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 ev..., Lizard tail tips were collected from Cyprus. Total genomic DNA was extracted from tissue using the DNeasy Blood and Tissue Kit (Qiagen, Hidden, Germany) following the manufacturer’s guidelines.Samples were amplified and sequenced for three mitochondrial gene fragments, cytochrome b (Cyt b), 16S ribosomal subunit (16S), and nicotinamide adenine dehydrogenase subunit 4 (ND4). Multiple sequence alignment was performed for each gene fragment separately using MAFFT v.7.520 with the default settings., , # Multiple Sequence Alignments (MSA) for comparative phylogeography of four lizard taxa within an Oceanic Island

[https://doi.org/10.5061/dryad.jh9w0vtn7](https://doi.org/10.5061/dryad.jh9w0vtn7)

## Description of the data and file structure

The datasets contain the multiple sequence alignments (MSA) required to replicate phylogenetic and cladochronological analyses in Antoniou et al. (in review) using three mtDNA genes (16S, Cyt *b* and ND4). The data cover sequences from samples of four lizards (*Acanthodactylus schreiberi*, *Ophisops elegans schlueteri*, *Phoenicolacerta troodica* and *Laudakia cypriaca*) collected from various localities within Cyprus, as well as outgroup sequences retrieved from GenBank. The length of each each gene for each taxon can be found at the following table.

| Taxon | 16S | Cyt *b* | ND4 |
| :---------------- | :---- | :------ | :------- |
| *Acanthodactylus* | 1-464 | 465-869 | 870-1711 |
| *Ophisops* | 1-495 | 496-886 | 887-...,