This README_Maier2022a.txt file was generated on 2022-02-21 by Paul Maier ------------------- GENERAL INFORMATION ------------------- Title of Dataset: YOTOAD_HUB_SATELLITE Author Information: Paul Maier paulm@genebygene.com San Diego State University 5500 Campanile Drive San Diego, CA 92182 Principal Investigator: Paul Maier Co-investigators: Amy Vandergast, Steve Ostoja, Andres Aguilar, Andrew Bohonak Date of data collection: 2011–2013 Geographic location of data collection: Yosemite National Park, Kings Canyon National Park Funding source: U.S. Geological Survey, Ecosystems Mission Area, Natural Resource Preservation Program Research grant -------------------------- SHARING/ACCESS INFORMATION -------------------------- No licenses/restrictions have been placed on the data. ** NOTE: ALL GEOGRAPHIC COORDINATES HAVE BEEN RANDOMLY JITTERED TO PROTECT THE LOCATION OF THIS FEDERALLY PROTECTED SPECIES ** ** PLEASE CONTACT THE CORRESPONDING AUTHOR TO REQUEST PERMISSION FOR THE ORIGINAL COORDINATES ** Recommended citation for the data: Maier P.A., Vandergast A.G., Ostoja S.M., Aguilar A., Bohonak A.J. (2022). Gene pool boundaries for the Yosemite toad (Anaxyrus canorus) reveal asymmetrical migration within meadow neighborhoods. Frontiers in Conservation Science, 3:851676. https://doi.org/10.3389/fcosc.2022.851676 Citation for and links to publications that cite or use the data: Main article DOI: https://doi.org/10.3389/fcosc.2022.851676 NCBI BioProject with links to Sequence Read Archive (SRA) fastq files: https://www.ncbi.nlm.nih.gov/sra/PRJNA558546 This Dryad DOI: https://doi.org/10.5061/dryad.xsj3tx99h USGS link to metadata for the article: https://doi.org/10.5066/P9KABYPU GitHub repository link for the fasta2genotype.py script: (This script was used to produce many of the genotypic data files that were subsequently analyzed. Please see the manual and example files on GitHub for instructions on usage.) https://github.com/paulmaier/fasta2genotype -------------------- DATA & FILE OVERVIEW -------------------- ├── README_Maier2022a.txt This readme file │ ├── ADMIXTURE.zip Script and input data for conducting ADMIXTURE analyses: │   ├── ADMIXTURE.R ADMIXTURE R script │   ├── kings │   │   ├── clumpp_files │   │   │   ├── clumpp_miscfile clumpp misc. param file │   │   │   ├── clumpp_paramfile clumpp param file │   │   │   └── clumpp_permutationfile clump permutations file │   │   ├── coords │   │   │   └── coords_kings.txt Coordinates for Kings Canyon NP, jittered to 1 km │   │   ├── data │   │   │   ├── kings.map Kings Canyon NP PLINK data │   │   │   └── kings.ped Kings Canyon NP PLINK data │   │   └── gis │   │   ├── KICAbndry.dbf Kings Canyon NP boundary shapefile │   │   ├── KICAbndry.prj Kings Canyon NP boundary shapefile │   │   ├── KICAbndry.shp Kings Canyon NP boundary shapefile │   │   ├── KICAbndry.shx Kings Canyon NP boundary shapefile │   │   ├── KICAdem.tif Kings Canyon NP elevation model │   │   └── KICAshade.tif Kings Canyon NP hillshade │   └── yose │   ├── clumpp_files │   │   ├── clumpp_miscfile clumpp misc. param file │   │   ├── clumpp_paramfile clumpp param file │   │   └── clumpp_permutationfile clump permutations file │   ├── coords │   │   └── coords_yose.txt Coordinates for Yosemite NP, jittered to 1km │   ├── data │   │   ├── yose.map Yosemite NP PLINK data │   │   └── yose.ped Yosemite NP PLINK data │   └── gis │   ├── YOSEbndry.dbf Yosemite NP boundary shapefile │   ├── YOSEbndry.prj Yosemite NP boundary shapefile │   ├── YOSEbndry.qpj Yosemite NP boundary shapefile │   ├── YOSEbndry.shx Yosemite NP boundary shapefile │   ├── YOSEdem.tif Yosemite NP elevation model │   └── YOSEshade.tif Yosemite NP hillshade │ ├── AMOVA.zip Script and input data for conducting AMOVA analyses: │   ├── AMOVA.R AMOVA R script │   ├── data_radsnp_allparks.stru Biallelic SNP data for both parks in STRUCTURE format │   └── hier.txt Hierarchy of population structure │ ├── HierarchicalStructure.zip Hierarchical directory containing STRUCTURE input files for each recursive analysis │   ├── A │   ├── B │   │   ├── North │   │   │   └── north.stru │   │   └── South │   │   └── south.stru │   ├── C │   │   ├── East │   │   │   └── east.stru │   │   ├── Isberg │   │   │   └── isberg.stru │   │   ├── NorthHybrids │   │   │   └── northhybrids.stru │   │   ├── Northwest │   │   │   └── northwest.stru │   │   ├── RancheriaCreek │   │   │   └── rancheriacreek.stru │   │   ├── Southwest │   │   │   └── southwest.stru │   │   └── West │   │   └── west.stru │   ├── D │   │   ├── BridalveilChilnualna │   │   │   └── bridalveilchilnualna.stru │   │   ├── East │   │   │   └── east.stru │   │   ├── KerrickWells │   │   │   └── kerrickwells.stru │   │   ├── Miller │   │   │   └── miller.stru │   │   ├── Porcupine │   │   │   └── porcupine.stru │   │   ├── RibbonWhiteWolf │   │   │   └── ribbonwhitewolf.stru │   │   ├── Rodgers │   │   │   └── rodgers.stru │   │   ├── Slide │   │   │   └── slide.stru │   │   ├── _NOSTRUCTURE │   │   │   └── StarrKing │   │   │   └── starrking.stru │   │   └── _SUBMEADOW │   │   ├── Bald │   │   │   └── bald.stru │   │   ├── Isberg1097 │   │   │   └── isberg1097.stru │   │   ├── Isberg942 │   │   │   └── isberg942.stru │   │   ├── Rancheria │   │   │   └── rancheria.stru │   │   ├── Summit │   │   │   └── summit.stru │   │   ├── Thompson │   │   │   └── thompson.stru │   │   ├── Tilden │   │   │   └── tilden.stru │   │   ├── TwinLakes │   │   │   └── twinlakes.stru │   │   └── Wawona │   │   └── wawona.stru │   ├── E │   │   ├── Bridalveil │   │   │   └── bridalveil.stru │   │   ├── Cathedral │   │   │   └── cathedral.stru │   │   ├── Chilnualna │   │   │   └── chilnualna.stru │   │   ├── CockscombTresidder │   │   │   └── cockscombtresidder.stru │   │   ├── Conness │   │   │   └── conness.stru │   │   ├── Ireland │   │   │   └── ireland.stru │   │   ├── Kerrick │   │   │   └── kerrick.stru │   │   ├── Lyell │   │   │   └── lyell.stru │   │   ├── Miller3400_3414 │   │   │   └── miller3400_3414.stru │   │   ├── Rodgers3384_3452 │   │   │   └── rodgers3384_3452.stru │   │   ├── Tioga │   │   │   └── tioga.stru │   │   ├── WhiteWolf2371_2385_2418 │   │   │   └── whitewolf2371_2385_2418.stru │   │   ├── _NOSTRUCTURE │   │   │   └── Ribbon1779_1841 │   │   │   └── ribbon1779_1841.stru │   │   └── _SUBMEADOW │   │   ├── Miller3342 │   │   │   └── miller3342.stru │   │   ├── Polly │   │   │   └── polly.stru │   │   └── Wells │   │   └── wells.stru │   ├── F │   │   ├── Bridalveil1040_1070_1171 │   │   │   └── bridalveil1040_1070_1171.stru │   │   ├── Conness │   │   │   └── conness.stru │   │   ├── Kerrick │   │   │   └── kerrick.stru │   │   ├── Lyell │   │   │   └── lyell.stru │   │   ├── WhiteWolf2371_2385 │   │   │   └── whitewolf2371_2385.stru │   │   └── _NOSTRUCTURE │   │   ├── Ireland1951_2021 │   │   │   └── ireland1951_2021.stru │   │   └── Tioga │   │   └── tioga.stru │   └── G │   └── _NOSTRUCTURE │   ├── Bridalveil1070_1171 │   │   └── bridalveil1070_1171.stru │   ├── Conness3200_3225 │   │   └── conness3200_3225.stru │   ├── Conness3272_3339_3371 │   │   └── conness3272_3339_3371.stru │   └── Lyell1815_1956 │   └── lyell1815_1956.stru │ ├── HubSatellite.zip Script and input data for conducting Hub-Satellite analyses: │   ├── HubSatellite.R Hub-Satellite R script │   ├── HubSatellite_functions.R Hub-Satellite R script functions to source │   ├── divM_G_martha.txt Asymmetrical Gst values for Martha neighborhood │   ├── divM_G_yose.txt Asymmetrical Gst values for Yosemite NP │   ├── heterozygosity.txt Expected heterozygosity values for all meadows │   ├── hier.txt Hierarchy of population structure │   ├── martha_cov10_haplo.gen Genotype data for Martha neighborhood in genpop format │   ├── martha_cov10_haplo.pops List of meadows in Martha neighborhood │   ├── meadow_attributes.txt Environmental data for Yosemite NP │   ├── yose_cov10_haplo.gen Genotype data for Yosemite NP in genpop format │   └── yose_cov10_haplo.pops List of meadows in Yosemite NP │ └── IBD.zip Script and input data for conducting IBD analyses:    ├── IBD.R IBD R script    └── IBD_data.txt Fst data for IBD analysis -------------------------- METHODOLOGICAL INFORMATION -------------------------- For all information about how the analyses were performed, which parameters were chosen, and for all sample meta-data, please refer to the main article and the supporting information.