Gray-Fox-Hybrid-Zone-Dynamics

Characterizing the dynamics of secondary contact between eastern and western gray fox lineages using whole genome and reduced-representation sequencing

Data Processing WGS

• Trim reads [Trim.sh]
• Align to reference [Align.sh]
• Merge (if split) and clean reads [Merge_Clean.sh]
• Calculate read depth across samples [ReadDepth.sh]

Data Processing GBS

• See Kierepka et al. 2022
• Details can be found in the github repository associated with that manuscript.

Local Ancestry Inference and Admixture Timing

Geographic Cline Analaysis

Run cline models for:

• All combined data [HZAR_ALLData.R]
• Western gray fox only [HZAR_West.R]
• Eastern gray fox only [HZAR_East.R]

Demographic History

PSMC Analysis

STEP0: Subset autosomes [subset_autosomes.sh]
STEP1: Convert bam to fastq file [bam2fastq.sh]
STEP2: Convert fastq to psmc fasta file [fastq2psmcfa.sh]
STEP3: Run PSMC for all files using Wang et al (2020) parameters [runPSMC.sh]
STEP4: Bootstrapping

Split fasta files for bootstrapping [bootstrap_split.sh]
Run bootstrapping [bootstrap.sh]

STEP5: Merge all .psmc files together [mergePSMC.sh]
STEP6: Plot PSMC trajectories [plotPSMC.sh]

Stairway Plot Analysis

Tajima's D and Fu's F

Heterozygosity

Ecological Niche Modeling