DOI: 10.5061/dryad.3xsj3txhm
title: 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

description: 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.
description: 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 <br>
 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) <br> 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.