This README_Maier2019.txt file was generated on 2019-10-30 by Paul Maier ------------------- GENERAL INFORMATION ------------------- Title of Dataset: YOTOAD_GLACIALPULSE 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. (2019). Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus). Evolution, 73(12):2476–2496. https://www.doi.org/10.1111/evo.13868 Citation for and links to publications that cite or use the data: Main article DOI: https://www.doi.org/10.1111/evo.13868 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 and phylogenetic data files that were subsequently analyzed. Please see the manual and example files on GitHub for instructions on usage.) https://github.com/paulmaier/fasta2genotype Journal Club Slides: https://figshare.com/articles/journal_contribution/Pleistocene_glacial_cycles_drove_lineage_diversification_and_fusion_in_the_Yosemite_toad_Anaxyrus_canorus_/10260362 -------------------- DATA & FILE OVERVIEW -------------------- ├── README_Maier2019.txt This readme file │ ├── fastsimcoal2.zip Input data for demographic analyses using fastsimcoal2: │   ├── README_FASTSIMCOAL2.txt README FILE FOR FASTSIMCOAL2 │   ├── NorthZone_MSFS.obs JOINT MINOR ALLELE FREQUENCY SPECTRUM – NORTH CONTACT ZONE │   ├── SouthZone_MSFS.obs JOINT MINOR ALLELE FREQUENCY SPECTRUM – SOUTH CONTACT ZONE │   ├── NorthZone-ISOLATION.tpl TEMPLATE FILE FOR SIMPLE ISOLATION MODEL – NORTH CONTACT ZONE │   ├── NorthZone-ISOLATION.est ESTIMATION FILE FOR SIMPLE ISOLATION MODEL – NORTH CONTACT ZONE │   ├── NorthZone-ISOMIGRATION.tpl TEMPLATE FILE FOR ISOLATION WITH MIGRATION MODEL – NORTH CONTACT ZONE │   ├── NorthZone-ISOMIGRATION.est ESTIMATION FILE FOR ISOLATION WITH MIGRATION MODEL – NORTH CONTACT ZONE │   ├── NorthZone-INTRO1.tpl TEMPLATE FILE FOR INTROGRESSION MODEL 1 – NORTH CONTACT ZONE │   ├── NorthZone-INTRO1.est ESTIMATION FILE FOR INTROGRESSION MODEL 1 – NORTH CONTACT ZONE │   ├── NorthZone-INTRO2.tpl TEMPLATE FILE FOR INTROGRESSION MODEL 2 – NORTH CONTACT ZONE │   ├── NorthZone-INTRO2.est ESTIMATION FILE FOR INTROGRESSION MODEL 2 – NORTH CONTACT ZONE │   ├── NorthZone-INTRO3.tpl TEMPLATE FILE FOR INTROGRESSION MODEL 3 – NORTH CONTACT ZONE │   ├── NorthZone-INTRO3.est ESTIMATION FILE FOR INTROGRESSION MODEL 3 – NORTH CONTACT ZONE │   ├── NorthZone-INTRO4.tpl TEMPLATE FILE FOR INTROGRESSION MODEL 4 – NORTH CONTACT ZONE │   ├── NorthZone-INTRO4.est ESTIMATION FILE FOR INTROGRESSION MODEL 4 – NORTH CONTACT ZONE │   ├── NorthZone-HYBRID1.tpl TEMPLATE FILE FOR HYBRID MODEL 1 – NORTH CONTACT ZONE │   ├── NorthZone-HYBRID1.est ESTIMATION FILE