DOI: 10.5061/dryad.c866t1gh7
title: Data from: Population structure, ancestral admixture, gene flow, and landscape association of blacklegged ticks during range expansion in the Midwestern U.S.

description: 42 populations totalling 517 individuals of Ixodes scapularis from
 different spatial locations were sampled and sequenced to study the
 neutral variation, population structure, ancestral admixture, genetic
 connectivity, and landscape influences on gene flow. We began with genomic
 data preprocessing, variant calling, variant filtering and concordance
 check. Then we used the finalized dataset in variant call format (VCF) and
 spatial locations to conduct genetic distance statistics, isolation by
 distance modeling and calculate summary statstics. Further we used VCF and
 sample metadata to conduct Pincipal Component analysis and clustering
 analysis for understanding population structure and ancestral admixture.
 To understand region-wide gene flow connectivity, we conducted effective
 migration surface analysis and graph network analyses to visualize
 dispersal route and extent. Lastly, we processed landscape and ecological
 data to conduct landscape genomic analyses to understand the impact of
 landscape on gene flow, and visualized routes of dispersal across
 favorable environmental conditions.
description: Table of Contents<br>Part 1. Genomic Data Preprocessing,
 Variant Calling, Variant filtering and concordance<br>1A.
 Demultiplex and assign ID - PROCESS_RADTAGS in STACKS 2.64 <br>1B.
 Adapter removal using CUTADAPT 3.5<br>1C. Read trimming with
 Trimmomatic 0.39<br>1D. Read mapping with reference genome using
 bwa-mem 0.7.17-r1188<br>1E. Alignment file conversion, and then
 resequencing bam merge - SAMTOOLS 1.16.1 <br>1F. Variant calling -
 GATK 4.4.0.0<br>1G. Sample missingness filtering - PLINK2 v2.00a3
 SSE4.2 <br>1H. Variant filtering - GATK 4.4.0.0<br>1I. Variant
 missingness filtering - VCFTOOLS 0.1.17 <br>1J. Genotype imputation
 in BEAGLE v5.4<br>1K. Genotype concordance between non-amplified and
 amplified ticks - GATK  Part 2. Genetic distance
 statistics, Isolation by distance and Summary stats<br>2A. Genetic
 distance via ADAGENET 2.1.10, GRAPH4LG 1.8.0, and MMOD 1.3.3<br>2B.
 Isolation by distance and mantel correlogram<br>2C. Expected
 heterozygosity and nucleotide diversity via POPULATIONS in STACKS
 2.64 <br>2D. Tajima's D via DADI<br>2E. Rarefied private
 alleles via ADZE-1.0 Part 3. Population structure via
 PCA, SNMF, and CONSTRUCT<br>3A. Principal component
 analysis<br>3B. SNMF via LEA 3.12.2<br>3C. CONSTRUCT
 1.0.5 Part 4. Effective Migration surface and Graph
 Networks<br>4A. Effective Migration surface via FEEMS<br>4B.
 Graph Networks via GRAPH4LG Part 5. Landscape
 ecological data collection and processing<br>5A. Landscape data
 download, reformat, variable selection, NA cell treatment, and
 aggregation Part 6. Isolation by resistance (IBR) and
 environment (IBE) analyses<br>6A. Isolation by resistance modeling,
 model selection, and resistance mapping via RADISH<br>6B. Current
 Flow map via CIRCUITSCAPE and visualization<br>6C. Isolation by
 Environment modeling, and co-estimating with Isolation by Distance and
 Isolation by Resistance via MMRR implemented in ALGATR
description: # **Population structure, ancestral admixture, gene flow, and landscape
 association of Blacklegged ticks during range expansion in the Midwestern
 U.S.** Main Author Information Name: Dahn-young Dong
 ORCID:0000-0001-6284-2738 Institution: University of Wisconsin - Madison
 Email: [ddong22@wisc.edu](mailto:ddong22@wisc.edu){.email} Co-Author
 Information Name: Sean Schoville ORCID:0000-0001-7364-434X Institution:
 University of Wisconsin - Madison Email:
 [sean.schoville@wisc.edu](mailto:sean.schoville@wisc.edu){.email} Date of
 data collection: from 2021 to 2023 Geographic location of data collection:
 See Metadata.xlsx SHARING/ACCESS INFORMATION Licenses/restrictions placed
 on the data: NA Links to publications that cite or use the data: Genetic
 and landscape connectivity of Blacklegged ticks during range expansion in
