Shawna J Zimmerman Cameron L Aldridge Michael S O'Donnell David R Edmunds Peter S Coates Brian G Prochazka Jennifer A Fike Todd B Cross Bradley C Fedy Sara J Oyler-McCance 20220729 tabular digital data https://doi.org/10.5066/P98Q5F6R Shawna J Zimmerman Cameron L Aldridge Michael S O'Donnell David R Edmunds Peter S Coates Brian G Prochazka Jennifer A Fike Todd B Cross Bradley C Fedy Sara J Oyler-McCance 2022 publication Monitoring change in genetic diversity in wildlife populations across multiple scales could facilitate prioritization of conservation efforts. We used microsatellite genotypes from 7,080 previously collected genetic samples from across the greater sage-grouse (Centrocercus urophasianus) range to develop a modelling framework for estimating genetic diversity within a recently developed hierarchically nested monitoring framework (clusters). The majority of these genetic samples (n=6560) were used in previous research (Oyler-McCance et al. 2014; Cross et. al 2018; Row et. al. 2018). Genetic diversity values associated with clusters across multiple scales could facilitate the identification of areas with low genetic diversity and inform the potential management or conservation priority and response. We also report the data used to define genetic diversity thresholds of conservation concern and a full reporting of the genetic diversity estimates associated with the evaluated clusters. Data were collected to explore range-wide population structure, and characterize local population structure. 2005 2017 year sample was collected Complete None planned -120.7000 -104.1000 50.1000 37.6000 Western United States and Southwestern Canada ISO 19115 Topic Category biota USGS Thesaurus genetics microsatellites birds greater sage-grouse USGS Metadata Identifier USGS:62854703d34e3bef0c9a687f Common geographic areas western United States California Colorado Idaho Montana North Dakota Nevada Oregon South Dakota Utah Washington Wyoming Canada Saskatchewan None. Please see 'Distribution Info' for details. None. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. Sara J Oyler-McCance U.S. Geological Survey, ROCKY MOUNTAIN REGION Research Geneticist mailing address

2150 Centre Avenue Bldg C

Fort Collins CO 80526 US 970-226-9197 970-226-9230 sara_oyler-mccance@usgs.gov Todd B. Cross Michael K. Schwartz David E. Naugle Brad C. Fedy Jeffrey R. Row Sara J. Oyler‐McCance 20180504 publication Ecology and Evolution vol. 8, issue 11 n/a Wiley ppg. 5394-5412 https://doi.org/10.1002/ece3.4056 Sara J. Oyler-McCance Michael L. Casazza Jennifer A. Fike Peter S. Coates 20140607 publication Conservation Genetics vol. 15, issue 6 n/a Springer Science and Business Media LLC ppg. 1299-1311 https://doi.org/10.1007/s10592-014-0618-8 Jeffrey R. Row Kevin E. Doherty Todd B. Cross Michael K. Schwartz Sara J. Oyler‐McCance Dave E. Naugle Steven T. Knick Bradley C. Fedy 20180512 publication Evolutionary Applications vol. 11, issue 8 n/a Wiley ppg. 1305-1321 https://doi.org/10.1111/eva.12627 Todd B. Cross David E. Naugle John C. Carlson Michael K. Schwartz 20160802 publication Conservation Genetics vol. 17, issue 6 n/a Springer Science and Business Media LLC ppg. 1417-1433 https://doi.org/10.1007/s10592-016-0872-z Jeffrey R. Row Sara J. Oyler‐McCance Jennifer A. Fike Michael S. O'Donnell Kevin E. Doherty Cameron L. Aldridge Zachary H. Bowen Bradley C. Fedy 201505 publication Ecology and Evolution vol. 5, issue 10 n/a Wiley ppg. 1955-1969 https://doi.org/10.1002/ece3.1479 None Centrocercus urophasianus Kingdom Animalia Subkingdom Bilateria Infrakingdom Deuterostomia Phylum Chordata Subphylum Vertebrata Infraphylum Gnathostomata Superclass Tetrapoda Class Aves Order Galliformes Family Phasianidae Subfamily Tetraoninae Genus Centrocercus Species Centrocercus urophasianus TSN: 175855 Positive and negative controls were included with each batch of reactions. To ensure correct genotypes from feather samples, each sample was PCR amplified at least twice across the 15 microsatellite loci to screen for allele dropout, stutter artifacts, and false alleles. Alleles for each locus were coded as missing if they did not match across at least two independent runs. Samples with missing data for more than 7 loci were removed. Genotypes were then screened to ensure consistency between allele length and length of the microsatellite repeat motif. To combine the genotype data sets from both labs, we first genotyped the same 70 individuals. For two loci, the labs had a two base pair difference across all allele calls (BG6 and SGCA5), for one locus there was a four base pair difference (SGCA11) and for another locus, a seven base pair difference (SGCTAT1) as well as two alleles called off-step on a dimer repeat motif changed to comply with the tetramer repeat motif. Each lab’s genotypes for these individuals were shifted to synchronize allele calls for all samples for these loci No