Data from: Phylogenetic relationships of Trachylepis skink species from Madagascar and the Seychelles (Squamata: Scincidae)

Lizards of the genus Trachylepis are a species-rich group of skinks mainly inhabiting Africa, Madagascar, and several other islands in the western Indian Ocean. All except one probably introduced species of Madagascan Trachylepis are endemic. Two species groups have been distinguished on the basis of subocular scale shape but their phylogenetic relationships remained unclear. We inferred a multilocus phylogeny of the Madagascan Trachylepis species, based on a concatenated dataset of 3261 bp from 3 mitochondrial and 4 nuclear genes with a dense Madagascan taxon sampling and find high support for the monophyly of the endemic Madagascan Trachylepis. The two species groups in Madagascar are highly supported as clades. The highland species T. boettgeri is nested in the T. aureopunctata species group of mainly arid-adapted species, suggesting a colonization of highland swamps by ancestors inhabiting dry western Madagascar. The Seychellois species were sister to the T. maculilabris/T. comorensis clade, suggesting their origin directly out of Africa as with Seychellois chameleons. In Madagascar, a high intraspecific molecular variation was confirmed for T. gravenhorstii, T. elegans, and T. vato, indicating a need for taxonomic revision.Trachylepis_alignment_partition_scheme_P5Interleaved alignment of all genes in Nexus format, with exclusion settings and partition scheme (P5) as used in the partitioned Bayesian analysis