","indexId":"70273218","displayToPublicDate":"2025-09-02T08:07:40","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1135,"text":"Bulletin of the Seismological Society of America","onlineIssn":"1943-3573","printIssn":"0037-1106","active":true,"publicationSubtype":{"id":10}},"title":"A scientific vision and roadmap for earthquake rupture forecast developments, a USGS perspective","docAbstract":"We articulate a scientific vision and roadmap for the development of improved Earthquake Rupture Forecast models, which are one of the two main modeling components used in modern seismic hazard and risk analysis. One primary future objective is to provide fully time-dependent models that include both elastic rebound and spatiotemporal clustering nationwide, which is particularly important for shorter-term hazard and risk considerations (e.g., earthquake insurance products). We also discuss the importance and perennial challenges associated with quantifying epistemic uncertainties, including those associated with deformation-model slip rates, un-quantified sampling errors with respect to off-fault seismicity, and any spatial covariances. The need for more physics-based approaches is also emphasized, as is the benefit of adding model valuation (quantifying usefulness) to our verification and validation protocols. Given the multidisciplinary and system-level nature of this activity, modular design is critical. Future updates will also draw from best-available science by both the United States Geological Survey and the external community. The primary goal of this paper is to highlight plans that guide research and facilitate community engagement with model development, especially with respect to lowering the entry barrier for early career scientists and engineers. The paper is written so readers can focus on the sections that interest them most (see table of contents), with the Introduction and Discussion providing a stand-alone overview and summary.","language":"English","publisher":"Seismological Society of America","doi":"10.1785/0120240217","usgsCitation":"Field, E.H., Hatem, A.E., Shaw, B.E., Page, M.T., Mai, P.M., Milner, K., Llenos, A.L., Michael, A.J., Pollitz, F., Jobe, J.A., Parsons, T.E., Zielke, O., Shelly, D.R., Gabriel, A., McPhillips, D., Briggs, R.W., Cochran, E.S., Luco, N., Petersen, M.D., Powers, P.M., Rubinstein, J., Shumway, A., van der Elst, N., Zeng, Y., DuRoss, C., and Altekruse, J.M., 2025, A scientific vision and roadmap for earthquake rupture forecast developments, a USGS perspective: Bulletin of the Seismological Society of America, v. 115, no. 6, p. 2523-2552, https://doi.org/10.1785/0120240217.","productDescription":"30 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U.S. Geological Survey
47914 252nd Street
Sioux Falls, SD 57198
The U.S. Geological Survey Earth Resources Observation and Science Calibration and Validation Center of Excellence Team assesses and calibrates Landsat remote-sensing data to ensure high-quality data products are publicly available. These data products are used to make informed decisions about natural resources and the environment. This report is part of a series of quarterly reports intended to provide updated observed geometric and radiometric analysis results for Landsats 8 and 9.
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We evaluate these questions in the St. Louis River estuary—a hydrologically and spatially complex coastal system within Lake Superior that supports a diverse assemblage of resident and migratory fish species—via comparison of eDNA metabarcoding (12S and 16S loci) to multigear capture survey data from 2 years and two seasons.
The eDNA and capture surveys collectively yielded 68 fish species: 2 species detected only by capture, 27 detected only by eDNA, and 39 shared across both survey types but having generally higher occurrence frequencies with eDNA than capture. Six species detected only by eDNA were unexpected, having no prior records in the Lake Superior basin. Data from paired eDNA and capture stations showed little relationship between the two survey types, with capture yielding species at stations that eDNA did not, eDNA detecting species in different habitats and distant locations from any captures, and assemblage patterns homogenized in eDNA surveys relative to capture surveys.
Our study finds that eDNA is a sensitive tool for assessing species presence at the system scale but that capture surveys may better yield the fine-scale spatial distribution information of interest to fisheries and habitat managers, especially in spatially and hydrologically complex systems.
No abstract available.