 the Midwestern U.S. In Review at Molecular Ecology Links to other publicly
 accessible locations of the data: NA Links/relationships to ancillary data
 sets: NA Was data derived from another source? No Recommended citation for
 this dataset: The publication mentioned above **DATA & FILE OVERVIEW**
 **Metadata file: Metadata.xlsx** **Genomic data processing files**:
 03.pruned.vcf.gz cohort.sample_map_wotbi.txt concordance calculation.xlsx
 contig.list imputation_exclude.txt input_files_QC.txt long_intervals.list
 short_intervals.list smaller.interval_list **Downstream Analysis data
 files**: 03_LD_IMPUTED.vcf.gz 03_MISS20.vcf.gz
 2024.10.04_03_LD_IMPUTED.geno ADZE_paramfile.txt Dgeo.rds
 GD.pop.new_03.rds Midwest triangles.shp PG_distance_mat.csv
 combined_vif_new.rds combined_vif_new_agg10.rds
 combined_vif_new_agg10_narm.rds coord_03 dps_distance_mat.csv
 fitted_resistance_est_PG_plus1.asc fitted_resistance_est_dps_plus1.asc
 fitted_resistance_est_linfst_plus1.asc genind_03.rds genpop_03.rds
 linfst_distance_mat.csv omniscape_PG.ini omniscape_dps.ini
 omniscape_linfst.ini polygon_outer population_stats.xlsx
 populationmap_03.txt populationmap_03_ind.txt private_allele_rich.csv
 sites.sf.rds sites.sp.rds surface_dir8_agg10.rds tick_private_popremoved
 ticks.eigenval ticks.eigenvec wildareas-v3-2009-human-footprint_geo.tif
 The use of these files are included in the script.txt files \[Description
 of each file]{.underline}: What is the file name, what does it do, where
 in the script you can find the use of the file **Metadata file:** *
 Metadata.xlsx * metadata of all samples, inclusive of 517 samples that are
 used for downstream genetic and landscape analyses. It is imported
 commonly in R scripts to obtain information such as sample ID, site names,
 acronyms, region names, lat-lon coordinates. It also contain information
 about tissue source and year of collection. You need some data wrangling
 to fit the R script input requirement. **Genomic data processing files:**
 * 03.pruned.vcf.gz * 03 is a internal code for versions. Pruned means
 Linkage disequilibrium (LD)-controlled variants. VCF means variant call
 format, and gz means gzipped compression. This is the variant call set
 that was pruned for LD but is not imputed for missingness after filtering
 highly missing variants. This file is used in 1J. Genotype imputation in
 BEAGLE v5.4 * cohort.sample_map_wotbi.txt * A mapping file linking sample
 same to directory file to allow building of GATK datastore. Used in
 #######1F. Variant calling - GATK 4.4.0.0 * concordance calculation.xlsx *
 concordance is needed to ensure whole genome amplified DNA can be used in
 same analyses as the ones without amplification. The concordance count of
 various categories are download from GATK output and manually calculated
 for genotype concordance. #1K. Genotype concordance between non-amplified
 and amplified ticks - GATK * contig.list * the contig.list provide the
 vcf.gz files with genomic contig names sorted in increasing order
 comformative to original reference genome call order, to keep
 scatter-gather process aligned, while allowing for parallelism.#######1F.
 Variant calling - GATK 4.4.0. * imputation_exclude.txt * Imputation of
 missing variant using BEAGLE. BEAGLE needs a minimal number of variants
 per contig to allow imputation. Some contigs have too few variants so
 needed to be excluded. ######1J. Genotype imputation in BEAGLE v5.4 *
 input_files_QC.txt * A list of Quality Control tick names to be included
 in GATK variant call pipeline.######1K. Genotype concordance between
 non-amplified and amplified ticks - GATK * long_intervals.list * a list of
 contigs that are long to optimize parallelization during RAM intensive
 step of GATK variant calling. #######1F. Variant calling - GATK 4.4.0.0 *
 short_intervals.list * a list of contigs that are short to optimize
 parallelization during RAM intensive step of GATK variant calling.
 #######1F. Variant calling - GATK 4.4.0.0 * smaller.interval_list * an
 initial interval list to allow the creation of gatk datastrore. #######1F.
