Pierson, Barbara J. (ORCID: 0000-0001-8233-874X) 20170725 tabular digital data Anchorage, Alaska U.S. Geological Survey, Alaska Science Center Suggested Citation: Pierson, B.J., 2017, Coho salmon (Oncorhynchus kisutch) genetic data, Glacier Bay National Park, Alaska (1994-1999): U.S. Geological Survey data release, https://doi.org/10.5066/F7V98657 https://doi.org/10.5066/F7V98657 These are genetic data collected from over 700 individual coho salmon (Oncorhynchus kisutch) from 17 streams and rivers within Glacier Bay Alaska and 2 rivers outside the bay. Data collected from all samples include one nuclear gene intron, Growth Hormone-1, and eight microsatellite loci. Samples were collected and analyzed to compare genetic signatures of populations by age of stream since deglaciation. 1994 1999 observed Complete None planned Alsek River in the west to Glacier Bay, Alaska, USA -138.55757 -135.52266 59.16582 58.37049 USGS Metadata Identifier USGS:ASC134 ISO 19115 Topic Category Biota Environment NASA GCMD Earth Science Keyword Thesaurus Animals/Vertebrates Terrestrial hydrosphere Glaciers/ice sheets Surface water Aquatic sciences Fisheries Climate indicators Range changes Species Migration USGS CSA Biocomplexity Thesaurus Fish Site Fidelity Gene Flow Population Genetics USGS Thesaurus Wildlife Aquatic ecosystems Genetics Polymerase chain reaction MeSH-National Library of Medicine DNA Genetic markers Microsatellite Repeats Oncorhynchus kisutch Rivers USGS Geographic Names Information System (GNIS) Alaska None Glacier Bay National Park None Animals Fish ITIS Integrated Taxonomic Information System Unknown online database online ITIS-North America Taxonomic details retrieved September 4, 2022, from the Integrated Taxonomic Information System online database https://www.itis.gov https://doi.org/10.5066/F7KH0KBK Woody, C. Unpublished material document Anchorage, Alaska U.S. Geological Survey, Alaska Science Center This document was an informal field guide for field collectors in proper identification to species level to reduce non-specific sample collection. Samples misidentified as Oncorhynchus kisutch in the field, were identified and eliminated from the study via non-specific DNA amplification products at the Growth Hormone 1 locus. Kingdom Animalia Subkingdom Bilateria Infrakingdom Deuterostomia Phylum Chordata Subphylum Vertebrata Infraphylum Gnathostomata Superclass Actinopterygii Class Teleostei Superorder Protacanthopterygii Order Salmoniformes Family Salmonidae Subfamily Salmoninae Genus Oncorhynchus Species Oncorhynchus kisutch Coho salmon Silver salmon TSN: 161977 No access constraints. No use constraints. We request that the suggested citation of this USGS data release be included in any publications that reference or utilize these data. U.S. Geological Survey, Alaska Science Center Mailing and Physical

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Anchorage Alaska 99508 USA 907-786-7000 gs-ak_asc_datamanagers@usgs.gov Department of Fisheries and Wildlife and Department of Integrative Biology, Michigan State University, East Lansing, MI 48824-1222, USA; Glacier Bay National Park and Preserve, P.O. Box 140, Gustavus, AK 99826, USA; Alaska Region, U.S. Geological Survey, 250 Egan Drive, Juneau, AK 99801, USA Scribner, K.T. Soiseth, C. McGuire, J. Sage, G.K. Thorsteinson, L. Nielsen, J.L. Knudsen, E. 2017 journal article Journal of Fish Biology 91(1):195–218 online Wiley Scribner, K.T., Soiseth, C., McGuire, J., Sage, G.K., Thorsteinson, L., Nielsen, J.L., Knudsen, E., 2017. Genetic assessment of the effects of streamscape succession on coho salmon Oncorhynchus kisutch colonization in recently deglaciated streams. Journal of Fish Biology 91(1):195–218, https://doi.org/10.1111/jfb.13337 https://doi.org/10.1111/jfb.13337 Individual sample ID's, collection dates, and sampling locations contained in the accompanying worksheet were verified and cross-referenced to field notes and the Glacier Bay National Park Service (NPS) Stream Database, National Hydrography Dataset (NHD) and manuscript (Scribner et al. 2017). Species identification by collectors were informally verified by confirming genetic "signatures" (e.g. microsatellite or Growth Hormone 1 sizes) fell within expected values for coho salmon (Oncorhynchus kisutch). We observed sterile technique in the handling of all DNA, and all procedures were performed with positive and negative controls to provide evidence of replication without contamination. All samples were scored independently by two experienced laboratory personnel. Exact sizes for GH-1 alleles were not determined, but any questionable allele results on an initial gel, were re-run on a subsequent gel adjacent to standards with known alleles. For microsatellite data, reported allele