FOR HYBRID MODEL 1 – NORTH CONTACT ZONE │   ├── NorthZone-HYBRID2.tpl TEMPLATE FILE FOR HYBRID MODEL 2 – NORTH CONTACT ZONE │   ├── NorthZone-HYBRID2.est ESTIMATION FILE FOR HYBRID MODEL 2 – NORTH CONTACT ZONE │   ├── NorthZone-HYBRID3.tpl TEMPLATE FILE FOR HYBRID MODEL 3 – NORTH CONTACT ZONE │   ├── NorthZone-HYBRID3.est ESTIMATION FILE FOR HYBRID MODEL 3 – NORTH CONTACT ZONE │   ├── NorthZone-HYBRID4.tpl TEMPLATE FILE FOR HYBRID MODEL 4 – NORTH CONTACT ZONE │   ├── NorthZone-HYBRID4.est ESTIMATION FILE FOR HYBRID MODEL 4 – NORTH CONTACT ZONE │   ├── SOUTHZone-ISOLATION1.tpl TEMPLATE FILE FOR SIMPLE ISOLATION MODEL 1 – SOUTH CONTACT ZONE │   ├── SOUTHZone-ISOLATION1.est ESTIMATION FILE FOR SIMPLE ISOLATION MODEL 1 – SOUTH CONTACT ZONE │   ├── SOUTHZone-ISOLATION2.tpl TEMPLATE FILE FOR SIMPLE ISOLATION MODEL 2 – SOUTH CONTACT ZONE │   ├── SOUTHZone-ISOLATION2.est ESTIMATION FILE FOR SIMPLE ISOLATION MODEL 2 – SOUTH CONTACT ZONE │   ├── SOUTHZone-ISOMIGRATION1.tpl TEMPLATE FILE FOR ISOLATION WITH MIGRATION MODEL 1 – SOUTH CONTACT ZONE │   ├── SOUTHZone-ISOMIGRATION1.est ESTIMATION FILE FOR ISOLATION WITH MIGRATION MODEL 1 – SOUTH CONTACT ZONE │   ├── SOUTHZone-ISOMIGRATION2.tpl TEMPLATE FILE FOR ISOLATION WITH MIGRATION MODEL 2 – SOUTH CONTACT ZONE │   ├── SOUTHZone-ISOMIGRATION2.est ESTIMATION FILE FOR ISOLATION WITH MIGRATION MODEL 2 – SOUTH CONTACT ZONE │   ├── SOUTHZone-INTRO1.tpl TEMPLATE FILE FOR INTROGRESSION MODEL 1 – SOUTH CONTACT ZONE │   ├── SOUTHZone-INTRO1.est ESTIMATION FILE FOR INTROGRESSION MODEL 1 – SOUTH CONTACT ZONE │   ├── SOUTHZone-INTRO2.tpl TEMPLATE FILE FOR INTROGRESSION MODEL 2 – SOUTH CONTACT ZONE │   ├── SOUTHZone-INTRO2.est ESTIMATION FILE FOR INTROGRESSION MODEL 2 – SOUTH CONTACT ZONE │   ├── SOUTHZone-HYBRID.tpl TEMPLATE FILE FOR HYBRID MODEL – SOUTH CONTACT ZONE │   └── SOUTHZone-HYBRID.est ESTIMATION FILE FOR HYBRID MODEL – SOUTH CONTACT ZONE │ ├── Phylogenetics.zip Input data for all phylogenetic analyses: │   ├── README_PHYLOGENETICS.txt README FILE FOR PHYLOGENETICS │   ├── RAXML_CANORUS-BOREAS-ALL RAXML FOR ALL NON-ADMIXED SAMPLES + EAST-NORTH-A1 ADMIXED MEADOWS, WHICH ARE PHYLOGENETICALLY DISTINCT │   │  ├── RAXML_CANORUS-BOREAS-ALL.phy PHYLIP FILE │   │  ├── part.txt PARTITION FILE TO BE USED WITH -q OPTION OF RAXML │   │  └── p1.txt COUNTS OF ACGT INVARIANT SITES │   ├── RAXML_CANORUS-BOREAS-BALANCED RAXML FOR BALANCED SUBSET OF SPECIES │   │ ├── RAXML_CANORUS-BOREAS-BALANCED.phy PHYLIP FILE │   │ ├── part.txt PARTITION FILE TO BE USED WITH -q OPTION OF RAXML │   │ └── p1.txt COUNTS OF ACGT INVARIANT