","largerWorkType":{"id":18,"text":"Report"},"largerWorkTitle":"The 2024 annual report of the International Red River Watershed Board","largerWorkSubtype":{"id":3,"text":"Organization Series"},"language":"English","publisher":"International Joint Commission","usgsCitation":"Thomas, D., 2025, USGS water resource investigations and activities: Annual Report, v. 25, 15 p.","productDescription":"15 p.","startPage":"88","endPage":"102","ipdsId":"IP-179575","costCenters":[{"id":34685,"text":"Dakota Water Science Center","active":true,"usgs":true}],"links":[{"id":501179,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":501178,"rank":1,"type":{"id":15,"text":"Index Page"},"url":"https://ijc.org/en/rrb/irrwb-annual-report-2024"}],"volume":"25","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Thomas, Daniel C 0009-0005-7051-9670","orcid":"https://orcid.org/0009-0005-7051-9670","contributorId":357351,"corporation":false,"usgs":true,"family":"Thomas","given":"Daniel C","affiliations":[{"id":34685,"text":"Dakota Water Science Center","active":true,"usgs":true}],"preferred":true,"id":941274,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":70272662,"text":"70272662 - 2025 - Critical mineral inventory of select IOA-IOCG deposits, southwestern USA","interactions":[],"lastModifiedDate":"2025-12-03T16:19:12.788724","indexId":"70272662","displayToPublicDate":"2025-09-01T10:11:28","publicationYear":"2025","noYear":false,"publicationType":{"id":24,"text":"Conference Paper"},"publicationSubtype":{"id":19,"text":"Conference Paper"},"title":"Critical mineral inventory of select IOA-IOCG deposits, southwestern USA","docAbstract":"Critical minerals are necessary for modern technology and strategic purposes. Their increasing importance requires finding new and nontraditional resources. Samples of ore, altered, and unaltered host rock were collected from 26 iron mines and prospects in California, Nevada, and Utah to assess the potential of these deposits to host economic quantities of different critical minerals. Geochemical analyses were conducted by 61 element ICP-OES-MS sodium peroxide fusion and major elements determined by WDXRF. These deposits concentrated many critical minerals beyond what is found in average upper crustal abundances, such as Sb, As, Bi, Co, Ga, Mg, Mn, Ni, Nb, Pd, REE, Sc, Te, Sn, Ti, W, V, and Zn. However, most of these are not concentrated enough in the ore to be considered as economic resources. Those critical minerals that are enriched enough in some of these deposits to possibly be considered as by-product commodities are Ni, REE, V, and potentially Co and Ga. These enrichments were not uniform, with REE more likely to be enriched in IOA deposits, whereas Co, Ga, Ni, and V could be found enriched in either IOA or IOCG deposits.","conferenceTitle":"18th SGA Biennial Meeting","conferenceDate":"August 3-7, 2025","conferenceLocation":"Golden, CO","language":"English","publisher":"Society for Geology Applied to Mineral Deposits","usgsCitation":"Taylor, R., Meighan, C.J., and Hofstra, A.H., 2025, Critical mineral inventory of select IOA-IOCG deposits, southwestern USA, 18th SGA Biennial Meeting, v. 3, Golden, CO, August 3-7, 2025, p. 963-966.","productDescription":"4 p.","startPage":"963","endPage":"966","ipdsId":"IP-176357","costCenters":[{"id":35995,"text":"Geology, Geophysics, and Geochemistry Science Center","active":true,"usgs":true}],"links":[{"id":497013,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":497012,"rank":1,"type":{"id":15,"text":"Index Page"},"url":"https://www.e-sga.org/publications/conference-proceedings"}],"country":"United States","state":"California, Nevada, Utah","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -114.96837443642112,\n 32.704121200218324\n ],\n [\n -114.90627175927149,\n 35.276512718803005\n ],\n [\n -113.85778870259917,\n 36.75952704897722\n ],\n [\n -111.12601522383044,\n 37.041029453418844\n ],\n [\n -111.18086370424344,\n 38.21185945627386\n ],\n [\n -113.95734086339156,\n 38.55172394057118\n ],\n [\n -113.9625620365557,\n 41.846893445470926\n ],\n [\n -120.18862063281,\n 42.02269387816904\n ],\n [\n -121.46065541607419,\n 41.96050209334149\n ],\n [\n -121.80133036685531,\n 39.645958588292274\n ],\n [\n -114.96837443642112,\n 32.704121200218324\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"3","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Taylor, Ryan