formal logical accuracy tests were conducted. Data set is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details. Genetic analysis was conducted at two molecular biological laboratories; the Molecular Ecology Lab at the U.S. Geological Survey Fort Collins Science Center (hereafter, FORT) and the National Genomics Center for Wildlife and Fish Conservation at the USFS Rocky Mountain Research Station (hereafter, NGC). At NGC feather DNA was extracted from the quill (calamus) using QIAGEN’s DNeasy Blood and Tissue Kit and a user-developed protocol for purification of total DNA from nails, hair, or feathers. We modified the protocol by incubating samples for a minimum of 8 hours after addition of Proteinase K and by eluting DNA with 100 microliters of Buffer AE (Cross et al. 2016). Feather samples from NGC were extracted in a lab used only for non-invasive DNA extraction in order to avoid potential contamination from samples with higher DNA concentrations. Blood samples were extracted using QIAGEN’s DNeasy Blood and Tissue Kit and the associated protocol for nucleated blood. At FORT, DNA from feather and blood samples were extracted using the same QIAGEN Kit following the user-developed protocol with portions of the extraction process automated using a Qiacube (QIAGEN). Both FORT and NGC amplified 15 microsatellite loci in eight multiplex polymerase chain reactions (PCR). At FORT, PCR products were multi-loaded based on product size and primer label, combined with GeneScan LIZ 600 internal lane size standard (Applied Biosystems), and electrophoresed through a capillary gel matrix using an AB3500 Automated DNA Sequencer (Applied Biosystems). Allele sizes were determined for each locus using GeneMapper v4.1 software (Applied Biosystems) (for details see Row et al. 2015). NGC electrophoresis methods can be found in Cross et al. (2016). We performed a systematic review of primary literature for estimates of allelic richness and expected heterozygosity for species of Phasianidae, Anatidae, Canidae, Felidae and all 7 bird and mammal species considered extinct in the wild to define genetic diversity thresholds associated with degree of conservation concern. We conducted our search for literature in Web of Science using the following keywords: species Latin name + ‘microsatellite’, species Latin name + ‘genetic’, and if the previous term returned more than 30 hits, we used the term ‘genetic diversity’ with the species Latin name. We considered only articles in the following research areas: genetics, heredity, environmental science, ecology, zoology, evolutionary biology, biodiversity, conservation, biology, and ornithology. We first examined abstracts to eliminate any article that clearly did not focus on a target species, evaluated captive (except for species extinct in the wild) or agricultural populations, used other than microsatellite loci for analyses, or did not include a genetic analysis. Articles that did not clearly warrant elimination based on the abstract were retained for further examination. We further required all articles to report estimates of allelic diversity and expected heterozygosity, sample size, and number of microsatellite loci. We also required allelic diversity to be reported as either the mean number of alleles per locus or the rarefied allelic richness. We eliminated individual populations that were reintroduced, captive, recipients of translocations, or were of special conservation concern relative to the rest of the species. We fit a single multinomial-Dirichlet model to our greater sage-grouse microsatellite data to estimate allelic richness and expected heterozygosity. Our model assumed microsatellite loci could be summarized as counts of different alleles at a locus, and the allele counts arise from a multinomial distribution centered on population specific allele frequencies modeled by the Dirichlet distribution. The conjugate relationship between the multinomial and the Dirichlet distributions allowed Gibbs sampling in an Markov chain Monte Carlo algorithm with R statistical software. The genetic diversity thresholds derived from the systematic review were used to determine whether individual clusters had genetic diversity levels denoting conservation concern. 