SITES │   ├── BEAST.XML XML FILE FOR BEAST │   └── SNAPP.XML XML FILE FOR SNAPP │ ├── NicheOverlap.zip Script and input data for conducting niche overlap analyses: │   ├── README_NICHEOVERLAP.txt README FILE FOR NICHE OVERLAP ANALYSIS │   ├── NicheOverlap.R R SCRIPT FILE │   ├── pops.txt MEADOWS, LINEAGES, AND COORDINATES │   └── GIS GIS FOLDER │   ├── YOSEbndry.shp YOSEMITE BOUNDARY SHAPEFILE │   ├── YOSEbndry.prj │   ├── YOSEbndry.dbf │   ├── YOSEbndry.shx │   ├── canorus.shp A. CANORUS DISTRIBUTION SHAPEFILE │   ├── canorus.prj │   ├── canorus.dbf │   ├── canorus.shx │   └── current_env FOLDER OF ENVIRONMENTAL GEOTIFF RASTERS FOR PRESENT DAY │   ├── bio_1.tif BIOCLIM VARIABLE 1 │   ├── bio_2.tif BIOCLIM VARIABLE 2 │   ├── bio_3.tif BIOCLIM VARIABLE 3 │   ├── bio_4.tif BIOCLIM VARIABLE 4 │   ├── bio_5.tif BIOCLIM VARIABLE 5 │   ├── bio_6.tif BIOCLIM VARIABLE 6 │   ├── bio_7.tif BIOCLIM VARIABLE 7 │   ├── bio_8.tif BIOCLIM VARIABLE 8 │   ├── bio_9.tif BIOCLIM VARIABLE 9 │   ├── bio_10.tif BIOCLIM VARIABLE 10 │   ├── bio_11.tif BIOCLIM VARIABLE 11 │   ├── bio_12.tif BIOCLIM VARIABLE 12 │   ├── bio_13.tif BIOCLIM VARIABLE 13 │   ├── bio_14.tif BIOCLIM VARIABLE 14 │   ├── bio_15.tif BIOCLIM VARIABLE 15 │   ├── bio_16.tif BIOCLIM VARIABLE 16 │   ├── bio_17.tif BIOCLIM VARIABLE 17 │   ├── bio_18.tif BIOCLIM VARIABLE 18 │   ├── bio_19.tif BIOCLIM VARIABLE 19 │   └── elevation.tif DEM DATA │ └── ContactZones.zip Script and input data for conducting analyses of contact zones: ├── README_CONTACTZONES.txt README FILE FOR CONTACT ZONE ANALYSIS ├── ContactZones.R R SCRIPT FILE ├── data DATA FOLDER │ ├── YOSEhaplo.stru GENOTYPE FILE, WITH MICROHAPLOTYPES, IN STRUCTURE FORMAT │ ├── YOSEsnp.stru GENOTYPE FILE, WITH ONE RANDOMLY PICKED SNP/LOCUS, IN STRUCTURE FORMAT │ ├── meadows.txt MEADOWS AND CONTACT ZONES │ └── coordinates.txt SAMPLES, MEADOWS, AND COORDINATES ├── GIS GIS FOLDER │  ├── YOSEbndry.shp YOSEMITE BOUNDARY SHAPEFILE │  ├── YOSEbndry.dbf │  ├── YOSEbndry.prj │  └── YOSEbndry.shx ├── scripts SCRIPTS FOLDER │  ├── filled.legend.R R SCRIPT OF PLOTTING FUNCTIONS │  ├── filled.contour3.R R SCRIPT OF PLOTTING FUNCTIONS │  └── sPCAplot.R R SCRIPT OF PLOTTING FUNCTIONS └── outfiles FOLDER FOR OUTPUT FILES └── structure FOLDER FOR STRUCTURE OUTPUT; INCLUDED, BECAUSE NOT CREATED BY SCRIPT ├── EN_ind.txt STRUCTURE OUTPUT FOR EAST-NORTH CONTACT ZONE ├── ES_ind.txt STRUCTURE OUTPUT FOR EAST-SOUTH CONTACT ZONE └── EW_ind.txt STRUCTURE OUTPUT FOR EAST-WEST CONTACT ZONE -------------------------- 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.