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