3.5.1 Structure and principal component analyses
Genetic structure analyses were done using the whole set of 5,702 SNP
with ADMIXTURE, without and with supervision (i.e., using the allopatric
samples as ancestry references) (Supplementary Figure S4). Analyses
without supervision indicated that the most likely number of ancestral
populations (i.e., the K with the lowest cv error) was K=2
(Supplementary Figure S5), but it should be noted that the cv errors for
K=2 and K=3 were similar. For K=2, the two genetic clusters corresponded
very well to I. graellsii and I. elegans , respectively,
and for K=3 a third cluster was found among I. eleganspopulations from the north-west hybrid region. For both K=2 and K=3,
many samples with admixed ancestry were present (Supplementary Figure
S4).
PCA allowed us to cluster I. elegans , I. graellsii and
hybrids from allopatry and from the three hybrid regions. The first axis
of the PCA explained 39% of the total variation and clearly separatedI. elegans and I. graellsii individuals from
allopatric localities, while the second axis explained 2% of the total
variation and separated some of the individuals from north-central and
north-west hybrid regions (Supplementary Figure S6). Consistent with the
ADMIXTURE results, many individuals from the three hybrid
regions appeared in the same PCA quadrant as those occupied by the pure
species from the allopatric distribution, while hybrids occupied
intermediate positions of the first axis.