Hybridization and interspecific gene flow play a substantial role in the evolution of plant taxa. The eastern North American white oak syngameon, a group of approximately 15 ecologically, morphologically and genomically distinguishable species, has long been recognised as a model system for studying introgressive hybridization in temperate trees. However, the prevalence, genomic context and environmental correlates of introgression in this system remain largely unknown. To assess introgression in the eastern North American white oak syngameon and population structure within the widespread Quercus macrocarpa, we conducted a rangewide survey of Q. macrocarpa and four sympatric eastern North American white oak species. Using a Hyb-Seq approach, we assembled a dataset of 3412 thinned single-nucleotide polymorphisms (SNPs) in 445 enriched target loci including 62 genes putatively associated with various ecological functions, as well as associated intronic regions and some off-target intergenic regions (not associated with the exons). Admixture analysis and hybrid class inference demonstrated species coherence despite hybridization and introgressive gene flow (due to backcrossing of F1s to one or both parents). Additionally, we recovered a genetic structure within Q. macrocarpa associated with latitude. Generalised linear mixed models (GLMMs) indicate that proximity to range edge predicts interspecific admixture, but rates of genetic differentiation do not appear to vary between putative functional gene classes. Our study suggests that gene flow between eastern North American white oak species may not be as rampant as previously assumed and that hybridization is most strongly predicted by proximity to a species' range margin.
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The global Landsat archive is made available in the Universal Transverse Mercator (UTM) projection system which preserves geographic shape across small area but introduces small errors in distance and area. As remote sensing-based studies develop from local scales to regional and global, they need to adopt more appropriate map projections from which accurate area measurements can be made. While effects of resampling on recorded values have been studied in the past, the impacts on higher-level results such as land cover have not been widely reported. This study investigates an approach for monitoring land cover and land change using two input datasets derived from identical source Landsat data, where one input dataset is transformed to an equal-area map projection and thereby resampled. Recorded surface reflectance values are changed through the reprojection/resampling process, and our study highlights observed differences in derived land cover from these two different input datasets throughout the various stages of deriving land cover and related characteristics. Our findings suggest that large-scale analyses of land cover will not be substantially impacted by reprojection of input data, but small-scale analyses should exercise caution when interpreting timing and magnitude of pixel-level change and classification dynamics.
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Providing unlimited harvest permits increased harvest, but the same increases were achieved by minimally increasing the number of limited harvest permits. Increasing the length of hunting season had a generally positive effect on antlerless harvest but the effect was non-linear and state dependent. The earn-a-buck incentive program resulted in the largest estimated increase in harvest. Finally, the number of licensed deer hunters in a state had a strong positive effect on the number of antlerless deer harvested. Our findings show that commonly applied changes in harvest regulations have a weak effect on the number of antlerless deer harvested, highlighting the challenges facing deer managers in the Midwestern US.
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sturgeon","interactions":[],"lastModifiedDate":"2025-07-18T14:34:21.386482","indexId":"70269296","displayToPublicDate":"2025-06-03T09:27:33","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1497,"text":"Endangered Species Research","active":true,"publicationSubtype":{"id":10}},"title":"New insights reveal a temporally distinct two-stock genetic structure for Suwannee River Gulf sturgeon","docAbstract":"Understanding population genetic structure and patterns of gene flow is important for effective decision making and the preservation of genetic diversity, especially when managing protected species. Historically, Gulf sturgeon have been managed by river system, with early evidence supporting spatially distinct genetic structure across 7 natal populations. However, an increasing number of studies recognize that some rivers possess 2 genetically distinct sturgeon stocks residing within the same drainage. This, combined with evidence of both spring and fall spawning events within these drainages, suggests the distinction between these stocks may be temporally mediated, as similarly exhibited by the closely related Atlantic sturgeon. We analyzed the movements of 136 Gulf sturgeon within the Suwannee River, Florida, USA, between 2008 and 2022 using acoustic telemetry. We assessed migratory patterns and presence within known spawning habitat to categorize individuals as exhibiting either spring, fall, or unknown spawning behaviors each year. These individuals were also genotyped for 14 microsatellite loci to assign them to a genetic group. Our results reinforce previous work suggesting the presence of 2 genetically distinct stocks in the Suwannee River and indicate this genetic structure is driven by fidelity to temporally distinct spawning events, with one stock spawning in the spring and the other in fall. The delineation of these 2 sympatric stocks, historically managed as one, has management implications for the recovery of this species.
","language":"English","publisher":"Inter-Research Science Publisher","doi":"10.3354/esr01418","usgsCitation":"Price, M.E., Kreiser, B., and Randall, M.T., 2025, New insights reveal a temporally distinct two-stock genetic structure for Suwannee River Gulf sturgeon: Endangered Species Research, v. 57, p. 289-298, https://doi.org/10.3354/esr01418.","productDescription":"10 p.","startPage":"289","endPage":"298","ipdsId":"IP-167683","costCenters":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"links":[{"id":492863,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.3354/esr01418","text":"Publisher Index Page"},{"id":492535,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Florida, Georgia","otherGeospatial":"Apalachicola River, Ochlockonee River, Suwannee River","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -85.5,\n 31.2\n ],\n [\n -85.5,\n 29\n ],\n [\n -82,\n 29\n ],\n [\n -82,\n 31.2\n ],\n [\n -85.5,\n 31.2\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"57","noUsgsAuthors":false,"publicationDate":"2025-06-03","publicationStatus":"PW","contributors":{"authors":[{"text":"Price, Melissa E. 0000-0002-4276-0855 mprice@usgs.gov","orcid":"https://orcid.org/0000-0002-4276-0855","contributorId":5875,"corporation":false,"usgs":true,"family":"Price","given":"Melissa","email":"mprice@usgs.gov","middleInitial":"E.","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"preferred":true,"id":943382,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kreiser, Brian","contributorId":210007,"corporation":false,"usgs":false,"family":"Kreiser","given":"Brian","affiliations":[{"id":38045,"text":"University of Southern Mississippi, Department of Biological Sciences, Hattiesburg, MS 39406","active":true,"usgs":false}],"preferred":false,"id":943383,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Randall, Michael T. 0000-0001-8805-0886 mrandall@usgs.gov","orcid":"https://orcid.org/0000-0001-8805-0886","contributorId":3127,"corporation":false,"usgs":true,"family":"Randall","given":"Michael","email":"mrandall@usgs.gov","middleInitial":"T.","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true},{"id":566,"text":"Southeast Ecological Science Center","active":true,"usgs":true}],"preferred":true,"id":943384,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70268776,"text":"70268776 - 2025 - Long-term surgery survival, body condition effects, and incision healing of Silver Carp and buffalo species comparing sedation methods across seasons","interactions":[],"lastModifiedDate":"2025-08-04T15:55:57.902628","indexId":"70268776","displayToPublicDate":"2025-06-03T09:25:54","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":21984,"text":"Transactions of the American Fishery Society","active":true,"publicationSubtype":{"id":10}},"title":"Long-term surgery survival, body condition effects, and incision healing of Silver Carp and buffalo species comparing sedation methods across seasons","docAbstract":"Internal tagging for telemetry studies requires invasive surgery procedures, necessitating sufficient sedation to support animal welfare. Challenges with existing chemical sedatives have resulted in technological alternatives, including electrosedation, with these newer methods less extensively studied. Our primary objective was to understand long-term survival, body-condition effects, and incision healing after surgical implantation of an imitation telemetry transmitter under three different sedation techniques.
We collected Silver Carp Hypophthalmichthys molitrix and buffalo Ictiobus spp. from the Missouri River watershed in 2022 and 2023, during each of the four seasons. One of three sedation techniques was applied: electric fish handling gloves, tricaine methanesulfonate (MS-222), and eugenol. Additionally, we observed a group of fish that were unsedated but subjected to handling similar to that experienced during surgery. Fish were monitored to determine the effects of treatment, individual characteristics, surgery characteristics, and time-varying environmental factors on survival, body condition, and incision healing over 69- to 85-d holding periods.
Long-term survival was higher for buffalo (86%) than Silver Carp (57%), with the fewest mortalities during the winter trial and most in summer, but sedation treatment did not affect survival. Smaller fish had a greater risk of mortality but better incision healing. Incision healing scores improved in warmer temperatures.
Difference in seasonal effects on survival and healing indicate a need to consider trade-offs when scheduling tagging for projects. However, a lack of difference in survival among treatments, including the group that was handled but did not undergo surgery, suggests no advantage of one sedative over another, but handling impacts may require more consideration.
Insecticide and fungicide seed coatings have become prevalent in conventional agriculture in recent decades. From 2015 to 2021, the AltEn bioenergy plant (Mead, Nebraska, USA) generated ethanol from almost 100% unused/expired treated corn seeds. This use of these seeds for ethanol production resulted in the accumulation of large amounts of contaminated wastewater and solid residue, a portion of which was applied to surrounding farmland. To better understand the potential long-term environmental effects from the processing of treated seeds at this facility, five nearby stream sites were sampled in 2022 after the closure of the plant; these included two sites directly impacted by AltEn, one upstream, and two downstream of the impacted sites. Water and sediment were collected in March through July, and algae and fish samples were collected in July for chemical analysis. Overall, 60 pesticide compounds (parents and transformation products) were detected in one or more matrices, including 23 fungicides, 20 insecticides, 16 herbicides, and 1 bacterial growth inhibitor. Pesticide results (maximum detection frequency, maximum concentration) varied substantially by environmental compartment: water (100% multiple pesticides; 4,600 ng L−1 thiamethoxam transformation product (NOA-407475)), algae (100% multiple pesticides, 190 ng g−1 atrazine), sediment (60% dithiopyr, 2.3 ng g−1 acetochlor) and fish (20% pyraclostrobin, 2.2 ng g−1 atrazine). Pesticides associated with treated corn seeds (e.g., insecticides clothianidin, thiamethoxam; fungicides fluoxastrobin, thiabendazole) were detected at significantly higher concentrations (p < 0.05) in stream water from sites impacted by the AltEn facility compared to non-impacted sites. Study results indicate that pesticides associated with the AltEn facility continue to be a source of contaminants to aquatic systems after the plant’s closure in 2021.
