Genomic phylogeography illuminates deep cyto-nuclear discordances in midwife toads (Alytes)

Through admixture and phylogenetic analyses of thousands of loci, we provide a comprehensive phylogeographic framework for the A. obstetricans complex, as well as a fully resolved phylogeny for the entire genus. As part of this effort, we carefully explore the influence of different sampling schemes and data filtering thresholds on tree reconstruction, showing that several, slightly different, yet robust topologies may be retrieved with small datasets obtained by stringent SNP calling parameters, especially when admixed individuals are included. In contrast, analyses of incomplete but larger datasets converged on the same phylogeny, irrespective of the reconstruction method used or the proportion of missing data.  Leer más.