Multiple Sequence Alignments (MSA) for comparative phylogeography of four lizard taxa within an Oceanic Island

Comparative phylogeography aims to detect common patterns of
differentiation among taxa attributed to the same geological or
environmental barriers, thus, to find shared drivers of genomic splits and
landscape features that explain patterns of occurrence and genetic
diversity. Following this approach, this work focuses on four endemic
lizard taxa, namely Acanthodactylus schreiberi schreiberi, Ophisops
elegans schlueteri, Phoenicolacerta troodica, and Laudakia cypriaca, that
co-occur in Cyprus, an isolated island of the Mediterranean. In an attempt
to discern possible effects of the geological and ecological history of
the region on diversity patterns along the lineages under study, samples
were collected from all parts of Cyprus and phylogenetic reconstructions,
species delimitation analyses, and biogeographic comparisons were
conducted at both genetic and genomic levels (Sanger and ddRAD sequencing
data, respectively) for all four taxa. The derived phylogenomic
relationships provide evidence of a strong genetic structure within the
island that agrees with the geographical origins of each population. A
rare case of an island-to-mainland dispersal event is confirmed for one of
the focal taxa, making it one of the few documented cases of this type.
Estimated diversification times during the Miocene reflect timing of first
arrival on the island, while further diversification seems to have been
strongly affected by the Pleistocene oscillations.