","language":"English","publisher":"Oxford Academic","doi":"10.1093/etojnl/vgaf139","usgsCitation":"Hladik, M.L., Kolpin, D., De Parsia, M., Snow, D.D., Bartelt-Hunt, S., Densmore, B., Hubbard, L.E., Rus, D., Spurgeon, J., Perrotta, B.G., Kidd, K.A., Kraus, J.M., Givens, C.E., Kotalik, C.J., and Walters, D., 2025, Pesticide concentrations in multiple physical and biological stream matrices are impacted by a bioenergy production facility receiving pesticide coated corn seeds: Environmental Toxicology and Chemistry, v. 44, no. 8, p. 2143-2153, https://doi.org/10.1093/etojnl/vgaf139.","productDescription":"11 p.","startPage":"2143","endPage":"2153","ipdsId":"IP-173482","costCenters":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"links":[{"id":491180,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"44","issue":"8","noUsgsAuthors":false,"publicationDate":"2025-05-30","publicationStatus":"PW","contributors":{"authors":[{"text":"Hladik, Michelle L. 0000-0002-0891-2712","orcid":"https://orcid.org/0000-0002-0891-2712","contributorId":203857,"corporation":false,"usgs":true,"family":"Hladik","given":"Michelle","middleInitial":"L.","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":941088,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kolpin, Dana W. 0000-0002-3529-6505","orcid":"https://orcid.org/0000-0002-3529-6505","contributorId":204154,"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":589,"text":"Toxic Substances Hydrology Program","active":true,"usgs":true}],"preferred":true,"id":941089,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"De Parsia, Matthew D. 0000-0001-5806-5403","orcid":"https://orcid.org/0000-0001-5806-5403","contributorId":204707,"corporation":false,"usgs":true,"family":"De Parsia","given":"Matthew D.","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":941090,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Snow, Daniel D.","contributorId":204934,"corporation":false,"usgs":false,"family":"Snow","given":"Daniel","email":"","middleInitial":"D.","affiliations":[{"id":6754,"text":"University of Missouri","active":true,"usgs":false}],"preferred":false,"id":941091,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Bartelt-Hunt, Shannon","contributorId":189223,"corporation":false,"usgs":false,"family":"Bartelt-Hunt","given":"Shannon","email":"","affiliations":[],"preferred":false,"id":941092,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Densmore, Brenda 0000-0003-2429-638X","orcid":"https://orcid.org/0000-0003-2429-638X","contributorId":215516,"corporation":false,"usgs":true,"family":"Densmore","given":"Brenda","affiliations":[{"id":464,"text":"Nebraska Water Science Center","active":true,"usgs":true}],"preferred":true,"id":941093,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"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":941094,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Rus, David L. 0000-0003-3538-7826","orcid":"https://orcid.org/0000-0003-3538-7826","contributorId":208516,"corporation":false,"usgs":true,"family":"Rus","given":"David L.","affiliations":[{"id":464,"text":"Nebraska Water Science Center","active":true,"usgs":true}],"preferred":true,"id":941095,"contributorType":{"id":1,"text":"Authors"},"rank":8},{"text":"Spurgeon, Jonathan J.","contributorId":146395,"corporation":false,"usgs":false,"family":"Spurgeon","given":"Jonathan J.","affiliations":[],"preferred":false,"id":941096,"contributorType":{"id":1,"text":"Authors"},"rank":9},{"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":941097,"contributorType":{"id":1,"text":"Authors"},"rank":10},{"text":"Kidd, Karen A.","contributorId":201554,"corporation":false,"usgs":false,"family":"Kidd","given":"Karen","email":"","middleInitial":"A.","affiliations":[{"id":25502,"text":"McMaster University","active":true,"usgs":false}],"preferred":false,"id":941098,"contributorType":{"id":1,"text":"Authors"},"rank":11},{"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":941099,"contributorType":{"id":1,"text":"Authors"},"rank":12},{"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 Center","active":true,"usgs":true}],"preferred":true,"id":941100,"contributorType":{"id":1,"text":"Authors"},"rank":13},{"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":941101,"contributorType":{"id":1,"text":"Authors"},"rank":14},{"text":"Walters, David 0000-0002-4237-2158","orcid":"https://orcid.org/0000-0002-4237-2158","contributorId":203410,"corporation":false,"usgs":true,"family":"Walters","given":"David","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":941102,"contributorType":{"id":1,"text":"Authors"},"rank":15}]}} ,{"id":70273657,"text":"70273657 - 2025 - Leucism in a family group and a review of color aberrations in Burrowing Owls (Athene cunicularia)","interactions":[],"lastModifiedDate":"2026-01-22T15:35:37.083978","indexId":"70273657","displayToPublicDate":"2025-05-29T08:25:39","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3784,"text":"Wilson Journal of Ornithology","active":true,"publicationSubtype":{"id":10}},"title":"Leucism in a family group and a review of color aberrations in Burrowing Owls (Athene cunicularia)","docAbstract":"Avian color aberrations capture public interest and sometimes indicate ecological problems. Diagnosing color aberration type can be difficult because nomenclature is inconsistent, appearance of color aberrations vary, typical coloration varies, and there are many undocumented color aberration types. One type of recognized avian color aberration is leucism. Leucism is often colloquially used to refer to all birds that are paler than normal but not albino, but it specifically refers to a plumage aberration in which, from hatching onward, birds are either all white or have patches of bilaterally symmetrical white feathers mixed with normally colored feathers, while retaining black pupils. Here, we document a case of leucism in a family of North American Burrowing Owls (Athene cunicularia). We observed a family group (two adults and five juveniles) of five leucistic, nearly all white owls, and two typically colored owls, in the Conata Basin, South Dakota, USA, in summer 2024. We also compiled all searchable records of color aberrations in Burrowing Owls across their North and South American range. We found 60 records of color aberrations, seven of which were cases of potential leucism. Twenty-five color aberrations were an unknown type in which only eye color was affected, all of them in Florida (USA) or south/central Brazil. Documenting color aberrations in birds can help expand our understanding of the types, causes, and consequences of color aberrations as well as the pigments and genetics that underly normal coloration.
","language":"English","publisher":"Taylor & Francis","doi":"10.1080/15594491.2025.2605827","usgsCitation":"Locatelli, A.J., Livieri, T.M., Forrest, S.C., Matchett, M.R., Conway, C.J., and Mangelsen, T.D., 2025, Leucism in a family group and a review of color aberrations in Burrowing Owls (Athene cunicularia): Wilson Journal of Ornithology, 10 p., https://doi.org/10.1080/15594491.2025.2605827.","productDescription":"10 p.","ipdsId":"IP-178133","costCenters":[{"id":200,"text":"Coop Res Unit Seattle","active":true,"usgs":true}],"links":[{"id":501110,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1080/15594491.2025.2605827","text":"Publisher Index Page"},{"id":498838,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"South Dakota","otherGeospatial":"Buffalo Gap National Grasslands, Conata Basin","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -103.22930479548828,\n 43.4255928036697\n ],\n [\n -103.22930479548828,\n 43.190598329342606\n ],\n [\n -102.87372783973137,\n 43.190598329342606\n ],\n [\n -102.87372783973137,\n 43.4255928036697\n ],\n [\n -103.22930479548828,\n 43.4255928036697\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","edition":"Online First","noUsgsAuthors":false,"publicationDate":"2026-01-09","publicationStatus":"PW","contributors":{"authors":[{"text":"Locatelli, Anthony J.","contributorId":365357,"corporation":false,"usgs":false,"family":"Locatelli","given":"Anthony","middleInitial":"J.","affiliations":[{"id":36394,"text":"University of Idaho","active":true,"usgs":false}],"preferred":false,"id":954201,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Livieri, Travis M.","contributorId":365358,"corporation":false,"usgs":false,"family":"Livieri","given":"Travis","middleInitial":"M.","affiliations":[{"id":6753,"text":"Prairie Wildlife Research","active":true,"usgs":false}],"preferred":false,"id":954202,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Forrest, Steven C.","contributorId":365359,"corporation":false,"usgs":false,"family":"Forrest","given":"Steven","middleInitial":"C.","affiliations":[{"id":87131,"text":"Truckee, CA","active":true,"usgs":false}],"preferred":false,"id":954203,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Matchett, Marc R.","contributorId":365360,"corporation":false,"usgs":false,"family":"Matchett","given":"Marc","middleInitial":"R.","affiliations":[{"id":36188,"text":"U.S. Fish and Wildlife Service","active":true,"usgs":false}],"preferred":false,"id":954204,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Conway, Courtney J. 0000-0003-0492-2953 cconway@usgs.gov","orcid":"https://orcid.org/0000-0003-0492-2953","contributorId":2951,"corporation":false,"usgs":true,"family":"Conway","given":"Courtney","email":"cconway@usgs.gov","middleInitial":"J.","affiliations":[{"id":200,"text":"Coop Res Unit Seattle","active":true,"usgs":true}],"preferred":true,"id":954205,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Mangelsen, Thomas D.","contributorId":365361,"corporation":false,"usgs":false,"family":"Mangelsen","given":"Thomas","middleInitial":"D.","affiliations":[{"id":87132,"text":"Images of Nature Moose Wyoming","active":true,"usgs":false}],"preferred":false,"id":954206,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70270725,"text":"70270725 - 2025 - First evidence of natural reproduction and recruitment of reintroduced Lake Sturgeon in the Coosa River, Georgia","interactions":[],"lastModifiedDate":"2025-08-25T15:12:18.431086","indexId":"70270725","displayToPublicDate":"2025-05-28T08:02:03","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2886,"text":"North American Journal of Fisheries Management","active":true,"publicationSubtype":{"id":10}},"title":"First evidence of natural reproduction and recruitment of reintroduced Lake Sturgeon in the Coosa River, Georgia","docAbstract":"Objective
Lake Sturgeon Acipenser fluences became extirpated from the Coosa River system in Georgia and Alabama during the 1970s. The Georgia Department of Natural Resources began stocking hatchery-raised Lake Sturgeon in 2002 with the goal of reestablishing a self-sustaining population. Stocking lapsed in 2020 due to the COVID-19 pandemic, which allowed an opportunity to assess natural recruitment to the reintroduced population.