sizes were reviewed to confirm they conform to expected distributions (e.g. dinucleotide repeats with 1 base pair differences were reviewed, gaps in allele sizes were reviewed, and single occurrences of an allele size were scrutinized). Data omissions for particular entities are explained in the Entity and Attribute definitions. Blank cells indicate no data were collected or not provided with the sample for a particular attribute. Geospatial data were acquired from the contributing data sources. These methods were not documented in the source data. All reported locations were verified with Glacier Bay National Park staff (Chad Soiseth) referencing available field sampling notes, the National Park Service stream catalog for Glacier Bay and confirmed congruent with reported National Hydrography Dataset and Alaska Department of Fish and Game Catalog of Anadromous Fish locators. Johnson, J. Litchfield, V. 2016 document Alaska Department of Fish and Game Special Publication No. 16-04 online Alaska Department of Fish and Game Johnson, J., Litchfield, V., 2016. Catalog of Waters Important for Spawning, Rearing, or Migration of Anadromous Fishes-Southeastern Region, Effective June 1, 2016. Alaska Department of Fish and Game Special Publication No. 16-04, accessed from the Alaska Resources Library and Information Services at: https://www.arlis.org/docs/vol1/B/19100834/2016/19100834-2016-AR.pdf https://www.arlis.org/docs/vol1/B/19100834/2016/19100834-2016-AR.pdf publication 2016 publication date Johnson and Litchfield 2016 Reference for placenames: 114-77-10900 (this study's "Gull Creek"); East Alsek River; Alsek River; 114-71-10240 (this study's "Berg Bay South"); Berg River (this study's "Berg Bay North"); >Bartlett River; Carolus River; Excursion River; Ice Valley Creek (this study's "Ice Valley River"); North Fingers Stream (this study's "N Fingers Bay, South/NPS Stream 141"); North Rush Point Creek (this study's North Rush Point (l)/NPS Stream 200"); Salmon River/114-23-10080; 114-60-10800-2004 (this study's "Seclusion River"); 114-75-10960-2031 (this study's "North Vivid Stream/NW Vivid Lake System"); Wolf Point Creek LAB: DNA was extracted via proteinase K digestion and phenol-chloroform methods following Sambrook et al (1989) and quantified via fluorometry. Loci were amplified using the polymerase chain reaction (PCR) as described in these references: GH-1 (Forbes et al. 1994); Okiµ1/Okiµ11 (Smith et al. 1998); Okeµ4 (Buchholz et al. 2001); Omy77 (Morris et al. 1996); Oneµ3-1/Oneµ3-2 (Scribner et al. 1996); Ots-1/Ots-2/Ots-4 (Banks et al. 1999+errata). Microsatellite genotype numbers were determined by visual scoring based on allele size relative to an M13 DNA sequence ladder and to samples established as size standards that were run on each gel. Growth Hormone-1 intron fragments were assigned manually by visualizing on 1% agarose gels stained with ethidium bromide where individuals of known genotype were run side by side with all samples to use as an allele identification standard. Additional downstream process steps and statistical analyses not included with this data have been published externally in Scribner, et. al. 2017. Unknown Full siblings were identified using likelihood-based analyses and the software KinGroup V. 2 (Konovalov et al. 2004). Only one full sibling was retained in published analyses, though results for all individuals for which data was collected are included here. Konovalov et al 2004 Unknown Watershed age was estimated as elapsed time since glacial ice recession from each stream mouth using published glacial records, historical documents, and aerial and oblique photographs to determine timing, location, and movement of ice masses. Watershed basin areas were estimated from scanned USGS 1:63360 series topographic maps using ArcView GIS, version 3.0. Cooper 1937 Field 1947 Unknown LITERATURE CITED: Banks, M.A., Blouin, M.S., Baldwin, B.A., Rashbrook, V.K., Fitzgerald, H.A., Blankenship, S.M., Hedgecock, D., 1999. Isolation and inheritance of novel microsatellites in chinook salmon (Oncorhynchus tshawytscha). Journal of Heredity 90(2):281-288, https://doi.org/10.1093/jhered/90.2.281 (see errata in May/June issue of same volume for corrected Table 1) Buchholz, W.G., Miller, S.J., Spearman, W.J., 2001. Isolation and characterization of chum salmon microsatellite loci and use across species. Animal Genetics 32(3):162-165 https://doi.org/10.1046/j.1365-2052.2001.0723b.x Cooper, W.S., 1937. The problem of Glacier Bay, Alaska: a study of glacier variations. Geographical Review 27(1):37-62, https://doi.org/10.2307/209660 Field, W.O., 1947. Glacier recession in Muir Inlet, Glacier Bay, Alaska. Geographical Review 37(3):369-399, https://doi.org/10.2307/211127 Forbes, S.H., Knudsen, K.L., North, T.W., Allendorf, F.W., 