 Variant calling - GATK 4.4.0.0 **Downstream Analysis data files:** *
 03_LD_IMPUTED.vcf.gz * Linkage disequilibrium controlled, missingness
 imputed set of variants that are ready for some of the downstream
 analyses. * 03_MISS20.vcf.gz * A set of variants for all tick samples that
 were only controlled for variant missingness by removing the variants that
 are missing in more than 80% of the biological samples. This is a file
 generated in ######1I. Variant missingness filtering - VCFTOOLS 0.1.17 ,
 and use to prune linkage disequilibrium variant in ######3A. Principal
 component analysis * 2024.10.04_03_LD_IMPUTED.geno * the file type that is
 readable by SNMF analysis to calculate ancestral admixture. I generated
 this file and read in R script found in ######3B. SNMF via LEA 3.12.2 *
 ADZE_paramfile.txt * parameter file to allow calculation of rarefied
 allele richness for each population. #######2E. Rarefied private alleles
 via ADZE-1.0 * Dgeo.rds * R data object that stores the Great Circle
 geographic distances among all populations. Used in many landscape
 genetics analyses R script. * GD.pop.new_03.rds * R data object Genetic
 Distance for populations contain a list of genetic distances calculated
 and accessed varyingly depending on the need. Used in many genetic
 distance, isolation by distance, and landscape association analyses in R
 scripts. * Midwest triangles.shp * The tesselation grod shapefile needed
 to generate the edges values in the migration surface in the gene flow
 analyses. #4A. Effective Migration surface via FEEMS * PG_distance_mat.csv
 * A matrix of resistance-optimized Pop Graph genetic distance used in
 generating combined modeling of isolation by environment and
 resistance.######6C. Isolation by Environment modeling, and co-estimating
 with Isolation by Distance and Isolation by Resistance via MMRR
 implemented in ALGATR * combined_vif_new.rds * landscape rasters in
 spatraster format in 1km resolution ready for landscape genetic analyses,
 after variable selection * combined_vif_new_agg10.rds * landscape rasters
 in spatraster format ready for landscape genetic analyses, after variable
 selection. Aggregated to 10km resolution * combined_vif_new_agg10_narm.rds
 * landscape rasters in spatraster format ready for landscape genetic
 analyses, after variable selection. Aggregated to 10km resolution and
 removing missing value cells after aggregation * coord_03 * population
 coordinates used in ######4A. Effective Migration surface via FEEMS *
 dps_distance_mat.csv * A matrix of resistance-optimized 1-proportion of
 share alleles (dps) genetic distance used in generating combined modeling
 of isolation by environment and resistance.######6C. Isolation by
 Environment modeling, and co-estimating with Isolation by Distance and
 Isolation by Resistance via MMRR implemented in ALGATR *
 fitted_resistance_est_PG_plus1.asc * raster values across the study region
 after fitted with isolation by resistance model using PG genetic distance.
 This file is used in Current Flow analysis in ######6B. Current Flow map
 via CIRCUITSCAPE and visualization * fitted_resistance_est_dps_plus1.asc *
 raster values across the study region after fitted with isolation by
 resistance model using dps genetic distance. This file is used in Current
 Flow analysis in ######6B. Current Flow map via CIRCUITSCAPE and
 visualization * fitted_resistance_est_linfst_plus1.asc * raster values
 across the study region after fitted with isolation by resistance model
 using linearized Fst genetic distance. This file is used in Current Flow
 analysis in ######6B. Current Flow map via CIRCUITSCAPE and visualization
 * genind_03.rds * genetic information of individuals in a R object data
 format. It is used in calculating some genetic distance in ######2A.
 Genetic distance via ADAGENET 2.1.10, GRAPH4LG 1.8.0, and MMOD 1.3.3. And
 some other plotting functions in #4B. Graph Networks via GRAPH4LG *
 genpop_03.rds * genetic information of individuals in a R object data
 format. It is used in calculating some genetic distance in ######2A.
 Genetic distance via ADAGENET 2.1.10, GRAPH4LG 1.8.0, and MMOD 1.3.3. Also
 used in calculating population allele frequency #######3C. CONSTRUCT
 1.0.5, code adapted from tutorial. * linfst_distance_mat.csv * A matrix of
 resistance-optimized linearized Fst genetic distance used in generating
 combined modeling of isolation by environment and resistance.######6C.