Methods
We conducted trammel-net surveys during May–August in 2022 and 2023 and removed a pectoral fin spine section from all captured individuals. We compared the fin spine sections of suspected naturally hatched juveniles with those from known-age, hatchery-raised juveniles to confirm our age estimates.
Results
We captured one age-2 juvenile Lake Sturgeon in 2022 and eight age-3 juveniles in 2023. This indicates the presence of natural recruitment due to the absence of stocking of hatchery individuals in 2020.
Conclusions
Documenting individuals of a year-class that was not created by hatchery-raised juveniles provides the first evidence that offspring of early reintroduced Lake Sturgeon are being recruited into the reintroduced population in the Coosa River, Georgia.
","language":"English","publisher":"American Fisheries Society","doi":"10.1093/najfmt/vqaf037","usgsCitation":"Hamel, M.J., Phillips, M.A., Perry, S.R., Irwin, B., and Damer, J.D., 2025, First evidence of natural reproduction and recruitment of reintroduced Lake Sturgeon in the Coosa River, Georgia: North American Journal of Fisheries Management, v. 45, no. 3, p. 516-522, https://doi.org/10.1093/najfmt/vqaf037.","productDescription":"7 p.","startPage":"516","endPage":"522","ipdsId":"IP-171293","costCenters":[{"id":198,"text":"Coop Res Unit Atlanta","active":true,"usgs":true}],"links":[{"id":494741,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Alabama, Georgia","otherGeospatial":"Coosa River system","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -88.17819090372103,\n 34.949541485813015\n ],\n [\n -88.44127214203048,\n 30.287215825336304\n ],\n [\n -87.3607540518563,\n 30.264942451616683\n ],\n [\n -87.49062855858051,\n 30.936194588981806\n ],\n [\n -85.07916672725408,\n 31.020018492584697\n ],\n [\n -84.674858734638,\n 30.673701378177704\n ],\n [\n -81.44970139212951,\n 30.55716772780623\n ],\n [\n -80.87214916269372,\n 31.931034572906817\n ],\n [\n -81.5735045337178,\n 33.0657629431891\n ],\n [\n -83.1899073469762,\n 34.99997683986355\n ],\n [\n -88.17819090372103,\n 34.949541485813015\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"45","issue":"3","noUsgsAuthors":false,"publicationDate":"2025-05-28","publicationStatus":"PW","contributors":{"authors":[{"text":"Hamel, Martin J.","contributorId":360226,"corporation":false,"usgs":false,"family":"Hamel","given":"Martin","middleInitial":"J.","affiliations":[{"id":12697,"text":"University of Georgia","active":true,"usgs":false}],"preferred":false,"id":946905,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Phillips, Matthew A.","contributorId":360229,"corporation":false,"usgs":false,"family":"Phillips","given":"Matthew","middleInitial":"A.","affiliations":[{"id":36378,"text":"Georgia Department of Natural Resources","active":true,"usgs":false}],"preferred":false,"id":946906,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Perry, Savannah R.","contributorId":360232,"corporation":false,"usgs":false,"family":"Perry","given":"Savannah","middleInitial":"R.","affiliations":[{"id":12697,"text":"University of Georgia","active":true,"usgs":false}],"preferred":false,"id":946907,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Irwin, Brian J. 0000-0002-0666-2641","orcid":"https://orcid.org/0000-0002-0666-2641","contributorId":280043,"corporation":false,"usgs":true,"family":"Irwin","given":"Brian J.","affiliations":[{"id":198,"text":"Coop Res Unit Atlanta","active":true,"usgs":true}],"preferred":true,"id":946908,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Damer, John D.","contributorId":360507,"corporation":false,"usgs":false,"family":"Damer","given":"John","middleInitial":"D.","affiliations":[{"id":36378,"text":"Georgia Department of Natural Resources","active":true,"usgs":false}],"preferred":false,"id":947156,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70269445,"text":"70269445 - 2025 - Leisure boat harbours, hidden alien species, and pollution: A case study of Hinsholmskilen harbour (Gothenburg, Sweden)","interactions":[],"lastModifiedDate":"2025-07-23T14:27:23.832772","indexId":"70269445","displayToPublicDate":"2025-05-26T09:22:43","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2391,"text":"Journal of Micropalaeontology","active":true,"publicationSubtype":{"id":10}},"title":"Leisure boat harbours, hidden alien species, and pollution: A case study of Hinsholmskilen harbour (Gothenburg, Sweden)","docAbstract":"Small leisure boat harbours have important aesthetic and recreational values in any country with a coastline. In Sweden, there are about 860 000 leisure boats, which is one of the world's highest numbers in relation to the country's population. However, small boat harbours also present a wide range of environmental problems, including the introduction of alien species and high pollution. In this study, we investigated the ecological quality status (EcoQS) of the Hinsholmskilen small boat harbour, located southwest of the city of Gothenburg (Sweden). We performed a reconnaissance survey of the harbour's previously unstudied benthic foraminiferal communities and analysed surface sediment (0–2 cm) samples for potentially toxic elements: copper (Cu), zinc (Zn), lead (Pb), cobalt (Co), nickel (Ni), chromium (Cr), mercury (Hg), and arsenic (As). The results show that, based on the total benthic foraminiferal distribution (dead and live specimens), the assemblages in Hinsholmskilen harbour represent a typical European estuarine community with highly abundant Ammonia and Elphidium species. Based on molecular and morphological data, we report the presence of two alien and putatively invasive species likely originating from Asia: Trochammina hadai and Ammonia confertitesta (phylotype T6). Both species have recently been identified elsewhere on the Swedish west coast based on molecular and morphological data but do not have a well-known distribution. The sediment analysis for potentially toxic elements showed that the harbour has good to high EcoQS corresponding to no or little deviation from reference conditions for Cd, Co, Ni, and Pb distribution. Some of the contaminants (Pb, As, Zn, and Cr) showed poor to bad EcoQS in the innermost harbour in proximity to high-pressure cleaning plants, where boats are usually lifted, cleaned, and prepared for winter storage on land. Finally, Cu and Hg showed consistently bad and poor EcoQS all over the harbour, reflecting the use of both metals as biocides in antifouling boat paints.