1994. One of two growth hormone genes in coho salmon is sex linked. Proceedings of the National Academy of Sciences 91(5):1628-1631, https://doi.org/10.1073/pnas.91.5.16 Konovalov, D.A., Manning, C., Henshaw, M.T., 2004. KINGROUP: a program for pedigree relationship reconstruction and kin group assignments using genetic markers. Molecular Ecology Notes 4(4):779-782, https://doi.org/10.1111/j.1471-8286.2004.00796.x Morris, D.B., Richard, K.R., Wright, J.M., 1996. Microsatellites from rainbow trout (Oncorhynchus mykiss) and their use for genetic study of salmonids. Canadian Journal of Fisheries and Aquatic Sciences 53(1):120-126, https://doi.org/10.1139/f95-161 Sambrook, J., Fritsch, E.F., Maniatis, T., 1989. Molecular cloning: a laboratory manual, 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA Scribner, K.T., Gust, J.R., Fields, R.L., 1996. Isolation and characterization of novel salmon microsatellite loci: cross-species amplification and population genetic applications. Canadian Journal of Fisheries and Aquatic Sciences 53(4):833-841, https://doi.org/10.1139/f95-254 Scribner, K.T., Soiseth, C., McGuire, J., Sage, G.K., Thorsteinson, L., Nielsen, J.L., Knudsen, E., 2017. Genetic assessment of the effects of streamscape succession on coho salmon Oncorhynchus kisutch colonization in recently deglaciated streams. Journal of Fish Biology 91(1):195–218, https://doi.org/10.1111/jfb.13337 Smith, C.T., Koop, B.F., Nelson, R.J., 1998. Isolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids. Molecular Ecology 7(11):1614-1616, https://doi.org/10.1046/j.1365-294X.1998.00474.x Unknown Several location methods have been provided with this dataset. Glacier Bay National Park maintains a stream locator database system for which their names are provided. Some streams can be identified with a unique National Hydrography Dataset identifier. Latitude and longitudes of stream mouths are provided for use in absence of access to either of the other databases referenced above and in the entity/attribute sections of this dataset. All reported locations were verified with Glacier Bay National Park staff (Chad Soiseth) referencing available field sampling notes, the National Park Service stream catalog for Glacier Bay and confirmed congruent with reported National Hydrography Dataset and Alaska Department of Fish and Game Catalog of Anadromous Fish locators. Point 0.0001 0.0001 Decimal degrees World Geodetic System of 1984 (WGS84) World Geodetic System of 1984 (WGS84) 6378137 298.257223563 cohoSalmon_microsat_glacierBay_pierson.csv Table with sample identifying information, collection location data, and genotype numbers for eight autosomal microsatellite loci (Okeµ4, Okiµ1, Okiµ11, Omy77, Oneµ3-1, Oneµ3-2, Ots-1, Ots-4)and one nuclear gene intron (Growth Hormone-1). Genotype numbers (nucleotide base pairs) were determined by scoring based on allele size relative to an M13 DNA sequence ladder and to samples established as size standards that were run on each gel. Presented in a Comma Separated Value (CSV) formatted table. Author defined Publication_Population_Label Sampling locations as referenced in Scribner et al. 2017 Author defined NPS Stream 317.5 Unnamed stream number 317.5 in the National Park Service Glacier Bay National Park stream catalog National Park Service NPS Stream 318 unnamed stream number 318 in the National Park Service Glacier Bay National Park stream catalog National Park Service NA This location was not included in manuscript publication, but data were collected concurrently with the published study. Author defined North Berg Stream Berg Bay North, stream number 205 in the National Park Service Glacier Bay National Park stream catalog National Park Service Bartlett River Bartlett River number 376 in the National Park Service Glacier Bay National Park stream catalog National Park Service Carolus River Carolus River number 198 in the National Park Service Glacier Bay National Park stream catalog National Park Service Excursion River Excursion River number 386 in the National Park Service Glacier Bay National Park stream catalog National Park Service Gull Creek Gull Lake (l) number 308 in the National Park Service Glacier Bay National Park stream catalog National Park Service Ice Valley River Ice Valley number 326 in the National Park Service Glacier Bay National Park stream catalog National Park Service NPS Stream 141 N Fingers Bay, South number 141 in the National Park Service Glacier Bay National Park stream National Park Service Reid Creek South Reid Creek (l) number 246 in the National Park Service Glacier Bay National Park stream catalog National Park Service NPS Stream 200 North Rush Point (l) number 200 in the National Park Service Glacier Bay National Park