Population structure, ancestral admixture, gene flow, and landscape association of blacklegged ticks during range expansion in the Midwestern U.S.

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 l..., Table of ContentsPart 1. Genomic Data Preprocessing, Variant Calling, Variant filtering and concordance1A. Demultiplex and assign ID - PROCESS_RADTAGS in STACKS 2.64 1B. Adapter removal using CUTADAPT 3.51C. Read trimming with Trimmomatic 0.391D. Read mapping with reference genome using bwa-mem 0.7.17-r11881E. Alignment file conversion, and then resequencing bam merge - SAMTOOLS 1.16.1 1F. Variant calling - GATK 4.4.0.01G. Sample missingness filtering - PLINK2 v2.00a3 SSE4.2 1H. Variant filtering - GATK 4.4.0.01I. Variant missingness filtering - VCFTOOLS 0.1.17 1J. Genotype imputation in BEAGLE v5.41K. Genotype concordance between non-amplified and amplified ticks - GATK 
Part 2. Genetic distance statistics, Isolation by distance and Summary stats2A. Genetic distance via ADAGENET 2.1.10, GRAPH4LG 1.8.0, and MMOD 1.3.32B. Isolation by distance and mantel correlogram2C. Expected heterozygosity and nucleotide diversity via POPULATIONS in STACKS 2.64 2D. Tajima's D via DADI2E. Rarefied priv..., , # **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: [[e-mail]](mailto:[e-mail]){.email}

Co-Author Information Name: Sean Schoville ORCID:0000-0001-7364-434X Institution: University of Wisconsin - Madison Email: [[e-mail]](mailto:[e-mail]){.email}

Date of data collection: from 2021 to 2023

Geographic location of data collection: See Metadata.xlsx

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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

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