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2025 - Foraging of wading birds on a patchy landscape: Simulating effects of social information, interference competition, and patch selection on prey intake and individual distribution","interactions":[],"lastModifiedDate":"2025-06-25T14:30:13.104344","indexId":"70268407","displayToPublicDate":"2025-05-21T09:26:42","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1458,"text":"Ecological Modelling","active":true,"publicationSubtype":{"id":10}},"title":"Foraging of wading birds on a patchy landscape: Simulating effects of social information, interference competition, and patch selection on prey intake and individual distribution","docAbstract":"Foragers on patchy landscapes must acquire sufficient resources despite uncertainty in the location and amount of the resources. Optimal Foraging Theory posits that foragers deal with this uncertainty by using strategies that optimize resource intake within foraging periods. For species such as wading birds, this optimization is closely linked to their survival and reproductive success. Understanding the influence of patch selection on individual resource intake and foraging distribution is therefore crucial. In this study, we simulated how resource distribution, interference competition, and social cues—such as aggregation behaviors—influence resource intake and foraging spatial distribution. We employed an individual-based model simulating wading bird foraging behaviors, with 900 individuals simultaneously foraging across a landscape with unknown resource distribution. Birds employed one of three patch-finding strategies: random, cue-searching, or hybrid, which uses both searching strategies. Each bird decided whether to remain in a patch based on a prey density threshold. We compared the daily resource intake and foraging distribution of birds across different modeled patch-finding strategies, resource distribution patterns, and the presence or absence of interference competition. Wading birds exhibiting aggregation behavior displayed increased intake rates when resources were concentrated and interference minimal. Aggregation behavior led to a closer match with the ideal free distribution when the prey density threshold was optimal. These findings provide theoretical support that aggregation behavior is effective in scenarios where resources are concentrated in a few patches, social cues are used by relatively few individuals, and interference competition is limited.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.ecolmodel.2025.111178","usgsCitation":"Lee, H.W., DeAngelis, D., Yurek, S., and Papastamatiou, Y., 2025, Foraging of wading birds on a patchy landscape: Simulating effects of social information, interference competition, and patch selection on prey intake and individual distribution: Ecological Modelling, v. 507, 111178, 14 p., https://doi.org/10.1016/j.ecolmodel.2025.111178.","productDescription":"111178, 14 p.","ipdsId":"IP-175552","costCenters":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"links":[{"id":491501,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1016/j.ecolmodel.2025.111178","text":"Publisher Index Page"},{"id":491277,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"507","noUsgsAuthors":false,"publicationDate":"2025-05-21","publicationStatus":"PW","contributors":{"authors":[{"text":"Lee, Hyo Won","contributorId":292184,"corporation":false,"usgs":false,"family":"Lee","given":"Hyo","email":"","middleInitial":"Won","affiliations":[{"id":7017,"text":"Florida International University","active":true,"usgs":false}],"preferred":false,"id":941239,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"DeAngelis, Donald L. 0000-0002-1570-4057","orcid":"https://orcid.org/0000-0002-1570-4057","contributorId":357336,"corporation":false,"usgs":false,"family":"DeAngelis","given":"Donald L.","affiliations":[{"id":7065,"text":"USGS emeritus","active":true,"usgs":false}],"preferred":false,"id":941240,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Yurek, Simeon 0000-0002-6209-7915","orcid":"https://orcid.org/0000-0002-6209-7915","contributorId":216733,"corporation":false,"usgs":true,"family":"Yurek","given":"Simeon","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"preferred":true,"id":941241,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Papastamatiou, Yannis P.","contributorId":356586,"corporation":false,"usgs":false,"family":"Papastamatiou","given":"Yannis P.","affiliations":[{"id":85026,"text":"Biological Sciences, Institute of Environment, Florida International University, 3000 NE 151st Street, 33181 North Miami (Florida), United States of America","active":true,"usgs":false}],"preferred":false,"id":941242,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70270741,"text":"70270741 - 2025 - Reconciling scale using the Resist-Accept-Direct (RAD) Framework to improve management of woody encroachment in grasslands","interactions":[],"lastModifiedDate":"2025-08-22T16:28:13.594774","indexId":"70270741","displayToPublicDate":"2025-05-21T09:19:19","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2258,"text":"Journal of Environmental Management","active":true,"publicationSubtype":{"id":10}},"title":"Reconciling scale using the Resist-Accept-Direct (RAD) Framework to improve management of woody encroachment in grasslands","docAbstract":"Implementing strategies to navigate large-scale ecological transitions in grasslands is one of this century's greatest conservation challenges. In the US Great Plains, managing areas impacted by woody transitions have been reactive, short-lived, costly, and ineffective. Along with current technological innovation in rangeland monitoring, the promise of early warning science is to provide managers with sufficient time to be better prepared for novel signals of ecological change. Combining the science of early warning signals and frameworks such as the Resist – Accept – Direct (RAD) can provide land managers with guidelines to identify proactive strategies when facing ecological change. Using this approach, we found that opportunities to resist woody transitions decreased from 84 % to 60 % between 1990 and 2020 over the entire biome but remained highest in the northern and western Great Plains, which contributes to large scale conservation targets. These are key areas to prioritize resist opportunities. In contrast, 11 % of the biome exhibited early warning transition signals across all hierarchical scales by 2020, a fourfold increase since 1990. Lastly by 2020, 30 % of the biome exhibited early warning signals across multiple but not all scales. Here, efforts may be more effective when management is directed to conserve fragmented grassland legacies within a woody-dominated matrix and avoid large-scale monocultures of problematic encroaching woody species. Our multi-scale study indicates that 1) anchoring to the last remaining grassland core areas with no early warning of transitions and 2) strategically investing in these intact grasslands may provide the best results for grassland conservation.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.jenvman.2025.125820","usgsCitation":"Scholtz, R., Uden, D.R., Allred, B.W., Donovan, V.M., Maestas, J.D., Morford, S.L., Jones, M.O., Naugle, D.E., Cady, S.M., Fogarty, D.T., Metcalf, A.L., Chaffin, B.C., Allen, C., Roberts, C.P., Rowen, E., Meredith, G.R., Nesbitt, H.K., Williamson, M.A., Gulab, S., Hamlin, S., Lohani, S., and Twidwell, D., 2025, Reconciling scale using the Resist-Accept-Direct (RAD) Framework to improve management of woody encroachment in grasslands: Journal of Environmental Management, v. 387, 125820, 13 p., https://doi.org/10.1016/j.jenvman.2025.125820.","productDescription":"125820, 13 p.","ipdsId":"IP-168014","costCenters":[{"id":198,"text":"Coop Res Unit Atlanta","active":true,"usgs":true}],"links":[{"id":495046,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1016/j.jenvman.2025.125820","text":"Publisher Index 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Gaussian process model of geochemistry, geophysics, and temperature for groundwater TDS in the San Ardo Oil Field, California, USA","docAbstract":"Critical flow theory provides a physical foundation for inferring discharge from measurements of wavelength and channel width made from images. In rivers with hydraulically steep local slopes greater than
∼0.01, flow velocities are high and the Froude number F r (ratio of inertial to gravitational forces) can approach 1.0 (critical flow) or greater. Under these conditions, undular hydraulic jumps (UHJ's) can form as standing wave trains at slope transitions or constrictions. The presence of UHJ's indicates that mean F r ≈ 1, implying that the velocity and depth of the flow and the spacing of the waves are uniquely related to one another. Discharges estimated from 82 Google Earth images agreed closely with discharges recorded at gaging stations (R2 = 0.98), with a mean bias of 1% ± 11%. This approach could provide reliable discharge information in many fluvial environments where critical flow occurs, which tend to be underrepresented in gage networks
Highly pathogenic H5N1 influenza A virus (HP H5N1) cases in wild mammals have been increasing globally. Carnivora has been the most affected mammal order; however, the extent of morbidity and mortality in carnivores exposed to HP H5N1 remains undefined. We assessed the presence of antibodies to H5 and N1 in the sera of 16 live-captured bobcats (Lynx rufus) in New York State, USA; reported on postcapture outcomes of HP H5N1-exposed bobcats; and reported on a case of HP H5N1 infection in one bobcat. In 2024, 4/16 bobcats (25%) tested positive for antibodies to H5 and N1. Two bobcats were confirmed alive as of November 2024 according to GPS data; the other two were alive as of June 2024, when their GPS collars stopped communicating. Another bobcat, which was negative for HP H5N1 antibodies at capture, died from HP H5N1 infection within 5 wks of capture. Our results provide evidence of bobcats both surviving and succumbing to HP H5N1 infection and highlight the importance of focused health studies paired with monitoring data to better understand exposure, infection, and outcomes for novel pathogens and species.
","language":"English","publisher":"BioOne","doi":"10.7589/jwd-d-24-00137","usgsCitation":"Turner, H., Fuller, A.K., Twining, J., Hitchener, G., Fadden, M., Stallknecht, D., Poulson, R., Carter, D., Watson, M., Schuler, K., and Bloodgood, J., 2025, Highly pathogenic avian influenza virus exposure and infection in free-ranging bobcats (Lynx rufus) in New York, USA: Journal of Wildlife Diseases, v. 61, no. 2, p. 515-521, https://doi.org/10.7589/jwd-d-24-00137.","productDescription":"7 p.","startPage":"515","endPage":"521","ipdsId":"IP-171388","costCenters":[{"id":199,"text":"Coop Res Unit Leetown","active":true,"usgs":true}],"links":[{"id":493708,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"New 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Lakes","interactions":[],"lastModifiedDate":"2025-08-08T13:18:23.449413","indexId":"70269924","displayToPublicDate":"2025-05-15T11:22:53","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1169,"text":"Canadian Journal of Fisheries and Aquatic Sciences","active":true,"publicationSubtype":{"id":10}},"title":"Integrating acoustic telemetry research into management: successes and challenges in the Laurentian Great Lakes","docAbstract":"In the Laurentian Great Lakes, the application of acoustic telemetry to track fish movements has evolved into an important part of multijurisdictional management. Nevertheless, barriers remain in translating telemetry research into management or conservation actions. Here, we synthesize acoustic telemetry literature within the Great Lakes basin to explore factors that have contributed to successes and failures of integrating research with the needs of decision-making processes. Collaboration between researchers and managers, facilitated by consistent opportunities for stakeholder engagement, stood out as one of the most effective means of integration. For example, 79% (95 of 127) of articles published (up to 2023) included co-authorship by both government and academic organizations. Case studies on lake sturgeon (Acipenser fulvescens), walleye (Sander vitreus), and sea lamprey (Petromyzon marinus) further highlight how telemetry has informed management through collaborative engagement among researchers, stakeholders, and managers, as well as ongoing challenges. By exploring facets of acoustic telemetry research and connections to conservation and fisheries concerns, we identify pathways to reduce knowledge–action gaps widely applicable within and outside of the Great Lakes.