2018 genotypes_clusters_final.csv Comma Separated Value (CSV) file containing data. Producer Defined unique_identifier Unique sample identifier Producer Defined The sample name assigned in the lab. year Year sample was collected. Producer Defined 2005 2017 state_province State or province where sample was collected. Producer Defined California Samples collected in the state of California. Producer defined Saskatchewan Samples collected in the province of Saskatchewan. Producer defined Colorado Samples collected in the state of Colorado. Producer defined Idaho Samples collected in the state of Idaho. Producer defined Montana Samples collected in the state of Montana. Producer defined North Dakota Samples collected in the state of North Dakota. Producer defined Nevada Samples collected in the state of Nevada. Producer defined Oregon Samples collected in the state of Oregon. Producer defined South Dakota Samples collected in the state of South Dakota. Producer defined Utah Samples collected in the state of Utah. Producer defined Washington Samples collected in the state of Washington. Producer defined Wyoming Samples collected in the state of Wyoming. Producer defined country Country where sample was collected. Producer Defined United States Samples collected in the United States. Producer defined Canada Samples collected in Canada. Producer defined BG6_allele1 Fragment size of microsatellite loci BG6, first allele. Producer Defined NA No Data Producer defined 197 301 base pairs BG6_allele2 Fragment size of microsatellite loci BG6, second allele. Producer Defined NA No Data Producer defined 197 309 base pairs SGMS064_allele1 Fragment size of microsatellite loci SGMS06.4, first allele. Producer Defined NA No Data Producer defined 118 178 base pairs SGMS064_allele2 Fragment size of microsatellite loci SGMS06.4, second allele. Producer Defined NA No Data Producer defined 126 182 base pairs SGMS066_allele1 Fragment size of microsatellite loci SGMS06.6, first allele. Producer Defined NA No Data Producer defined 122 182 base pairs SGMS066_allele2 Fragment size of microsatellite loci SGMS06.6, second allele. Producer Defined NA No Data Producer defined 128 185 base pairs SGMS068_allele1 Fragment size of microsatellite loci SGMS06.8, first allele. Producer Defined NA No Data Producer defined 103 159 base pairs SGMS068_allele2 Fragment size of microsatellite loci SGMS06.8, second allele. Producer Defined NA No Data Producer defined 107 159 base pairs MSP11_allele1 Fragment size of microsatellite loci MSP11, first allele. Producer Defined NA No Data Producer defined 206 262 base pairs MSP11_allele2 Fragment size of microsatellite loci MSP11, second allele. Producer Defined NA No Data Producer defined 206 280 base pairs MSP18_allele1 Fragment size of microsatellite loci MSP18, first allele. Producer Defined NA No Data Producer defined 94 120 base pairs MSP18_allele2 Fragment size of microsatellite loci MSP18, second allele. Producer Defined NA No Data Producer defined 98 124 base pairs SG28_allele1 Fragment size of microsatellite loci SG28, first allele. Producer Defined NA No Data Producer defined 107 167 base pairs SG28_allele2 Fragment size of microsatellite loci SG28, second allele. Producer Defined NA No Data Producer defined 113 171 base pairs SG29_allele1 Fragment size of microsatellite loci SG29, first allele. Producer Defined NA No Data Producer defined 110 150 base pairs SG29_allele2 Fragment size of microsatellite loci SG29, second allele. Producer Defined NA No Data Producer defined 118 150 base pairs SG36_allele1 Fragment size of microsatellite loci SG36, first allele. Producer Defined NA No Data Producer defined 203 243 base pairs SG36_allele2 Fragment size of microsatellite loci SG36, second allele. Producer Defined NA No Data Producer defined 203 255 base pairs SG39_allele1 Fragment size of microsatellite loci SG39, first allele. Producer Defined NA No Data Producer defined 148 184 base pairs SG39_allele2 Fragment size of microsatellite loci SG39, second allele. Producer Defined NA No Data Producer defined 148 187 base pairs reSGCA5_allele1 Fragment size of microsatellite loci reSGCA5, first allele. Producer Defined NA No Data Producer defined 118 140 base pairs reSGCA5_allele2 Fragment size of microsatellite loci reSGCA5, second allele. Producer Defined NA No Data Producer defined 118 140 base pairs reSGCA11_allele1 Fragment size of microsatellite loci reSGCA11, first allele. Producer Defined NA No Data Producer defined 177 197 base pairs reSGCA11_allele2 Fragment size of microsatellite loci reSGCA11, second allele. Producer Defined NA No Data Producer defined 177 199 base pairs SGCTAT1_allele1 Fragment size of microsatellite loci SGCTAT1, first allele. Producer Defined NA No Data Producer defined 82 118 base pairs SGCTAT1_allele2 Fragment size of microsatellite loci SGCTAT1, second allele. Producer Defined NA No Data Producer defined 82 126 base pairs TUT3_allele1 Fragment size of microsatellite loci TUT3, first allele. Producer Defined NA No Data Producer defined 140 168 base pairs TUT3_allele2 Fragment size of microsatellite loci TUT3, second allele. Producer Defined NA No Data Producer defined 144 168 base pairs TUT4_allele1 Fragment size of microsatellite loci TUT4, first allele. Producer Defined NA No Data Producer defined 163 199 base pairs TUT4_allele2 Fragment size of microsatellite loci TUT4, second allele. Producer Defined NA No Data Producer defined 163 203 base pairs climate_cluster_name Name of climate of cluster to which the sample belongs. Producer Defined Climate