D. 0000-0002-8845-5290","orcid":"https://orcid.org/0000-0002-8845-5290","contributorId":201948,"corporation":false,"usgs":true,"family":"Taylor","given":"Ryan D.","affiliations":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":951245,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Meighan, Corey J. 0000-0002-5668-1621 cmeighan@usgs.gov","orcid":"https://orcid.org/0000-0002-5668-1621","contributorId":5892,"corporation":false,"usgs":true,"family":"Meighan","given":"Corey","email":"cmeighan@usgs.gov","middleInitial":"J.","affiliations":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":951246,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Hofstra, Albert H. 0000-0002-2450-1593 ahofstra@usgs.gov","orcid":"https://orcid.org/0000-0002-2450-1593","contributorId":1302,"corporation":false,"usgs":true,"family":"Hofstra","given":"Albert","email":"ahofstra@usgs.gov","middleInitial":"H.","affiliations":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":951247,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70272004,"text":"70272004 - 2025 - Assessing diet and genotyping success of goat pellet surveys from 2019 in Glacier National Park","interactions":[],"lastModifiedDate":"2025-09-30T15:06:54.506965","indexId":"70272004","displayToPublicDate":"2025-09-01T10:03:46","publicationYear":"2025","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":1,"text":"Federal Government Series"},"displayTitle":"Assessing Diet and Genotyping Success of Goat Pellet Surveys from 2019 in Glacier National Park","title":"Assessing diet and genotyping success of goat pellet surveys from 2019 in Glacier National Park","docAbstract":"Fecal pellets contain genetic information and can be used to identify individuals, their diet, and more. Individual identification can be useful in understanding movements of individuals, developing population estimates, assessing vital rates, genetic diversity and structure, and evaluating trends over time (e.g., Epps et al 2024). Successful genotyping depends on the quality of the sample, which can be influenced by many things including the initial state of the sample, environmental conditions that the pellets were exposed to, and the method of storage.
The diet of mountain goats (Oreamnos americanus) is hard to study as they are habitat specialists in some of the most remote and rugged alpine environments (Festa-Bianchet & Côté 2012). These iconic ungulates epitomize the renowned wilderness character of Glacier National Park (GNP), yet the population has declined by 45% since 2008 likely due at least in part to changing climate (Graves et al. 2025). This is well above the International Union for the Conservation of Nature’s population decline criterion used to designate a species as vulnerable (IUCN 2012).
Mountain goats are known as dietary generalists employing highly variable diets across systems, but diets have not been identified for GNP. Identifying goat diet composition in GNP can provide the information needed to determine whether this population decline could be related to climate-change induced shifts in forage phenology, diversity, productivity, and plant community structure. Other anthropogenic changes in GNP, such as increases in exotic and invasive plant species, will continue to affect plant community composition (Lesica et al. 1993). These alterations may reduce optimal forage availability and quality, which could have a deleterious effect on mountain goat survival. To examine these possibilities, we must first ask- What precisely are the mountain goats of Glacier National Park eating?
DNA metabarcoding of fecal pellets provides a cutting-edge, non-invasive method for assessing herbivore diet. Previous studies of mountain goat diet have used methods such as fecal crude protein analysis (Festa-Bianchet & Côté 2012), rumen analysis (Saunders 1955), fecal microhistology (Cobb et al. 2012), and bite-for-bite feeding observations (Daily et al. 1984). Many of these studies have only been able to identify diet components to functional plant type and the methods used are biased towards less digestible diet components such as grasses (McInnis et al. 1983). Metabarcoding of fecal pellets can provide a higher taxonomic resolution than previous methods (Scasta et al. 2019, Stapleton et al. 2022) and open the field for increased participation of volunteers, also called community or citizen scientists.