","language":"English","publisher":"Canadian Science Publishing","doi":"10.1139/cjfas-2024-0335","usgsCitation":"Klinard, N.V., Vandergoot, C.S., Briggs, A.S., Elliott, C.W., Faust, M.D., Fielder, D.G., Gorsky, D., Hartman, T., Holbrook, C., Isermann, D.A., Midwood, J.D., Siefkes, M.J., Justin VanDeHey, Wilfond, D., Wills, T.C., Zorn, T., Barbosa Martins, A.P., Oakley-Cogan, A., Fisk, A.T., and Matley, J.K., 2025, Integrating acoustic telemetry research into management: successes and challenges in the Laurentian Great Lakes: Canadian Journal of Fisheries and Aquatic Sciences, v. 80, p. 1-20, https://doi.org/10.1139/cjfas-2024-0335.","productDescription":"20 p.","startPage":"1","endPage":"20","ipdsId":"IP-172320","costCenters":[{"id":199,"text":"Coop Res Unit Leetown","active":true,"usgs":true}],"links":[{"id":493727,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Canada, United States","otherGeospatial":"Laurentian 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V.","contributorId":359090,"corporation":false,"usgs":false,"family":"Klinard","given":"Natalie","middleInitial":"V.","affiliations":[{"id":24650,"text":"Dalhousie University","active":true,"usgs":false}],"preferred":false,"id":944958,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Vandergoot, Christopher S.","contributorId":359091,"corporation":false,"usgs":false,"family":"Vandergoot","given":"Christopher","middleInitial":"S.","affiliations":[{"id":6601,"text":"Michigan State University","active":true,"usgs":false}],"preferred":false,"id":944959,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Briggs, Andrew S.","contributorId":359094,"corporation":false,"usgs":false,"family":"Briggs","given":"Andrew","middleInitial":"S.","affiliations":[{"id":36986,"text":"Michigan Department of Natural Resources","active":true,"usgs":false}],"preferred":false,"id":944960,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Elliott, Connor W.","contributorId":359097,"corporation":false,"usgs":false,"family":"Elliott","given":"Connor","middleInitial":"W.","affiliations":[{"id":34006,"text":"Queen’s University","active":true,"usgs":false}],"preferred":false,"id":944961,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Faust, Matthew D.","contributorId":359100,"corporation":false,"usgs":false,"family":"Faust","given":"Matthew","middleInitial":"D.","affiliations":[{"id":16232,"text":"Ohio Department of Natural Resources","active":true,"usgs":false}],"preferred":false,"id":944962,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Fielder, David G.","contributorId":359103,"corporation":false,"usgs":false,"family":"Fielder","given":"David","middleInitial":"G.","affiliations":[{"id":36986,"text":"Michigan Department of Natural Resources","active":true,"usgs":false}],"preferred":false,"id":944963,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Gorsky, 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Arun","contributorId":359125,"corporation":false,"usgs":false,"family":"Oakley-Cogan","given":"Arun","affiliations":[{"id":24650,"text":"Dalhousie University","active":true,"usgs":false}],"preferred":false,"id":944975,"contributorType":{"id":1,"text":"Authors"},"rank":18},{"text":"Fisk, Aaron T.","contributorId":359126,"corporation":false,"usgs":false,"family":"Fisk","given":"Aaron","middleInitial":"T.","affiliations":[{"id":48871,"text":"University of Windsor","active":true,"usgs":false}],"preferred":false,"id":944976,"contributorType":{"id":1,"text":"Authors"},"rank":19},{"text":"Matley, Jordan K.","contributorId":359127,"corporation":false,"usgs":false,"family":"Matley","given":"Jordan","middleInitial":"K.","affiliations":[{"id":40595,"text":"Flinders University","active":true,"usgs":false}],"preferred":false,"id":944977,"contributorType":{"id":1,"text":"Authors"},"rank":20}]}} ,{"id":70266895,"text":"ofr20241070 - 2025 - Calibration of the Stream Salmonid Simulator (S3) model to estimate annual survival, movement, and food consumption by juvenile Chinook salmon (Oncorhynchus tshawytscha) in the restoration reach of the Trinity River, California, 2006–18","interactions":[],"lastModifiedDate":"2025-05-16T14:44:27.229198","indexId":"ofr20241070","displayToPublicDate":"2025-05-15T07:39:36","publicationYear":"2025","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":330,"text":"Open-File Report","code":"OFR","onlineIssn":"2331-1258","printIssn":"0196-1497","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"2024-1070","displayTitle":"Calibration of the Stream Salmonid Simulator (S3) Model to Estimate Annual Survival, Movement, and Food Consumption by Juvenile Chinook Salmon (Oncorhynchus tshawytscha) in the Restoration Reach of the Trinity River, California, 2006–18","title":"Calibration of the Stream Salmonid Simulator (S3) model to estimate annual survival, movement, and food consumption by juvenile Chinook salmon (Oncorhynchus tshawytscha) in the restoration reach of the Trinity River, California, 2006–18","docAbstract":"The Trinity River is managed in two sections: (1) from the upper 64-kilometer “restoration reach” downstream from Lewiston Dam to the confluence with the North Fork Trinity River, and (2) the 120-kilometer lower Trinity River downstream from the restoration reach. The Stream Salmonid Simulator (S3) has been previously applied to these reaches and the Klamath River. To estimate fish growth, past S3 calibration efforts in the Trinity and Klamath Rivers used maximum likelihood methods that considered only the abundance of juvenile Chinook salmon (Oncorhynchus tshawytscha) passing a fish trap to estimate survival and movement parameters, but not fish consumption. Previous calibrations did not estimate the average proportion of maximum consumption (Cy) when estimating survival (Sy) and movement (M0y) parameters across years (y) of data, but because no other information was available in the literature a fixed value of Cy=0.66 was assumed. Therefore, the goal of this report is to present an alternative approach that calibrates the S3 model to multivariate data (that is, abundance and size), enabling the estimation of the average proportion of maximum consumption, in conjunction with survival and movement parameters for a particular migration year. We fit the S3 model to individual years of weekly trap abundance estimates and mean fish sizes (fork length) at the Pear Tree Gulch (hereafter referred to as Pear Tree) fish trap representing the restoration reach. We used the Earth Mover’s Distance (EMD) as the objective value to be minimized in parameter optimization. This approach estimated survival, movement, and consumption parameters for each migration year. Because we had information on the abundance of natural and hatchery produced juvenile salmon at the fish traps, we estimated survival and movement for natural and hatchery fish.
S3 is a deterministic life-stage-structured population model that tracks daily growth, movement, and survival of juvenile Chinook Salmon. A key theme of the model is that river discharge affects habitat availability and capacity, which in turn drives density-dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily timeseries of discharge, water temperature, and useable habitat area or carrying capacity. In turn, the physical characteristics of each habitat unit and the number of fish occupying each unit drive survival and growth within each habitat unit and movement of fish among habitat units.
The physical template of the restoration reach of the Trinity River was classified into 356 meso-habitat units comprised of runs, riffles, and pools. For each habitat unit, we developed a timeseries of daily discharge, water temperature, amount of available spawning habitat, and fry and parr carrying capacity. Capacity time series were constructed using state-of-the-art models of spatially explicit hydrodynamics and quantitative fish habitat relationships developed for the Trinity River. These variables were then used to drive population dynamics such as egg maturation and survival, and in turn, juvenile movement, growth, and survival.
We estimated movement, survival, and consumption parameters by calibrating the model to 12 years of weekly juvenile abundance estimates and fish sizes at the Pear Tree fish trap near the downstream end of the restoration reach. We estimated parameters for 12 years that included a wide range of female spawner abundances (1,414–11,494) and water year types (critically dry–extremely wet). We contrast the estimated parameters to the corresponding number of female spawners and the total annual volume of water discharged for the Trinity River (Trinity River Restoration Program; https://www.trrp.net/restoration/flows/summary/).
The calibration consisted of replicating historical conditions as closely as possible (for example, discharge; temperature; spawner abundance, spawning location and timing, and hatchery releases), and then running the model to predict weekly abundance passing the trap location from each brood year of adults and subsequent migration year of their juvenile progeny. Because density-dependent movement was favored in past evaluations, we estimated S3 parameters based on density-independent survival and density-dependent movement. Likewise, each year’s estimated survival parameter for natural (SNy) and hatchery (SHy) fish may be interpreted as the mean daily survival probability from emergence or hatchery release to the Pear Tree fish trap. Under density dependence, the estimated movement parameter for natural (M0Ny) and hatchery (M0Hy) fish represents the intercept of the Beverton-Holt model; the probability of remaining in a habitat at near-zero abundance.
We estimated Cy by using EMD and incorporating abundance and fish size into model calibration. Average daily proportions of maximum consumption, , across the years were generally high (=0.640; standard deviation (SD) SD=0.176), suggesting that fish were feeding at about two-thirds of expected maximum consumption rates. This average proportion of maximum consumption,is very similar to what has been assumed (=0.66) in previous Trinity and Klamath River S3 calibration and simulation efforts. In 2017, we estimated the lowest Cy, suggesting lower average consumption for juvenile salmon in high-discharge water years. When this high discharge year was excluded, there was no apparent trend in Cy with annual water volume. Estimates of survival showed little trend over the range in spawner abundances, but a trend towards higher natural and hatchery fish survival with higher annual volumes of water was apparent. Over the 12 years, the average survival of hatchery fish was =0.888 (SD=0.079) and the average survival natural fish was=0.969 (SD=0.01).
With respect to fish movement, we estimated higher M0Ny and M0Hy with higher annual volumes of water in the Trinity River. Higher MN0y or MH0y suggest greater probability of remaining in a habitat at low fish densities, with potential for density-dependent processes in movement to occur. The highest M0Ny = 0.676 was estimated during brood year 2012, and the overall average for natural fish was =0.276 (SD=0.188) and for hatchery fish was=0.467 (SD=0.235). Under the Beverton-Holt model, as M0Ny or M0Hy approach zero, there is less capacity for change in fish movement as fish density increases.
The S3 model was initialized with only the spatiotemporal distribution of spawners, so it performed well at capturing the essential outmigration features that are ultimately governed by rates of growth, movement, and mortality. We used a new optimization method that could accommodate multivariate data on abundance and fish size collected at the Pear Tree fish trap, enabling the calibration of S3 to estimate five parameters for 12 separate years of data. Incorporating weekly fish size data for each year in our parameter optimization process made the estimation of Cy possible and represents a step forward in the fitting of the S3 model to fish trap data for the purposes of parameter calibration and the estimation of growth parameters with respect to annual conditions. We identified lack of fit and adding important effects into the S3 model may improve the S3 estimation and simulation of water scenarios.
