Multilocus phylogeny of the land snail Helix differs substantially from the mitochondrial gene tree

The phylogeny of the western Palaearctic land snail genus Helix was previously studied using only a few partial mitochondrial genes. The mitochondrial phylogeny was not well resolved, and frequent mitochondrial introgressions indicated that the mitochondrial phylogeny may not correspond to the species tree. We analysed genome-wide ddRAD data to obtain a reliable species tree and re-analysed the mitochondrial phylogeny with mitogenome-scale data from selected species to investigate the extent and causes of mitonuclear discordance. The ddRAD phylogeny resolved the position of previously problematic species, elucidated the biogeographic history of the genus, and confirmed the monophyly of some species that was not unambiguously supported by the mitochondrial data. Helix arnautorum is shown here to be a distinct species, separate from Helix dormitoris. Mitochondrial introgressions indeed cause discordances between the mitochondrial and species trees. The most significant case, the nearly complete replacement of the original mitochondrion of Helix buchii, is associated with relaxed selection and accelerated substitution rate in the original mitochondrial lineage. However, robustly estimating the mitochondrial phylogeny turned out to be difficult even with complete mitochondrial genomes. This is probably due to a combination of short internal branches and variation in substitution rate and nucleotide composition. Alignment filtering and site-heterogeneous mixture models yielded estimates more concordant with the species tree than partitioned analysis of complete protein-coding sequences.