Molecular data and analysis specifications for a study on Atriophallophorus parasites from New Zealand

This dataset accompanies the manuscript \"Phylogeography and Cryptic Species Structure of a Locally Adapted Parasite in New Zealand\". In our study we have shown that multiple species of the trematode parasite from the Atriophallophorus genus co-exist within the same lakes. When focusing on the most common of these species, Atriophallophorus winterbourni, we found that the Southern Alps and Pleistocene glaciation are a likely explanation for its phylogeographic patterns.
This dataset consists of three parts: (I) An Excel file containing SNP data, all sample information and the output of phylogeographic analysis with MASCOT1, (II) all sequence alignments, including NADH5, 28S, ITS2 and COI, as they are used for the manuscript and (III) input files for the various analyses as they were prepared for the analysis.
1MASCOT: marginal approximation of the structured coalescent as implemented in BEAST2