The Trinity River Restoration Program (TRRP) Science Advisory Board recommended that the TRRP focus on developing core elements of a decision support system (DSS; Buffington and others, 2014). Toward that end, the habitat and S3 models described in this report are both core elements of the DSS. The structure of S3 makes it a particularly useful fish production model for the DSS because population dynamics are sensitive to (1) water temperature, (2) daily discharge management, and (3) habitat quality and quantity. Each of these variables are key management parameters under consideration in the TRRP. As such, the S3 model may provide valuable insights into the potentially variable effects of different management decisions on the Trinity River.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ofr20241070","collaboration":"Prepared in cooperation with U.S. Bureau of Reclamation","usgsCitation":"Plumb, J.M., Perry, R.W., and De Juilio, K., 2025, Calibration of the Stream Salmonid Simulator (S3) model to estimate annual survival, movement, and food consumption by juvenile Chinook salmon (Oncorhynchus tshawytscha) in the restoration reach of the Trinity River, California, 2006–18: U.S. Geological Survey Open-File Report 2024–1070, 21 p., https://doi.org/10.3133/ofr20241070.","productDescription":"vii, 22 p.","onlineOnly":"Y","ipdsId":"IP-156648","costCenters":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"links":[{"id":485969,"rank":4,"type":{"id":34,"text":"Image Folder"},"url":"https://pubs.usgs.gov/of/2024/1070/images"},{"id":485968,"rank":3,"type":{"id":39,"text":"HTML Document"},"url":"https://pubs.usgs.gov/publication/ofr20241070/full","text":"Report","linkFileType":{"id":5,"text":"html"},"description":"OFR 2024-1070"},{"id":485967,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/of/2024/1070/ofr20241070.pdf","text":"Report","size":"7.9 MB","linkFileType":{"id":1,"text":"pdf"},"description":"OFR 2024-1070"},{"id":485966,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/of/2024/1070/coverthb.jpg"},{"id":485970,"rank":5,"type":{"id":31,"text":"Publication XML"},"url":"https://pubs.usgs.gov/of/2024/1070/ofr20241070.XML"}],"country":"United States","state":"California","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -123.1406578585185,\n 40.785753827016435\n ],\n [\n -123.1406578585185,\n 40.69151845163566\n ],\n [\n -122.79146166523228,\n 40.69151845163566\n ],\n [\n -122.79146166523228,\n 40.785753827016435\n ],\n [\n -123.1406578585185,\n 40.785753827016435\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","contact":"Director, Western Fisheries Research Center
U.S. Geological Survey
6505 NE 65th Street
Seattle, Washington 98115-5016
Lampreys (Petromyzontiformes) are an ancient group of fishes with complex life histories. We created a life cycle model that includes an R Shiny interactive web application interface to simulate abundance by life stage. This will allow scientists and managers to connect available demographic information in a framework that can be applied to questions regarding lamprey biology and conservation. We used Pacific lamprey (Entosphenus tridentatus) as a case study to highlight the utility of this model. We applied a global sensitivity analysis to explore the importance of individual life stage parameters to overall population size, and to better understand the implications of existing gaps in knowledge. We also provided example analyses of selected management scenarios (dam passage, fish translocations, and hatchery additions) influencing Pacific lamprey in fresh water. These applications illustrate how the model can be applied to inform conservation efforts. This tool will provide new capabilities for users to explore their own questions about lamprey biology and conservation. Simulations can hone hypotheses and predictions, which can then be empirically tested in the real world.
","language":"English","publisher":"PLOS","doi":"10.1371/journal.pone.0323408","usgsCitation":"Gomes, D.G., Benjamin, J.R., Clemens, B.J., Lampman, R., and Dunham, J., 2025, New technology for an ancient fish: A lamprey life cycle modeling tool with an R Shiny application: PLoS ONE, v. 20, no. 5, e0323408, 25 p., https://doi.org/10.1371/journal.pone.0323408.","productDescription":"e0323408, 25 p.","ipdsId":"IP-172919","costCenters":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"links":[{"id":489170,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1371/journal.pone.0323408","text":"Publisher Index Page"},{"id":486169,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"20","issue":"5","noUsgsAuthors":false,"publicationDate":"2025-05-14","publicationStatus":"PW","contributors":{"authors":[{"text":"Gomes, Dylan Gerald-Everett 0000-0002-2642-3728","orcid":"https://orcid.org/0000-0002-2642-3728","contributorId":346160,"corporation":false,"usgs":true,"family":"Gomes","given":"Dylan","email":"","middleInitial":"Gerald-Everett","affiliations":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":937518,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Benjamin, Joseph R. 0000-0003-3733-6838 jbenjamin@usgs.gov","orcid":"https://orcid.org/0000-0003-3733-6838","contributorId":3999,"corporation":false,"usgs":true,"family":"Benjamin","given":"Joseph","email":"jbenjamin@usgs.gov","middleInitial":"R.","affiliations":[{"id":289,"text":"Forest and Rangeland Ecosys Science Center","active":true,"usgs":true},{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":937519,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Clemens, Benjamin J.","contributorId":195098,"corporation":false,"usgs":false,"family":"Clemens","given":"Benjamin","email":"","middleInitial":"J.","affiliations":[],"preferred":false,"id":937520,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Lampman, Ralph","contributorId":215233,"corporation":false,"usgs":false,"family":"Lampman","given":"Ralph","email":"","affiliations":[],"preferred":true,"id":937521,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Dunham, Jason 0000-0002-6268-0633","orcid":"https://orcid.org/0000-0002-6268-0633","contributorId":220078,"corporation":false,"usgs":true,"family":"Dunham","given":"Jason","affiliations":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":937522,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70267437,"text":"70267437 - 2025 - Regional analysis of the dependence of peak-flow quantiles on climate with application to adjustment to climate trends","interactions":[],"lastModifiedDate":"2025-05-23T15:07:59.713754","indexId":"70267437","displayToPublicDate":"2025-05-14T10:05:31","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":10778,"text":"Hydrology","active":true,"publicationSubtype":{"id":10}},"title":"Regional analysis of the dependence of peak-flow quantiles on climate with application to adjustment to climate trends","docAbstract":"Standard flood-frequency analysis methods rely on an assumption of stationarity, but because of growing understanding of climatic persistence and concern regarding the effects of climate change, the need for methods to detect and model nonstationary flood frequency has become widely recognized. In this study, a regional statistical method for estimating the effects of climate variations on annual maximum (peak) flows that allows for the effect to vary by quantile is presented and applied. The method uses a panel–quantile regression framework based on a location-scale model with two fixed effects per basin. The model was fitted to 330 selected gauged basins in the midwestern United States, filtered to remove basins affected by reservoir regulation and urbanization. Precipitation and discharge simulated using a water-balance model at daily and annual time scales were tested as climate variables. Annual maximum daily discharge was found to be the best predictor of peak flows, and the quantile regression coefficients were found to depend monotonically on annual exceedance probability. Application of the models to gauged basins is demonstrated by estimating the peak-flow distributions at the end of the study period (2018) and, using the panel model, to the study basins as-if-ungauged by using leave-one-out cross validation, estimating the fixed effects using static basin characteristics, and parameterizing the water-balance model discharge using median parameters. The errors of the quantiles predicted as-if-ungauged approximately doubled compared to the errors of the fitted panel model.
","language":"English","publisher":"MDPI","doi":"10.3390/hydrology12050119","usgsCitation":"Over, T.M., Marti, M.K., and Podzorski, H.L., 2025, Regional analysis of the dependence of peak-flow quantiles on climate with application to adjustment to climate trends: Hydrology, v. 12, no. 5, 119, 43 p., https://doi.org/10.3390/hydrology12050119.","productDescription":"119, 43 p.","ipdsId":"IP-167316","costCenters":[{"id":36532,"text":"Central Midwest Water Science Center","active":true,"usgs":true}],"links":[{"id":487957,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.3390/hydrology12050119","text":"Publisher Index Page"},{"id":486509,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"12","issue":"5","noUsgsAuthors":false,"publicationDate":"2025-05-14","publicationStatus":"PW","contributors":{"authors":[{"text":"Over, Thomas M. 0000-0001-8280-4368","orcid":"https://orcid.org/0000-0001-8280-4368","contributorId":204650,"corporation":false,"usgs":true,"family":"Over","given":"Thomas","email":"","middleInitial":"M.","affiliations":[{"id":344,"text":"Illinois Water Science Center","active":true,"usgs":true},{"id":36532,"text":"Central Midwest Water Science Center","active":true,"usgs":true}],"preferred":true,"id":938195,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Marti, Mackenzie K. 0000-0001-8817-4969 mmarti@usgs.gov","orcid":"https://orcid.org/0000-0001-8817-4969","contributorId":289738,"corporation":false,"usgs":true,"family":"Marti","given":"Mackenzie","email":"mmarti@usgs.gov","middleInitial":"K.","affiliations":[{"id":36532,"text":"Central Midwest Water Science Center","active":true,"usgs":true}],"preferred":true,"id":938196,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Podzorski, Hannah Lee 0000-0001-5204-2606 hpodzorski@usgs.gov","orcid":"https://orcid.org/0000-0001-5204-2606","contributorId":333626,"corporation":false,"usgs":true,"family":"Podzorski","given":"Hannah","email":"hpodzorski@usgs.gov","middleInitial":"Lee","affiliations":[{"id":36532,"text":"Central Midwest Water Science Center","active":true,"usgs":true}],"preferred":true,"id":938197,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70267492,"text":"70267492 - 2025 - Using distance sampling with camera traps to estimate densities of ungulates on tropical oceanic islands","interactions":[],"lastModifiedDate":"2025-05-27T14:44:08.288888","indexId":"70267492","displayToPublicDate":"2025-05-13T09:40:39","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2487,"text":"Journal of Tropical Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Using distance sampling with camera traps to estimate densities of ungulates on tropical oceanic islands","docAbstract":"Reliable population estimates are one of the most elementary needs for the management of wildlife, particularly for introduced ungulates on oceanic islands. We aimed to produce accurate and precise density estimates of Philippine deer (Rusa marianna) and wild pigs (Sus scrofa) on Guam using motion-triggered cameras combined with distance sampling to estimate densities from observations of unmarked animals while accounting for imperfect detection. We used an automated digital data processing pipeline for species recognition and to estimate the distance to detected species. Our density estimates were slightly lower than published estimates, consistent with management to reduce populations. We estimated the number of camera traps needed to obtain a 0.1 coefficient of variation was substantial, requiring > ten-fold increase in camera traps, while estimates with precision of 0.2 or 0.3 were more achievable, requiring doubling to quadrupling the number of camera traps. We provide best practices for establishing and conducting distance sampling with camera trap surveys for density estimation based on lessons learned during this study. Future studies should consider distance sampling with camera traps to efficiently survey and monitor unmarked animals, particularly medium-sized ungulates, in tropical, oceanic island ecosystems.
