Population differentiation and genetic diversity
The TASSEL derived vcf was converted to formats compatible with
downstream analyses using PGDSpider v2.0.9.0 (Lischer and Excoffier
2012). Population summary statistics were generated using ‘basic.stats’,
‘fstat’, and ‘pairwise.WCfst’ from the hierfstat v0.5-7 package (Goudet
2005) in the R v4.0.4 computing environment (RC Team 2013). Poppr v2.9.0
(Kamvar, Tambia and Grünwald 2014) was used to analyze genetic distances
between populations and conduct AMAOVAs across hosts and populations.
Nei’s genetic distance was calculated across the full set of SNPs while
‘missingno’ was used to purge markers with missing data from the SNP
dataset to conduct the AMOVAs and test isolation by distance. IBD was
tested using ‘mantel.randtest’ from the adegenet v2.1.3 package (Jombart
and Ahmed 2011) on distance matricies generated using ‘dist.genepop’
(with Edwards’ distance) for SNPs and ‘dist’ on latitude and longitude
(decimal degrees) for each population.