3.3. Phylogeographic scenario
Prior to phylogenetic reconstruction, we assessed past migration events
among populations using allele frequencies on Treemix and OptM analysis
to support the best number of edges. OptM analysis indicated a single
migration edge explaining 98.9% of the variance. The event with the
greatest weight occurred from Colomer into Cabrera-Escatlasang (mean
migration weight: 0.454032, mean p-value: 3.22478e-11), followed by a
migration event from Dragonera into Escatlasang-Cabrera (mean migration
weight: 0.380029, mean p-value: 6.71e-05) (Figure S1).
A midpoint rooted ML tree was then built using consensus sequences for
each population on the concatenated SNP dataset (Figure 6). The
phylogenetic tree supports the major grouping obtained by the ADMIXTURE,
Fst and DAPC analyses, largely in line with the population geographic
distribution (Figure 1). Menorcan and Cabrera/Mallorca populations
formed clearly distinct phylogenetic clades (bootstrap, bs =100%).
Within the Mallorca/Cabrera clade, further substructuring indicated
three well differentiated clades: i) the southern Mallorca islets of en
Curt, Moltona and Guardia (bs= 99%)), ii) Cabrera islets of Foradada
and Esclatasang (bs=76%), with Cabrera as a basal lineage, and iii) the
two northern Mallorcan islands of Colomer and Dragonera (bs=80%)
(Figure 1 and Figure 6). Within the Menorca clade, substantial support
is given only to the grouping of Porros de Cavalleria (PRCV) and Revells
(RAVL) (bs=73%), while the small islet of Porros de Fornells (PORROS)
represents an independent lineage, highly differentiated from to the
rest of Menorcan populations (bs=89%). The remaining Menorcan
populations were poorly resolved, consistently with their lower Fst
values (Figure 4) and higher admixture levels (Figure 5B).
Tree rooting using non-reversible models on IQ-tree consistently
identified the population of Colomer (Mallorca) as the most likely
ancestral lineage. The island showed the highest rootstrap value
(86,13%, after 10K bootstrapping on consensus sequences, all sites;
values <2% for all other branches) (Figure S2). This result
was robust to the use of consensus sequences with variant sites only and
to subsampling to one random specimen per population, all consistently
recovering the highest rootstrap value for Colomer (71.35 and 69.54,
respectively). Root testing provided the maximum p-value of the
approximately-unbiased (AU) test for the branch leading to Colomer
(p=0.85). All branches within the Menorca clade showed a
p<0.05, significantly excluding Menorca as a potential source
of the ancestral population. Rootstrap values and root testing
considering only the archipelago of Menorca did not provide any clear
root support within Menorca.