Testing spatial clustering by genetic cline
To test whether the genetic clusters from sNMF are the consequence of
natural genetic clusters or isolation by distance (IBD) with
discontinuous sampling, we used the R package conStruct version 1.0.4
(Bradburd, Coop, & Ralph, 2018). We compare the non-spatial (cluster)
and spatial (IBD) models for K=1 to K=10 ancestral populations. The
input allele frequencies of SNPs from fully-filtered dataset were
calculated using VCFtools version 0.1.17 (Danecek et al., 2011), and the
geographical distances among populations were calculated using R package
geodist version 0.0.4 (Karney, 2013). In the conStruct package, we ran
cross-validation analysis through K=3 to K=10 with ten replicates and
100,000 iterations of the MCMC chains for each K. The predictive
accuracies were estimated with 90% training and 10% test data.
Two-sample t-tests were used to test differences between spatial and
non-spatial models for each K. Moreover, we also consider the preferred
models by examining the layer contributions from K=1 to K=10 using the
construct function, with two MCMC chains of 100,000 iterations
(Bradburd, Coop, & Ralph, 2018).