stream catalog National Park Service N. Sebree Creek Unnamed number 327 in the National Park Service Glacier Bay National Park stream National Park Service Salmon River Salmon River number 377.4 in the National Park Service Glacier Bay National Park stream catalog National Park Service Seclusion River Seclusion River number 185.1 in the National Park Service Glacier Bay National Park stream catalog National Park Service North Vivid Stream NW Vivid Lake system number 101 in the National Park Service Glacier Bay National Park stream catalog National Park Service Wolf Point Creek This represents Wolf Point Creek (l) system number 336 in the National Park Service Glacier Bay National Park stream catalog with a mouth at latitude 58.99487917 N, longitude 136.1619958 W. C. Soiseth, National Park Service South Berg Stream Berg Bay South system number 202 in the National Park Service Glacier Bay National Park stream catalog National Park Service NPS_Stream_Database_Locator Stream name includes official USGS water body names designated on 1:63,360 scale topo maps or are unofficial local names. If value is a number, it indicates the Glacier Bay National Park Service stream catalog numerical indicator for which names have not been assigned. National Park Service NPS Stream 317.5 Unnamed stream number 317.5 in the National Park Service Glacier Bay National Park stream catalog National Park Service NPS Stream 318 Unnamed stream number 318 in the National Park Service Glacier Bay National Park stream catalog National Park Service Alsek River Alsek River number 61 in the National Park Service Glacier Bay National Park stream catalog National Park Service Berg Bay North Berg Bay North number 205 in the National Park Service Glacier Bay National Park stream catalog National Park Service Bartlett River Bartlett River number 376 in the National Park Service Glacier Bay National Park stream catalog National Park Service Berg Bay South Berg Bay South number 202 in the National Park Service Glacier Bay National Park stream catalog National Park Service Carolus River Carolus River number 198 in the National Park Service Glacier Bay National Park stream catalog National Park Service East Alsek River East Alsek River number 60 in the National Park Service Glacier Bay National Park stream catalog National Park Service Excursion River Excursion River number 386 in the National Park Service Glacier Bay National Park stream catalog National Park Service Gull Lake (l) Gull Lake (l) number 308 in the National Park Service Glacier Bay National Park stream catalog National Park Service Ice Valley Ice Valley number 326 in the National Park Service Glacier Bay National Park stream catalog National Park Service N Fingers Bay, South N Fingers Bay, South number 141 in the National Park Service Glacier Bay National Park stream catalog National Park Service South Reid Creek (l) South Reid Creek (l) number 246 in the National Park Service Glacier Bay National Park stream catalog National Park Service North Rush Point (l) North Rush Point (l) number 200 in the National Park Service Glacier Bay National Park stream catalog National Park Service NPS Stream 327 Unnamed number 327 in the National Park Service Glacier Bay National Park stream catalog National Park Service Salmon River Salmon River number 377.4 in the National Park Service Glacier Bay National Park stream catalog National Park Service Seclusion River Seclusion River number 185.1 in the National Park Service Glacier Bay National Park stream catalog National Park Service NW Vivid Lake System NW Vivid Lake system number 101 in the National Park Service Glacier Bay National Park stream catalog National Park Service Wolf Point Creek (l) Wolf Point Creek (l) system number 336 in the National Park Service Glacier Bay National Park stream catalog National Park Service NHD_Reach_Code National Hydrography Dataset (NHD) reach code. The first eight digits represent the Hydrologic Unit Code (HUC) for the subbasin in which the reach exists, and the last six digits are a sequential number assigned when reach codes are allocated in the subbasin. U.S. Geological Survey 19010302000015 19010406000789 National Hydrography Dataset https://www.usgs.gov/national-hydrography/national-hydrography-dataset [Accessed 2016-06-17]. NA The NHD Reach Code not provided for this location Author defined Stream_Mouth_or_Reach_Latitude This is the GIS derived latitudeof referenced stream mouth or reach, presumably derived from original NAD27 datum field coordinates. C. Soiseth, National Park Service 58.38104838 59.18663219 Decimal degrees Stream_Mouth_or_Reach_Longitude This is the GIS derived longitude of referenced stream mouth or reach, presumably derived from original NAD27 datum field coordinates. C. Soiseth, National