Here, we use mountain goat fecal pellets to conduct 1) an evaluation of which conditions might influence genotyping success and 2) a preliminary assessment of diet using metabarcoding. This pilot study allowed us to evaluate which pellets to focus on collecting, identify the best storage methods, explore approaches for analyzing metabarcoding data, examine the utility of metabarcoding for acquiring taxonomically specific diet information, and to identify genetic sequences that could not be resolved to genus or species levels using these methods. We examined the frequency of occurrence and relative diet composition of identified forbs, shrubs, graminoids, mosses, and trees in mountain goat diets.
","language":"English","publisher":"National Park Service","usgsCitation":"Scoresby, S., Dose, L.M., Belt, J., and Graves, T., 2025, Assessing diet and genotyping success of goat pellet surveys from 2019 in Glacier National Park, 23 p.","productDescription":"23 p.","ipdsId":"IP-174564","costCenters":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"links":[{"id":496262,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":496254,"rank":1,"type":{"id":15,"text":"Index Page"},"url":"https://irma.nps.gov/DataStore/Reference/Profile/2311387"}],"country":"United States","state":"Montana","otherGeospatial":"Glacier National Park","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -113.60109929508316,\n 49.00250961037867\n ],\n [\n -114.47247108032799,\n 49.00250961037867\n ],\n [\n -114.08980516405627,\n 48.48262143393191\n ],\n [\n -113.89155655683145,\n 48.4856773542281\n ],\n [\n -113.53655323691696,\n 48.22526656841134\n ],\n [\n -113.20921251335938,\n 48.41534459946189\n ],\n [\n -113.60109929508316,\n 49.00250961037867\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Scoresby, Salix","contributorId":352228,"corporation":false,"usgs":false,"family":"Scoresby","given":"Salix","affiliations":[{"id":84134,"text":"Contractor, USGS (Northern Arizona University)","active":true,"usgs":false}],"preferred":false,"id":949691,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Dose, Lindsay M","contributorId":361945,"corporation":false,"usgs":false,"family":"Dose","given":"Lindsay","middleInitial":"M","affiliations":[{"id":27609,"text":"Contractor to USGS","active":true,"usgs":false}],"preferred":false,"id":949692,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Belt, Jami","contributorId":177314,"corporation":false,"usgs":false,"family":"Belt","given":"Jami","affiliations":[],"preferred":false,"id":949693,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Graves, Tabitha A. 0000-0001-5145-2400","orcid":"https://orcid.org/0000-0001-5145-2400","contributorId":202084,"corporation":false,"usgs":true,"family":"Graves","given":"Tabitha A.","affiliations":[{"id":481,"text":"Northern Rocky Mountain Science Center","active":true,"usgs":true}],"preferred":true,"id":949694,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70272285,"text":"70272285 - 2025 - Disturbance is the primary determinant of food chain length when the top predator is constant","interactions":[],"lastModifiedDate":"2025-11-20T16:30:30.424268","indexId":"70272285","displayToPublicDate":"2025-09-01T09:24:13","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2299,"text":"Journal of Freshwater Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Disturbance is the primary determinant of food chain length when the top predator is constant","docAbstract":"Food chain length (FCL) is a primary determinant of food web structure and is hypothesized to be influenced by habitat size, productivity, and disturbance. Understanding the environmental characteristics that determine food chain length can assist in understanding how food webs may be impacted due to changes in habitats and environmental characteristics. This study examines the impact of hydrologic disturbance on stream food webs when the top predator is constant. We analyzed FCL in less disturbed groundwater flashy streams and more disturbed runoff flashy streams using stable isotopes. Despite no difference in species richness or fish density, food chains in more disturbed streams had a lower FCL compared to food chains in more stable streams. Assemblage analysis showed that flow regime and drainage area significantly impacted individual species abundances. The more disturbed runoff flashy streams had higher proportions of primary consumer fish, such as the algivorous Campostoma sp. (Stonerollers), which likely drives the reduced FCL. Drainage area and land cover had non-significant relationships with FCL. Shifting community structure due to hydrologic variability likely leads to differences in diet of Micropterus dolomieu (Smallmouth Bass), and thus a difference in FCL.