clusters to which each sample belongs, enumerated A through F. neighborhood_cluster_name Name of neighborhood of cluster to which the sample belongs. Producer Defined Neighborhood cluster to which each sample belongs, enumerated as A-001 - F-056. level_1 Level 1 cluster to which the sample belongs. Producer Defined 1 650 level_2 Level 2 cluster to which the sample belongs. Producer Defined 1 473 level_3 Level 3 cluster to which the sample belongs. Producer Defined 1 192 level_4 Level 4 cluster to which the sample belongs. Producer Defined 1 146 level_5 Level 5 cluster to which the sample belongs. Producer Defined 1 77 level_6 Level 6 cluster to which the sample belongs. Producer Defined 1 70 level_7 Level 7 cluster to which the sample belongs. Producer Defined 1 39 level_8 Level 8 cluster to which the sample belongs. Producer Defined 1 33 level_9 Level 9 cluster to which the sample belongs. Producer Defined 1 20 level_10 Level 10 cluster to which the sample belongs. Producer Defined 1 17 level_11 Level 11 cluster to which the sample belongs. Producer Defined 1 14 level_12 Level 12 cluster to which the sample belongs. Producer Defined 1 10 level_13 Level 13 cluster to which the sample belongs. Producer Defined 1 6 sytematic_review_for_thresholds.csv Comma Separated Value (CSV) file containing data. Producer Defined Species Species Latin name. Producer Defined The species Latin name. Family Family the species belongs to. Producer Defined Family the species belongs to. IUCN_code Species conservation status as defined by the International Union for Conservation of Nature (IUCN). Producer Defined LC Least Concern Producer defined NT Near Threatened Producer defined EN Endangered Producer defined EW Extinct in the Wild Producer defined CR Critically Endangered Producer defined VU Vulnerable Producer defined Number_of_loci Number of microsatellite loci the reported genetic diversity. Producer Defined 3.0 88.0 Sample_size Sample size the reported expected heterozygosity estimates are based on . Producer Defined 1.0 1075.0 Sample_size_adjusted Sample size the reported allelic richness estimates are based on. Producer Defined NA No Data Producer defined 1.0 1075.0 Expected_heterozygosity Reported expected heterozygosity estimate. Producer Defined NA No Data Producer defined 0.08 0.94 Allelic_richness Reported allelic richness estimate. Producer Defined NA No Data Producer defined 1.26 24.29 Source Source of the genetic diversity values. Producer Defined Reference information for the reported number of loci, sample size, and estimates of genetic diversity (expected heterozygosity and allelic richness). genetic_diverisity_values.csv Comma Separated Value (CSV) file containing data. Producer Defined Cluster_Level One of two spatial cluster levels. Producer Defined climate Coarse-scale, regional spatial cluster. Producer defined neighborhood Local-scale spatial cluster . Producer defined Cluster_ID Unique identifier for climate and neighborhood clusters. Producer Defined The unique identifier for each reported climate or neighborhood cluster. Allelic_richness_mean_1 Mean allelic richness estimate for independent model fit 1. Producer Defined 3.67 7.27 number of alleles Allelic_richness_lower_1 Lower 95% credible interval for the allelic richness estimate for independent model fit 1. Producer Defined 3.33 6.67 number of alleles Allelic_richness_upper_1 Upper 95% credible interval for the allelic richness estimate for independent model fit 1. Producer Defined 4.0 7.87 number of alleles Allelic_richness_mean_2 Mean allelic richness estimate for independent model fit 2. Producer Defined 3.67 7.27 number of alleles Allelic_richness_lower_2 Lower 95% credible interval for the allelic richness estimate for independent model fit 2. Producer Defined 3.33 6.67 number of alleles Allelic_richness_upper_2 Upper 95% credible interval for the allelic richness estimate for independent model fit 2. Producer Defined 4.0 7.87 number of alleles Allelic_richness_GR Gelman-Rubin diagnostic for convergence of the two independent model fits estimating allelic richness. Producer Defined 0.98 1.01 Expected_heterozygosity_mean_1 Mean expected heterozygosity estimate for independent model fit 1. Producer Defined 0.58 0.86 proportion heterozygous loci Expected_heterozygosity_lower_1 Lower 95% credible interval for the expected heterozygosity estimate for independent model fit 1. Producer Defined 0.55 0.85 proportion heterozygous loci Expected_heterozygosity_upper_1 Upper 95% credible interval for the expected heterozygosity estimate for independent model fit 1. Producer Defined 0.62 0.86 proportion heterozygous loci Expected_heterozygosity_mean_2 Mean expected heterozygosity estimate for independent model fit 2. Producer Defined 0.58 0.86 proportion heterozygous loci Expected_heterozygosity_lower_2 Lower 95% credible interval for the expected heterozygosity estimate for