Park Service -138.3736117 -135.5224048 Decimal degrees Stream_Location This designation corresponds with the relative time since deglaciation of various sampling locations ranging from "Outside Bay" (not glaciated during last glacial advance), "Lower Bay," "Middle Bay," to "Upper Bay" (youngest, most recently deglaciated). Author defined Upper Bay This area encompasses sampling locations that were the youngest, most recently deglaciated (50-68 yrs. BP) and colonized, and were located in the upper reaches of the east arm of Glacier Bay, Alaska. Author defined NA This is an area outside Glacier Bay, Alaska not analyzed in the associated manuscript. Author defined Lower Bay This area encompasses sampling locations that were the oldest watersheds in the deglaciated region of the lower bay (152-197 yrs. BP) of Glacier Bay, Alaska. Author defined Outside Bay This area encompasses sampling locations that were not glaciated during the last glacial advance (with the exception of Salmon River; 230 BP: referring to before the time of sampling). These locations represent the most geographically proximal sources for colonization of streams inside Glacier Bay proper. Author defined Middle Bay This area encompasses sampling locations that were of intermediate age (117-130 yrs. BP) and were situated in the mid to lower reaches of the west and east arm, of Glacier Bay, Alaska, respectively. Author defined Watershed_Age Watershed age (years) is generally defined as the time since ice recession from stream mouths using historical and aerial photographs, journal articles, and unpublished data. Milner, A.M. et al. 2000. Colonization and development of stream communities across a 200-year gradient in Glacier Bay National Park, Alaska, U.S.A. Can. J. Fish. Aquat. Sci. 57: 2319-2335. 50 14,000 Years Old NA Age of watershed was not calculated since this location was not included in the associated manuscript. Author defined Basin_Area Watershed area (km2) and gradient were estimated from scanned USGS 1:63360 series topographic maps using ArcView GIS (version 3.0). Scribner, K.T. et al. 2017 0.6 190.6 square kilometers NA Area of watershed was not calculated since this location was not included in the associated manuscript. Author defined Sample_ID This is a U.S. Geological Survey, Alaska Science Center, Molecular Ecology Laboratory name that uniquely identifies each sample using an abbreviation of sampling location, 2-digit year sampled, and 3 digit individual ID. Author defined This is a unique alphanumeric code incorporating population, sample year, and individual identifiers. Publication_Status This indicates whether each sample was included in the analyses for the manuscript (Scribner et al 2017) accompanying this dataset. Author defined Analyzed This indicates the individual was included in analyses of the accompanying manuscript (Scribner et al 2017). Author defined Removed This indicates the individual was not included in analyses of the accompanying manuscript (Scribner et al 2017). Author defined GH-1_1 Allele one from the GH-1 locus: genotype numbers were assigned based on size relative to individuals of known genotype run on each gel. Blank cells indicate no data were collected for that individual. Author defined Six different allele sizes were identified among samples in this dataset. Exact sizes were not determined, but relative sizes in descending order are: 6, 5, 1, 2, 3, 4. GH-1_2 Allele two from the GH-1 locus: genotype numbers were assigned based on size relative to individuals of known genotype run on each gel. Blank cells indicate no data were collected for that individual. Author defined Six different allele sizes were identified among samples in this dataset. Exact sizes were not determined, but relative sizes in descending order are: 6, 5, 1, 2, 3, 4. Okeµ4_1 through Ots-4_2 These 16 columns present the genotype number (nucleotide base pairs) for each of eight autosomal microsatellite loci. Each microsatellite locus genotype is represented by two adjacent columns (i.e., allele1 and allele2). Blank cells indicate that the genotype number of this locus was not collected for this sample. Locus names and order of presentation: Okeµ4, Okiµ1, Okiµ11, Omy77, Oneµ3-1, Oneµ3-2, Ots-1, Ots-4 These microsatellite data cannot be combined with data generated outside the Alaska Science Center without molecular size calibration between laboratories. Author defined Genotype number (nucleotide base pairs) for each microsatellite locus from each sample. U.S. Geological Survey USGS ScienceBase Team Mailing and Physical

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Anchorage Alaska 99508 USA 907-786-7000 gs-ak_asc_datamanagers@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata (CSDGM) FGDC-STD-001.1-1999