Data from: Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera, Podarcis pityusensis (Squamata: Lacertidae)

Two monophyletic sister species of wall lizards inhabit the two main
groups of Balearic Islands: Podarcis lilfordi from islets and small
islands around Mallorca and Menorca and Podarcis pityusensis from Ibiza,
Formentera and associated islets. Genetic diversity within the endangered
P. lilfordi has been well characterized, but P. pityusensis has not been
studied in depth. Here, 2430 bp of mtDNA and 15 microsatellite loci were
analysed from P. pityusensis populations from across its natural range.
Two main genetic groupings were identified, although geographical
structuring differed slightly between the mtDNA and the nuclear loci. In
general, individuals from islets/islands adjacent to the main island of
Ibiza were genetically distinct from those from Formentera and the
associated Freus islands for both mtDNA and the nuclear loci. However,
most individuals from the island of Ibiza were grouped with neighbouring
islets/islands for nuclear loci, but with Formentera and Freus islands for
the mitochondrial locus. A time-calibrated Bayesian tree was constructed
for the principal mitochondrial lineages within the Balearics, using the
multispecies coalescent model, and provided statistical support for
divergence of the two main P. pityusensis lineages 0.111–0.295 Ma. This
suggests a mid-late Pleistocene intraspecific divergence, compared with an
early Pleistocene divergence in P. lilfordi, and postdates some major
increases in sea level between 0.4 and 0.6 Ma, which may have flooded
Formentera. The program IMa2 provided a posterior divergence time of
0.089–0.221 Ma, which was similar to the multispecies coalescent tree
estimate. More significantly, it indicated low but asymmetric effective
gene copy migration rates, with higher migration from Formentera to Ibiza
populations. Our findings suggest that much of the present-day diversity
may have originated from a late Pleistocene colonization of one island
group from the other, followed by allopatric divergence of these
populations. Subsequent gene flow between these insular groups seems
likely to be explained by recent human introductions. Two evolutionary
significant units can be defined for P. pityusensis but these units would
need to exclude the populations that have been the subjects of recent
admixture.