Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus Ommatotriton) from the Near East has been proposed to contain three species (O. nesterovi, O. ophryticus and O. vittatus) with unclear phylogenetic relationships, apparently limited interspecific gene flow and deep intraspecific geographic mtDNA structure. We use parallel tagged amplicon sequencing to obtain 177 nuclear DNA markers for 35 banded newts sampled throughout the range. We determine population structure (with Bayesian clustering and principal component analysis), interspecific gene flow (by determining the distribution of species-diagnostic alleles) and phylogenetic relationships (by maximum likelihood inference of concatenated sequence data and based on a summary-coalescent approach). We confirm that the three proposed species are genetically distinct. A sister relationship between O. nesterovi and O. ophryticus is suggested. We find evidence for introgression between O. nesterovi and O. ophryticus, but this is geographically limited. Intraspecific structuring is extensive, with the only recognized banded newt subspecies, O. vittatus cilicensis, representing the most distinct lineage below the species level. While mtDNA mostly mirrors the pattern observed in nuclear DNA, all banded newt species show mito-nuclear discordance as well.

This Dryad package contains the sequence data and input and output files associated with:

van Riemsdijk, I. Arntzen, J.W., Babik, W., Bogaerts, S., Franzen, M., Kalaentzis, K., Litvinchuk, S.N., Olgun, K. Wijnands, J.W.P.M., Wielstra, B. (2022). Next-generation phylogeography of the banded newts (Ommatotriton): a phylogenetic hypothesis for three ancient species with geographically restricted interspecific gene flow and deep intraspecific genetic structure. Molecular Phylogenetics and Evolution [issue details pending at the moment of uploading] https://doi.org/10.1016/j.ympev.2021.107361

Provided are the raw Ion Torrent reads (Raw_reads.zip) and the reads processed (Processed_reads.zip) through the bioinformatics pipeline described in:

Wielstra, B., Duijm, E., Lagler, P., Lammers, Y., Meilink, W.R.M., Ziermann, J.M., Arntzen, J.W. (2014). Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform. Molecular Ecology Resources 14(5): 1080-1089. (https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12242)

The input and output files of analyses described in the paper are as follows:

1) Structure_nuDNA.zip - contains the input and output files of the STRUCTURE analysis for nuDNA.

2) PCA_nuDNA.zip - contains the input and output files of the PCA analysis for nuDNA.

3) FASTA_nuDNA.zip - contains the sequences for each gene for each individual.

4) Concensus_nuDNA.zip - contains single sequences for each individual with polymorphic sites encoded with IUPAC codes, to be used downstream (in RAXML and ASTRAL).

5) RAXML_nuDNA.zip - contains the input and output files of the concatenated maximum likelihood phylogenetic analysis in RAXML for nuDNA.

6) ASTRAL_nuDNA.zip - contains the input and output files of the summary-coalescent species tree inference in ASTRAL for nuDNA.

7) MrBayes_mtDNA.zip - contains the input and output files of the Bayesian phylogenetic analysis in MrBayes for mtDNA.