This readme file was generated on 2022-09-22 by Ellen Haynes GENERAL INFORMATION 1. Title of Dataset: Survey for selected parasites in Alaska brown bears (Ursus arctos) 2. Author Information Corresponding Author 1 Name: Ellen Haynes Institution: Southeastern Cooperative Wildlife Disease Study, University of Georgia College of Veterinary Medicine, Athens, GA, USA Email: ellen.haynes@uga.edu Corresponding Author 2 Name: Christopher A. Cleveland Institution: Southeastern Cooperative Wildlife Disease Study, University of Georgia College of Veterinary Medicine, Athens, GA, USA Email: ccleve@uga.edu Co-Investigator 1 Name: Sarah Coker Institution: Southeastern Cooperative Wildlife Disease Study, University of Georgia College of Veterinary Medicine, Athens, GA, USA Co-Investigator 2 Name: Michael J. Yabsley Institution: Southeastern Cooperative Wildlife Disease Study, University of Georgia College of Veterinary Medicine, Athens, GA, USA Co-Investigator 3 Name: Kevin D. Niedrighaus Institution: Southeastern Cooperative Wildlife Disease Study, University of Georgia College of Veterinary Medicine, Athens, GA, USA Co-Investigator 4 Name: Andrew M. Ramey Institution: U.S. Geological Survey Alaska Science Center, Anchorage, AK, USA Co-Investigator 5 Name: Guilherme G. Verocai Institution: Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA Co-Investigator 6 Name: Grant V. Hilderbrand Institution at time of study: U.S. Geological Survey Alaska Science Center, Anchorage, AK, USA Current affiliation: National Park Service, Alaska Region, Anchorage, AK, USA Co-Investigator 7 Name: Kyle Joly Institution: National Park Service, Gates of the Arctic National Park and Preserve, Fairbanks, AK, USA Co-Investigator 8 Name: David D. Gustine Institution at time of study: U.S. Geological Survey Alaska Science Center, Anchorage, AK, USA Current affiliation: U.S. Fish and Wildlife Service, Alaska Region, Anchorage, AK, USA Co-Investigator 9 Name: Buck Mangipane Institution: National Park Service, Lake Clark National Park and Preserve, Port Alsworth, AK, USA Co-Investigator 10 Name: William B. Leacock Institution at time of study: U.S. Fish and Wildlife Service, Kodiak National Wildlife Refuge, Kodiak, AK, USA Current affiliation: U.S. Fish and Wildlife Service, Arctic National Wildlife Refuge, Fairbanks, AK, USA Co-Investigator 11 Name: Anthony P. Crupi Institution: Alaska Department of Fish and Game, Division of Wildlife Conservation, Juneau, AK, USA 3. Date of data collection: 2013-2017 4. Geographic location of data collection: Gates of the Arctic National Park and Preserve, Katmai National Park, Kodiak Island, Lake Clark National Park and Preserve, and Yakutat Forelands, AK, USA 5. Funding sources that supported the collection of the data: Alaska Department of Fish and Game, National Park Service, U.S. Fish and Wildlife Service, U.S. Geological Survey, and Southeastern Cooperative Wildlife Disease Study 6. Links to publications that cite or use the data: Paper currently in review with the Journal of Wildlife Diseases. 7. Recommended citation for this dataset: Haynes, Ellen et al. (2022), Results of survey for selected parasites in alaska brown bears (Ursus arctos), Dryad, Dataset, https://doi.org/10.5061/dryad.xd2547dm3 DATA & FILE OVERVIEW 1. Description of dataset These data were generated to assess infection with or exposure to endo- and ectoparasites in Alaska brown bears (Ursus arctos). Blood and fecal samples were collected during 2013 – 2017 from five locations: Gates of the Arctic National Park and Preserve, Katmai National Park, Lake Clark National Park and Preserve, Yakutat Forelands, and Kodiak Island. Standard fecal centrifugal-flotation was used to screen for gastrointestinal parasites, molecular techniques were used to test blood for the presence of Bartonella and Babesia spp., and an enzyme-linked immunosorbent assay (ELISA) was used to detect antibodies to Sarcoptes scabiei, a species of mite recently associated with mange in American black bears (Ursus americanus). 2. File List: File Name: Haynes_2022_AK_bear_parasite_data File Description: Results of diagnostic testing for each bear sampled at various time points METHODOLOGICAL INFORMATION As part of ongoing inter-agency research, personnel from the Alaska Department of Fish and Game, National Park Service, U.S. Fish and Wildlife Service, and U.S. Geological Survey sampled 166 brown bears during July 2013–July 2017 at five locations: Gates of the Arctic National Park and Preserve (GAAR), Katmai National Park (KATM), Kodiak Island (KOD), Lake Clark National Park and Preserve (LACL), and the Yakutat Forelands. Bears were captured and handled as reported by Ramey et al. (2019), with all capture, handling, and sampling procedures approved by Animal and Care Use Committees for Alaska Department of Fish and Game (2013-028), NPS (2014.A2, 2014.A3), USFWS (2012-14), and USGS (2014-1, 2014-10, 2015-4, 2015-6). Feces were collected opportunistically from the rectums of 114 anesthetized bears from GAAR, KATM, KOD, and LACL one to five times during the study period, stored in 70% ethanol, then processed using double centrifugal flotation with Sheather’s sucrose solution (specific gravity 1.25). Blood was collected as described by Ramey et al. (2019) from 156 bears from all sites and tested for Bartonella and Babesia species, with 44 bears screened twice. Genomic DNA was extracted using a DNeasy® Blood