Ceratonia siliqua
For the Treemix analysis, we rooted C. siliqua phylogenetic tree
with SM following SVDquartets reconstructions (Fig. 2). Tree topology
reconstructed by Treemix (Fig. 3) is highly similar to that of
SVDquartets, showing the same strong west-east differentiation. The
position of NM was resolved as intermediate between Western (SM, SWS,
SES) and Central and Eastern CEUs (CM, NEM, SEM), which agrees with the
highly admixed pattern in NM inferred by snmf (Fig. 2 A) and with its
low to moderate differentiation with respect to other CEUs (Tab. S2 in
supplementary material). The Treemix model without migrations explained
96 % of the covariance (Fig. 3A), and the addition of four migrations
resulted in 99.8 % of the total covariance explained (Fig. 3B). Three
of the four migrations identified SEM as the source of introgression,
into SM, SWS and NM, whereas the fourth migration connected the
central-eastern CEUs to SES, again indicating a westward migration.
Impact of carob cultivation effort on carob genetic diversity
Overall genetic diversity values are reported in Table 1. The Nei
diversity (Hexp) values decrease from west CEUs and natural or
seminatural habitats to east and/or cultivated habitats, regardless of
the markers. Interestingly, this trend is negatively correlated with the
association index (rbardD), which reports the highest lack of mixing in
cultivated CM carobs. The fixation index (f) suggests a lack of
heterozygosity in SM, NM, and NEM (and SEM only for SSR), significant
excess in CM, but was non significantly different from zero in SWS and
SES (and SEM too for RADseq. Based on the differentiation between
genetic groups formed by the combination of CEUs and habitats (Table 1),
OUTFLANK did not detect candidate loci with a false discovery rate
(qvalue) below 0.05, which indicates that the hypothesis of neutrality
cannot been rejected (Fig. S6 in supplementary material).