 Isolation by Environment modeling, and co-estimating with Isolation by
 Distance and Isolation by Resistance via MMRR implemented in ALGATR *
 omniscape_PG.ini * The init file to provide parameters to run omniscape to
 generate gene flow current map for the study area by providing landscape
 resistance map generated by Pop Graph genetic distance. ######6B. Current
 Flow map via CIRCUITSCAPE and visualization * omniscape_dps.ini * The init
 file to provide parameters to run omniscape to generate gene flow current
 map for the study area by providing landscape resistance map generated by
 Dps genetic distance. ######6B. Current Flow map via CIRCUITSCAPE and
 visualization * omniscape_linfst.ini * The init file to provide parameters
 to run omniscape to generate gene flow current map for the study area by
 providing landscape resistance map generated by linearized Fst genetic
 distance. ######6B. Current Flow map via CIRCUITSCAPE and visualization *
 polygon_outer * A self-enclosing set of coordinates that formulate the
 spatial boundary of the study region. Used in #######5A. Landscape data
 download, reformat, and variable selection and ######4A. Effective
 Migration surface via FEEMS * population_stats.xlsx * genomic summary
 statistics of populations on Expected heterozygosity, nucleotide
 diversity, with sample size and Tajima's D. It is used in mapping and
 plotting of the results. ######2D. Tajima's D via DADI ######2C.
 Expected heterozygosity and nucleotide diversity via POPULATIONS in STACKS
 2.64 * populationmap_03.txt * a file linking sample name and population
 sampling location. Used in generation of ######2C. Expected heterozygosity
 and nucleotide diversity via POPULATIONS in STACKS 2.64, ######2D.
 Tajima's D via DADI, Rarefied private alleles via ADZE-1.0, and
 ancestral clustering using #######3C. CONSTRUCT 1.0.5, code adapted from
 tutorial * populationmap_03_ind.txt * this file is a list of sample name
 IDs. Used in ######3B. SNMF via LEA 3.12.2 * private_allele_rich.csv *
 rarefied private allelic richness generated by ADZE. The file include site
 name, rarefied sample size (loci), mean, variance, and standardized error.
 The mean values are taken for visusalization. Used in #######2E. Rarefied
 private alleles via ADZE-1.0 * sites.sf.rds * R data object of sampling
 sites/population coordinates transformed into SF objects useful for
 downstream spatial analyses. * sites.sp.rds * R data object of sampling
 sites/population coordinates transformed into SP objects useful for
 downstream spatial analyses. * surface_dir8_agg10.rds * R data object of
 conductance surface generated by RADISH R package to prepare for landscape
 genetic regression analyses. It is generated by setting direction of
 neighbor to 8 and aggregation to 10km resolution. It is used in ######6A.
 Isolation by resistance modeling, model selection, and resistance mapping
 via RADISH * tick_private_popremoved * The actual ADZE output and later
 manually imported to private_allele_rich.csv for further visualization.
 The file is mentioned in #######2E. Rarefied private alleles via ADZE-1.0
 * ticks.eigenval * The eigenvalues, an input component to generate
 Pincipal component plot. This is used in ######3A. Principal component
 analysis * ticks.eigenvec * The eigenvector, an input component to
 generate Pincipal component plot. This is used in ######3A. Principal
 component analysis * wildareas-v3-2009-human-footprint_geo.tif * The tif
 file (Venter et al., 2016) I downloaded from
 https://www.earthdata.nasa.gov/data/catalog/sedac-ciesin-sedac-lwp3-hf-2009-2018.00 to generate human footprint raster. The file is used in #######5A. Landscape data download, reformat, and variable selection. This dataset is not my own, and included here for the sake of reproducibility. It is under "Creative Commons Zero (CC0). There are no restrictions on the use of these data." https://www.earthdata.nasa.gov/engage/open-data-services-software-policies/data-use-policy Relationship between files, if important: N/A Additional related data collected that was not included in the current data package: N/A Are there multiple versions of the dataset? No Read quality control were assessed using FastQC and MultiQC. Quality control of Whole-genome Amplification described in Data_prep_script.txt ######1K. Genotype concordance between non-amplified and amplified ticks - GATK People involved with sample collection, processing, analysis and/or submission: See manuscript acknowledgement DATA-SPECIFIC INFORMATION: see script files marked out comments among the codes **Reference** Venter, O., Sanderson, E. W., Magrach, A., Allan, J. R., Beher, J., Jones, K. R., . . . Watson, J. E. M. (2016). Global terrestrial Human Footprint maps for 1993 and 2009. *Scientific Data, 3*(1), 160067. doi:10.1038/sdata.2016.67