Multivariate statistics
SNP metrics were recalculated in R for post-filtered data using the
‘DArTR package’ (Gruber, Unmack, Berry, & Georges, 2018). PCoAs were
constructed from individual larval SNP genotypes with Gower PCoA
ordination and Euclidean distances using the packages ‘Adegenet’ and
‘DArTR’ (Gruber et al., 2018; Jombart, 2008). Clusters of genetically
related individuals were inferred using Discriminant Analysis of
Principal Components (Jombart, Devillard, & Balloux, 2010) constructed
with and without the between- and within- group variance components from
PCoA outputs. Multiple loading thresholds were explored, including the
default value of the third quartile (75%) of x-values (Grünwald,
Kamvar, & Everhart, Jombart & Collins, 2015). Diversity metrics were
calculated using ‘DArTR’ following (Sherwin, Chao, Jost, & Smouse,
2017). These analyses are similar to classic population genetic analyses
that measure differentiation via Fst, in which high
allele frequency differentiation suggests population differentiation
although they can be fraught with false positives (Rajora, 2019).
Given the influence of close relationships in STRUCTURE analyses
(Anderson & Dunham, 2008), DAPC was used as an alternative method to
infer admixture (Grünwald et al., 2010). Hence, “true k ” was
calculated based on Bayesian Information Criteria (BIC, Jombart et al.,
2010), in which the largest drop in BIC was at k = 5.