and Tissue Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol. Nested PCR was performed using GoTaq® Flexi DNA Polymerase (Promega, Madison, Wisconsin, USA). For Bartonella spp., the ITS gene was targeted using the primers and cycling conditions described by Trataris et al. (2012). Primary PCR primers were QHVE-1 and QHVE-3; secondary primers were QHVE-12 and QHVE-14b. For Babesia spp., the 18S gene was targeted using primers and cycling conditions described by Yabsley et al. (2005). Primary PCR primers were 3.1 and 5.1; secondary primers were RLB-F and RLB-R. Amplicons were purified using the QIAquick gel extraction kit (Qiagen) and submitted for bi-directional sequencing at the Georgia Genomics and Bioinformatics Core (Athens, Georgia, USA). Serum samples (n=59) were collected from 53 individual bears in 2016 and 2017 from GAAR, LACL, and KATM and tested for antibodies to Sarcoptes scabiei using a commercial indirect ELISA kit designed for domestic dogs (Sarcoptes-ELISA 2001, Afosa, Germany). Modifications for use in black bears (Ursus americanus) were implemented as described (Niedringhaus et al. 2020). Relevent Citations: Niedringhaus KD, Brown JD, Ternent M, Peltier SK, Van Wick P, Yabsley MJ. 2020. Serology as a tool to investigate sarcoptic mange in American black bears (Ursus americanus) J Wildl Dis 56:350-358. Ramey AM, Cleveland CA, Hilderbrand GV, Joly K, Gustine DD, Mangipane B, Leacock WB, Crupi AP, Hill DE, Dubey JP, Yabsley MJ. 2019. Exposure of Alaska brown bears (Ursus arctos) to bacterial, viral, and parasitic agents varies spatiotemporally and may be influenced by age. J Wildl Dis 55:576-588. Trataris AN, Rossouw J, Arntzen L, Karstaedt A, Frean J. 2012. Bartonella spp. in human and animal populations in Gauteng, South Africa, from 2007 to 2009. J Vet Res 79:E1–8 Yabsley MJ, Davidson WR, Stallknecht DE, Varela AS, Swift PK, Devos Jr. JC, Dubay SA. 2005. Evidence of tick-borne organisms in Mule deer (Odocoileus hemionus) from the Western United States. Vector Borne Zoonotic Dis 5:351-362. DATA-SPECIFIC INFORMATION FOR: Haynes_2022_AK_bear_parasite_data 1. Number of variables: 17 2. Number of cases/rows: 238 3. Variable List: Location_Captured: Site where bear was captured; GAAR = Gates of the Arctic National Park and Preserve, KATM = Katmai National Park, KOD = Kodiak Island, LACL = Lake Clark National Park and Preserve, YAK = Yakutat Forelands Bear_ID: Unique numerical identifier for the individual bear Month_Captured: Month when bear was captured; April - October Year_Captured: Year when bear was captured; 2013 - 2017 Bear_Sex: Biological sex of the captured bear; F = female, M = male Bear_Age: Age of the bear at capture; ages given in years to the nearest 0.5 year, 'adult' is listed for two individuals for whom a more exact age was not estimated Fecal_Flotation_Performed?: Indication (Yes or No) of whether a fecal flotation was performed on a fecal sample collected from that bear at that time point Baylisascaris: Indication of the detection (1) or lack of detection (0) of Baylisascaris sp. eggs in the feces based on fecal flotation; n/a is listed if no fecal flotation was performed Uncinaria: Indication of the detection (1) or lack of detection (0) of Uncinaria sp. eggs in the feces based on fecal flotation; n/a is listed if no fecal flotation was performed Dibothriocephalus: Indication of the detection (1) or lack of detection (0) of Dibothriocephalus sp. eggs in the feces based on fecal flotation; n/a is listed if no fecal flotation was performed Taeniid-type: Indication of the detection (1) or lack of detection (0) of Taeniid-type eggs in the feces based on fecal flotation; n/a is listed if no fecal flotation was performed Other_fecal_findings: Notation of any additional findings on fecal flotation; comments are listed when applicable, 0 = no additional findings, n/a is listed if no fecal flotation was performed Bartonella/Babesia_Testing_Performed?: Indication (Yes or No) of whether PCR testing was performed on a sample collected from that bear at that time point to detect Bartonella and Babesia Bartonella/Babesia_Result: Outcome of testing for Babesia and Bartonella; Negative = negative results for both tests, n/a is listed if testing was not performed Sarcoptes_ELISA_Performed?: Indication (Yes or No) of whether a sample collected from that bear at that time point was run on the ELISA to detect antibodies against Sarcoptes scabei Sarcoptes_result_bear_control: Result of the Sarcoptes scabei ELISA interpreted using data derived from a positive control sample from a black bear; Positive = antibodies detected; Negative = antibodies not detected, Doubtful = borderline result, n/a is listed if testing was not performed Sarcoptes_result_dog_control: Result of the Sarcoptes scabei ELISA interpreted using data derived from a positive control sample from a domestic dog; Positive = antibodies detected; Negative = antibodies not detected, Doubtful = borderline result, n/a is listed if testing was not performed 4. Missing data codes: None 5. Specialized formats or other abbreviations used: n/a: not applicable 6. Other relevant information: Bear sex and age were determined by biologists with extensive experience working with brown bears. Fecal flotations were performed by a single veterinary parasitologist with extensive parasite identification experience and eggs were identified based on morphological characteristics.