","language":"English","publisher":"Cambridge University Press","doi":"10.1017/S0266467425000033","usgsCitation":"Camp, R.J., Bak, T.M., Burt, M., and Vogt, S., 2025, Using distance sampling with camera traps to estimate densities of ungulates on tropical oceanic islands: Journal of Tropical Ecology, v. 41, e12, https://doi.org/10.1017/S0266467425000033.","productDescription":"e12","ipdsId":"IP-154449","costCenters":[{"id":521,"text":"Pacific Island Ecosystems Research Center","active":false,"usgs":true}],"links":[{"id":486578,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"otherGeospatial":"Guam","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n 144.96784988323265,\n 13.61173385872614\n ],\n [\n 144.8366796899819,\n 13.68869399233894\n ],\n [\n 144.63621203614423,\n 13.440889342095488\n ],\n [\n 144.62136258030552,\n 13.248242573805925\n ],\n [\n 144.72778368049006,\n 13.221741661313231\n ],\n [\n 144.79955605038276,\n 13.274740600770016\n ],\n [\n 144.81688041552877,\n 13.419224264484484\n ],\n [\n 144.96042515531252,\n 13.525123785236971\n ],\n [\n 144.96784988323265,\n 13.61173385872614\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"41","noUsgsAuthors":false,"publicationDate":"2025-05-13","publicationStatus":"PW","contributors":{"authors":[{"text":"Camp, Richard J. 0000-0001-7008-923X rick_camp@usgs.gov","orcid":"https://orcid.org/0000-0001-7008-923X","contributorId":189964,"corporation":false,"usgs":true,"family":"Camp","given":"Richard","email":"rick_camp@usgs.gov","middleInitial":"J.","affiliations":[{"id":521,"text":"Pacific Island Ecosystems Research Center","active":false,"usgs":true},{"id":5049,"text":"Pacific Islands Ecosys Research Center","active":true,"usgs":true}],"preferred":true,"id":938391,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Bak, Trevor M.","contributorId":317824,"corporation":false,"usgs":false,"family":"Bak","given":"Trevor","email":"","middleInitial":"M.","affiliations":[{"id":13341,"text":"Hawai‘i Cooperative Studies Unit, University of Hawai‘i at Hilo","active":true,"usgs":false}],"preferred":false,"id":938392,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Burt, Matthew D","contributorId":355925,"corporation":false,"usgs":false,"family":"Burt","given":"Matthew D","affiliations":[{"id":84860,"text":"Naval Facilities Marianas","active":true,"usgs":false}],"preferred":false,"id":938393,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Vogt, Scott","contributorId":355926,"corporation":false,"usgs":false,"family":"Vogt","given":"Scott","affiliations":[{"id":84860,"text":"Naval Facilities Marianas","active":true,"usgs":false}],"preferred":false,"id":938394,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70268342,"text":"70268342 - 2025 - Shifting baselines of coral-reef species composition from the Late Pleistocene to the present in the Florida Keys","interactions":[],"lastModifiedDate":"2025-06-23T14:20:17.616459","indexId":"70268342","displayToPublicDate":"2025-05-13T09:14:05","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":5781,"text":"The Depositional Record","active":true,"publicationSubtype":{"id":10}},"title":"Shifting baselines of coral-reef species composition from the Late Pleistocene to the present in the Florida Keys","docAbstract":"The ongoing global-scale reassembly of modern coral reefs is unprecedented compared with the observed stability of most late Quaternary reef assemblages. One notable exception is the marine isotope stage (MIS) 5e (ca 130–116 thousand years ago [ka]) reefs in the Florida Keys, where the ubiquitous shallow-water coral, Acropora palmata, was near absent. Little is known, however, about reefs that grew during MIS5d–a (ca 116–74 ka), between MIS5e and the Holocene. It is therefore unclear whether Florida's unique MIS5e coral assemblages represent a geologically brief anomaly or a more persistent departure from the western Atlantic coral-reef archetype. We addressed that question by reconstructing the composition of MIS5d–a reefs within 29 coral-reef cores collected throughout the Florida Keys. We then compared the relative composition of corals during MIS5d–a to existing datasets from MIS5e, Holocene and modern (1996 and 2022) reefs to evaluate how far today's reef assemblages have diverged from geological baselines. We show that although the proportion of reef frameworks built by corals was remarkably consistent (ca 38%), species composition changed significantly through time. Acropora palmata was rare throughout MIS5, which we hypothesise was due to greater cold-temperature stress in Florida's subtropical reefs compared with the more climatically stable tropics. In contrast, the massive reef-building coral, Orbicella spp., was regionally dominant throughout the late Quaternary, but has become increasingly rare on modern reefs. By 2022, reefs in the Florida Keys were characterised by a truly novel coral assemblage dominated by Porites astreoides and Siderastrea siderea. In many ways, Florida's reefs defy the concept of a natural baseline; instead, their most persistent characteristic since the Late Pleistocene is their uniqueness. Yet, as reefs are increasingly subjected to unprecedented levels of environmental change, the exceptions to what was normal in the past could, paradoxically, provide the best geological analogues for the future.
","language":"English","publisher":"WIley","doi":"10.1002/dep2.70009","usgsCitation":"Toth, L., Stathakopoulos, A., Hsia, S., and Weinstein, D.A., 2025, Shifting baselines of coral-reef species composition from the Late Pleistocene to the present in the Florida Keys: The Depositional Record, v. 11, no. 3, p. 893-916, https://doi.org/10.1002/dep2.70009.","productDescription":"24 p.","startPage":"893","endPage":"916","ipdsId":"IP-173487","costCenters":[{"id":574,"text":"St. Petersburg Coastal and Marine Science Center","active":true,"usgs":true},{"id":40020,"text":"Florence Bascom Geoscience Center","active":true,"usgs":true}],"links":[{"id":491456,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1002/dep2.70009","text":"Publisher Index Page"},{"id":491097,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Florida","otherGeospatial":"Florida Keys","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -80.17917140030995,\n 25.383351188271973\n ],\n [\n -81.59701661611159,\n 24.90866922937429\n ],\n [\n -83.02465696293855,\n 24.77579446049141\n ],\n [\n -83.06138870428032,\n 24.366054515738625\n ],\n [\n -81.8345485434568,\n 24.395013657422012\n ],\n [\n -80.65178647224371,\n 24.557720553123204\n ],\n [\n -80.17917140030995,\n 25.383351188271973\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"11","issue":"3","noUsgsAuthors":false,"publicationDate":"2025-05-13","publicationStatus":"PW","contributors":{"authors":[{"text":"Toth, Lauren T. 0000-0002-2568-802X ltoth@usgs.gov","orcid":"https://orcid.org/0000-0002-2568-802X","contributorId":181748,"corporation":false,"usgs":true,"family":"Toth","given":"Lauren","email":"ltoth@usgs.gov","middleInitial":"T.","affiliations":[{"id":574,"text":"St. Petersburg Coastal and Marine Science Center","active":true,"usgs":true}],"preferred":true,"id":940869,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Stathakopoulos, Anastasios 0000-0002-4404-035X astathakopoulos@usgs.gov","orcid":"https://orcid.org/0000-0002-4404-035X","contributorId":147744,"corporation":false,"usgs":true,"family":"Stathakopoulos","given":"Anastasios","email":"astathakopoulos@usgs.gov","affiliations":[{"id":574,"text":"St. Petersburg Coastal and Marine Science Center","active":true,"usgs":true}],"preferred":true,"id":940870,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Hsia, Scarlette Shan-Hwei 0000-0002-2230-9004","orcid":"https://orcid.org/0000-0002-2230-9004","contributorId":346523,"corporation":false,"usgs":true,"family":"Hsia","given":"Scarlette Shan-Hwei","affiliations":[{"id":40020,"text":"Florence Bascom Geoscience Center","active":true,"usgs":true}],"preferred":true,"id":940871,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Weinstein, David A.","contributorId":206027,"corporation":false,"usgs":false,"family":"Weinstein","given":"David","email":"","middleInitial":"A.","affiliations":[{"id":12722,"text":"Cornell University","active":true,"usgs":false}],"preferred":false,"id":940872,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70267387,"text":"70267387 - 2025 - Linking permafrost to the abundance, biomass, and energy density of fish in Arctic headwater streams","interactions":[],"lastModifiedDate":"2025-05-21T14:10:33.157869","indexId":"70267387","displayToPublicDate":"2025-05-13T08:59:33","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":"Linking permafrost to the abundance, biomass, and energy density of fish in Arctic headwater streams","docAbstract":"Permafrost thaw alters groundwater flow, river hydrology, stream-catchment interactions, and the availability of carbon and nutrients in headwater streams. The impact of permafrost on watershed hydrology and biogeochemistry of headwater streams has been demonstrated, but there is little understanding of how permafrost influences fish in these ecosystems. We examined relations among permafrost characteristics, the resulting changes in water temperature, stream hydrology (e.g., discharge flashiness), and macroinvertebrates, with the abundance, biomass, and energy density of juvenile Dolly Varden (Salvelinus malma) and Arctic Grayling (Thymallus arcticus) across 10 headwater streams in northwestern Alaska. Macroinvertebrate density was driven by concentrations of dissolved carbon and nutrients supporting stream food webs. Dolly Varden abundance was primarily related to water temperature with fewer fish in warmer streams, whereas Dolly Varden energy density decreased with the flashiness of the headwater streams. Dolly Varden biomass was related to both temperature and bottom-up food web effects. The energy density of Arctic Grayling decreased with warmer temperatures and discharge flashiness. These relations demonstrate the importance of terrestrial–aquatic connections in permafrost landscapes and indicate the complexity of landscape effects on fish. Because permafrost thaw is one of the most impactful changes occurring as the Arctic warms, an improved understanding of how stream temperature, hydrology, and bottom-up food web processes influence fish populations can aid forecasting of future conditions across the Arctic.