independent model fit 2. Producer Defined 0.55 0.85 proportion heterozygous loci Expected_heterozygosity_upper_2 Upper 95% credible interval for the expected heterozygosity estimate for independent model fit 2. Producer Defined 0.62 0.86 proportion heterozygous loci Expected_heterozygosity_GR Gelman-Rubin diagnostic for convergence of the two independent model fits estimating expected heterozygosity. Producer Defined 0.99 1.01 GWS_Watch Indicator of exceeding a genetic diversity watch threshold. Producer Defined NA No Data Producer defined 0 threshold not exceeded Producer defined 1 threshold exceeded Producer defined GWS_Warning Indicator of exceeding a genetic diversity warning threshold. Producer Defined NA No Data Producer defined 0 threshold not exceeded Producer defined 1 threshold exceeded Producer defined TAWS_Watch Indicator of exceeding a population trend watch threshold. Producer Defined NA No Data Producer defined 1 threshold exceeded Producer defined 0 threshold not exceeded Producer defined TAWS_Warning Indicator of exceeding a population trend warning threshold. Producer Defined NA No Data Producer defined 0 threshold not exceeded Producer defined 1 threshold exceeded Producer defined Time_Frame Indicator of the timing of genetic data collection relative to detected population trend decline. Producer Defined NA designation not applicable Producer defined after data were collected after the detected population trend decline Producer defined before data were collected before the detected population trend decline Producer defined Scenario Categorical designation of the combination of genetic and population trend watches and warnings and the timing of genetic sample collection. Producer Defined NA No Data Producer defined 2 genetic warning, population trend watch, genetic samples collected after population trend decline Producer defined 4 genetic watch, population trend watch, genetic samples collected after population trend decline Producer defined 1 genetic warning, population trend warning, genetic samples collected after population trend decline Producer defined 5 genetic warning, population trend warning, genetic samples collected before population trend decline Producer defined 10 genetic watch, no population trend watch or warning, genetic sample collection not relevant Producer defined 15 no genetic or population trend watch or warning Producer defined 12 no genetic watch or warning, population trend warning, genetic samples collected before population trend decline Producer defined 14 no genetic watch or warning, population trend watch, genetic samples collected before population trend decline Producer defined 11 no genetic watch or warning, population trend warning, genetic samples collected after population trend decline Producer defined 9 genetic warning, no population trend watch or warning, genetic sample collection not relevant Producer defined 7 genetic watch, population trend warning, genetic samples collected before population trend decline Producer defined 13 no genetic watch or warning, population trend watch, genetic samples collected after population trend decline Producer defined 3 genetic watch, population trend warning, genetic samples collected after population trend decline Producer defined 8 genetic watch, population trend watch, genetic samples collected before population trend decline Producer defined Priority Hypothetical conservation priority groups based on the number and severity of genetic and population trend thresholds exceeded. Producer Defined NA No Data Producer defined 1 first (highest) priority group Producer defined 2 second priority group Producer defined 3 third priority group Producer defined 0 no thresholds exceeded Producer defined 4 fourth priority group Producer defined Example_Response Examples of potential conservation or management responses based on the combination of genetic and population trend thresholds exceeded. Producer Defined NA No Data Producer defined Examples of potential responses: action = habitat restoration/improvement, translocation; extra monitoring = more frequent or more intensive lek/population monitoring; re-sample = collect and analyze additional genetic samples to confirm observed low genetic diversity or evaluate for further genetic diversity erosion. GS ScienceBase U.S. Geological Survey mailing address

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Denver CO 80225 United States 1-888-275-8747 sciencebase@usgs.gov Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. Digital Data https://doi.org/10.5066/P98Q5F6R None 20230111 FORT Metadata Specialist U.S. Geological Survey, Fort Collins Science Center FORT Metadata Specialist mailing address

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Fort Collins CO 80526 US 970-226-9100 970-226-9230 fortdatamanagement@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata FGDC-STD-001.1-1999