","language":"English","publisher":"Taylor & Francis","doi":"10.1080/02705060.2025.2552789","usgsCitation":"Sorensen, S.F., and Magoulick, D.D., 2025, Disturbance is the primary determinant of food chain length when the top predator is constant: Journal of Freshwater Ecology, v. 40, no. 1, 2552789, 13 p., https://doi.org/10.1080/02705060.2025.2552789.","productDescription":"2552789, 13 p.","ipdsId":"IP-158669","costCenters":[{"id":198,"text":"Coop Res Unit Atlanta","active":true,"usgs":true}],"links":[{"id":496764,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1080/02705060.2025.2552789","text":"Publisher Index Page"},{"id":496698,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Arkansas, Missouri, Oklahoma","otherGeospatial":"Boston Mountains, Ozark Highlands","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -94.36140202738136,\n 36.86778775165942\n ],\n [\n -95.16750642659139,\n 35.284730700987836\n ],\n [\n -90.54968868524054,\n 35.4188870788884\n ],\n [\n -89.35998010774131,\n 36.86867805963976\n ],\n [\n -92.3624285247389,\n 37.51630205547987\n ],\n [\n -93.33606079252797,\n 37.097059236951665\n ],\n [\n -94.36140202738136,\n 36.86778775165942\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"40","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Sorensen, Sarah F.","contributorId":362643,"corporation":false,"usgs":false,"family":"Sorensen","given":"Sarah","middleInitial":"F.","affiliations":[{"id":6623,"text":"University of Arkansas","active":true,"usgs":false}],"preferred":false,"id":950684,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Magoulick, Daniel D. 0000-0001-9665-5957 danmag@usgs.gov","orcid":"https://orcid.org/0000-0001-9665-5957","contributorId":2513,"corporation":false,"usgs":true,"family":"Magoulick","given":"Daniel","email":"danmag@usgs.gov","middleInitial":"D.","affiliations":[{"id":198,"text":"Coop Res Unit Atlanta","active":true,"usgs":true},{"id":200,"text":"Coop Res Unit Seattle","active":true,"usgs":true}],"preferred":true,"id":950685,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70273401,"text":"70273401 - 2025 - Newly released Grand Canyon flash flood incident report","interactions":[],"lastModifiedDate":"2026-01-12T16:09:12.732432","indexId":"70273401","displayToPublicDate":"2025-09-01T09:22:30","publicationYear":"2025","noYear":false,"publicationType":{"id":25,"text":"Newsletter"},"publicationSubtype":{"id":30,"text":"Newsletter"},"seriesTitle":{"id":8569,"text":"Boatman's Quarterly Review","active":true,"publicationSubtype":{"id":30}},"title":"Newly released Grand Canyon flash flood incident report","docAbstract":"No abstract available.
","language":"English","publisher":"Grand Canyon River Guides","usgsCitation":"Byerley, E.P., 2025, Newly released Grand Canyon flash flood incident report: Boatman's Quarterly Review, v. 38, no. 3.","productDescription":"1 p.","startPage":"13","ipdsId":"IP-181804","costCenters":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"links":[{"id":498535,"rank":2,"type":{"id":15,"text":"Index Page"},"url":"https://www.gcrg.org/bqr"},{"id":498549,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Arizona","otherGeospatial":"Grand Canyon","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -111.37659635793055,\n 36.92768493688186\n ],\n [\n -114.02194696398374,\n 36.92768493688186\n ],\n [\n -114.02194696398374,\n 35.784272392896824\n ],\n [\n -111.37659635793055,\n 35.784272392896824\n ],\n [\n -111.37659635793055,\n 36.92768493688186\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"38","issue":"3","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Byerley, Erica Paige 0009-0003-8483-7528","orcid":"https://orcid.org/0009-0003-8483-7528","contributorId":333657,"corporation":false,"usgs":true,"family":"Byerley","given":"Erica","email":"","middleInitial":"Paige","affiliations":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"preferred":true,"id":953587,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ]}