","language":"English","publisher":"Ecological Society of America","doi":"10.1002/ecs2.70270","usgsCitation":"Carey, M.P., Koch, J.C., O’Donnell, J.A., Poulin, B., and Zimmerman, C.E., 2025, Linking permafrost to the abundance, biomass, and energy density of fish in Arctic headwater streams: Ecosphere, v. 16, no. 5, e70270, 20 p., https://doi.org/10.1002/ecs2.70270.","productDescription":"e70270, 20 p.","ipdsId":"IP-168519","costCenters":[{"id":65299,"text":"Alaska Science Center Ecosystems","active":true,"usgs":true}],"links":[{"id":486925,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1002/ecs2.70270","text":"Publisher Index Page"},{"id":486281,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Alaska","otherGeospatial":"Noatak National Preserve","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -164,\n 69\n ],\n [\n -164,\n 66.7\n ],\n [\n -156,\n 66.7\n ],\n [\n -156,\n 69\n ],\n [\n -164,\n 69\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"16","issue":"5","noUsgsAuthors":false,"publicationDate":"2025-05-13","publicationStatus":"PW","contributors":{"authors":[{"text":"Carey, Michael P. 0000-0002-3327-8995 mcarey@usgs.gov","orcid":"https://orcid.org/0000-0002-3327-8995","contributorId":5397,"corporation":false,"usgs":true,"family":"Carey","given":"Michael","email":"mcarey@usgs.gov","middleInitial":"P.","affiliations":[{"id":120,"text":"Alaska Science Center Water","active":true,"usgs":true},{"id":117,"text":"Alaska Science Center Biology WTEB","active":true,"usgs":true},{"id":114,"text":"Alaska Science Center","active":true,"usgs":true},{"id":116,"text":"Alaska Science Center Biology MFEB","active":true,"usgs":true}],"preferred":true,"id":938061,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Koch, Joshua C. 0000-0001-7180-6982 jkoch@usgs.gov","orcid":"https://orcid.org/0000-0001-7180-6982","contributorId":202532,"corporation":false,"usgs":true,"family":"Koch","given":"Joshua","email":"jkoch@usgs.gov","middleInitial":"C.","affiliations":[{"id":116,"text":"Alaska Science Center Biology MFEB","active":true,"usgs":true},{"id":114,"text":"Alaska Science Center","active":true,"usgs":true},{"id":120,"text":"Alaska Science Center Water","active":true,"usgs":true}],"preferred":true,"id":938062,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"O’Donnell, Jonathan A. 0000-0001-7031-9808","orcid":"https://orcid.org/0000-0001-7031-9808","contributorId":191423,"corporation":false,"usgs":false,"family":"O’Donnell","given":"Jonathan","email":"","middleInitial":"A.","affiliations":[],"preferred":false,"id":938063,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Poulin, Brett 0000-0002-5555-7733","orcid":"https://orcid.org/0000-0002-5555-7733","contributorId":260893,"corporation":false,"usgs":false,"family":"Poulin","given":"Brett","affiliations":[{"id":52706,"text":"Department of Environmental Toxicology, University of California Davis, Davis, CA 95616, USA","active":true,"usgs":false}],"preferred":false,"id":938064,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Zimmerman, Christian E. 0000-0002-3646-0688 czimmerman@usgs.gov","orcid":"https://orcid.org/0000-0002-3646-0688","contributorId":410,"corporation":false,"usgs":true,"family":"Zimmerman","given":"Christian","email":"czimmerman@usgs.gov","middleInitial":"E.","affiliations":[{"id":116,"text":"Alaska Science Center Biology MFEB","active":true,"usgs":true},{"id":120,"text":"Alaska Science Center Water","active":true,"usgs":true},{"id":114,"text":"Alaska Science Center","active":true,"usgs":true}],"preferred":true,"id":938065,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70266906,"text":"70266906 - 2025 - Assessing potential collateral effects on amphibians from insecticide applications for flea control and plague mitigation","interactions":[],"lastModifiedDate":"2025-05-15T14:58:27.853948","indexId":"70266906","displayToPublicDate":"2025-05-12T09:46:05","publicationYear":"2025","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2980,"text":"PLoS ONE","active":true,"publicationSubtype":{"id":10}},"title":"Assessing potential collateral effects on amphibians from insecticide applications for flea control and plague mitigation","docAbstract":"Ideal disease mitigation measures for wildlife are safe and benign for target species, non-target organisms, the environment, and humans. Identifying collateral (i.e., unintended) effects is a key consideration in implementing such actions. Deltamethrin dust and fipronil-laced baits represent a group of insecticides that target fleas (pulicides) and are used to control flea (Siphonaptera) vectors of the plague bacterium Yersinia pestis to protect prairie dogs (Cynomys spp.) and their plague-susceptible obligate predators, endangered black-footed ferrets (Mustela nigripes). A variety of animals use prairie dog burrows as refuge, which potentially exposes them to deltamethrin, and to fipronil and its metabolites in fecal pellets excreted by prairie dogs and other mammals that have eaten fipronil baits. We assessed the potential effects of deltamethrin and fipronil residues on survival, body mass, and activity of western tiger salamanders (Ambystoma mavortium), a burrow-inhabiting amphibian. Pulicides were applied at realistic concentrations in mesocosms mimicking burrows. Treatments included (1) deltamethrin dust and non-treated prairie dog fecal pellets, (2) prairie dog fecal pellets containing fipronil and fipronil sulfone, and (3) un-treated prairie dog fecal pellets as controls. All 29 salamanders survived the experiment. We did not detect pulicide residues in any control salamanders. Fipronil sulfone was detected in tissues from 3 of 10 salamanders in the fipronil treatment and deltamethrin was detected in tissues from 9 of 11 salamanders in the deltamethrin treatment. Salamanders were observed outside of burrows more frequently after treatments than before. Deltamethrin concentrations in whole body samples correlated positively with the amount of time salamanders were inside burrows. Acute, lethal effects were not detected, but uptake of deltamethrin and, to a lesser extent fipronil sulfone, into salamander tissues indicated the potential for long-term effects on this non-target species. Identifying potential collateral effects is an important aspect of evaluating mitigation actions implemented to protect endangered species.
","language":"English","publisher":"PLoS","doi":"10.1371/journal.pone.0320382","usgsCitation":"Eads, D.A., Shriner, S.A., Ellis, J.W., Cryan, P.M., Hladik, M.L., Dooley, G.P., and Muths, E., 2025, Assessing potential collateral effects on amphibians from insecticide applications for flea control and plague mitigation: PLoS ONE, v. 20, no. 5, e0320382, 15 p., https://doi.org/10.1371/journal.pone.0320382.","productDescription":"e0320382, 15 p.","ipdsId":"IP-160537","costCenters":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"links":[{"id":488598,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1371/journal.pone.0320382","text":"Publisher Index Page"},{"id":486312,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P9NR46X4","text":"USGS data release","linkHelpText":"Data on tiger salamander body mass, behavioral activity, and insecticide residues"},{"id":485994,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"20","issue":"5","noUsgsAuthors":false,"publicationDate":"2025-05-12","publicationStatus":"PW","contributors":{"authors":[{"text":"Eads, David A. 0000-0002-4247-017X deads@usgs.gov","orcid":"https://orcid.org/0000-0002-4247-017X","contributorId":173639,"corporation":false,"usgs":true,"family":"Eads","given":"David","email":"deads@usgs.gov","middleInitial":"A.","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":false,"id":937098,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Shriner, Susan A.","contributorId":168690,"corporation":false,"usgs":false,"family":"Shriner","given":"Susan","email":"","middleInitial":"A.","affiliations":[{"id":13407,"text":"Colorado State Univ.","active":true,"usgs":false}],"preferred":false,"id":937099,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Ellis, Jeremy W.","contributorId":212846,"corporation":false,"usgs":false,"family":"Ellis","given":"Jeremy","email":"","middleInitial":"W.","affiliations":[{"id":36589,"text":"USDA","active":true,"usgs":false}],"preferred":false,"id":937100,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Cryan, Paul M. 0000-0002-2915-8894 cryanp@usgs.gov","orcid":"https://orcid.org/0000-0002-2915-8894","contributorId":147942,"corporation":false,"usgs":true,"family":"Cryan","given":"Paul","email":"cryanp@usgs.gov","middleInitial":"M.","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":true,"id":937101,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Hladik, Michelle L. 0000-0002-0891-2712","orcid":"https://orcid.org/0000-0002-0891-2712","contributorId":221229,"corporation":false,"usgs":true,"family":"Hladik","given":"Michelle","middleInitial":"L.","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":937102,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Dooley, Gregory P.","contributorId":347021,"corporation":false,"usgs":false,"family":"Dooley","given":"Gregory","email":"","middleInitial":"P.","affiliations":[{"id":6621,"text":"Colorado State University","active":true,"usgs":false}],"preferred":false,"id":937103,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Muths, Erin L. 0000-0002-5498-3132","orcid":"https://orcid.org/0000-0002-5498-3132","contributorId":245922,"corporation":false,"usgs":true,"family":"Muths","given":"Erin L.","affiliations":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"preferred":true,"id":937104,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ]}