DOI: 10.5061/dryad.jh9w0vtn7
title: Multiple Sequence Alignments (MSA) for comparative phylogeography of four lizard taxa within an Oceanic Island

description: 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.
description: 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 <em>b)</em>, 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.
description: # 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 | 887-1728 | | *Phoenicolacerta* | 1-422 | 423-807 | 808-1664 | | *Laudakia* | 1-489 | 490-826 | 827-1659 | ### Files and variables #### File: MSA\_16S\_CytB\_ND4\_Acanthodactylus\_Aligned.fasta **Description:** Multiple Sequence Alignment for *Acanthodactylus* #### File: MSA\_16S\_CytB\_ND4\_Troodica\_Aligned.fasta **Description:** Multiple Sequence Alignment for *Phoenicolacerta* #### File: MSA\_16S\_CytB\_ND4\_Laudakia\_Aligned.fasta **Description:** Multiple Sequence Alignment for *Laudakia* #### File: MSA\_16S\_CytB\_ND4\_Ophisops\_Aligned.fasta **Description:** Multiple Sequence Alignment for *Ophisops* ## Code/software The data are in fasta format and were edited using the software MEGA X v. 10.1.8. ## Access information Data was derived from the following sources: * Some of the data were retrieved from GenBank ([https://www.ncbi.nlm.nih.gov/genbank/](https://www.ncbi.nlm.nih.gov/genbank/))