Koppetsch T, Pabijan M, Hutter CR, Köhler J, Gehring P-S, Rakotoarison A, Ratsoavina FM, Scherz MD, Vieites DR, Glaw F, Vences M (2023)

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Explanation note: Table S1. Primers and thermal cycling profiles used for the amplification of DNA fragments used in this study (see Materials and Methods). Fragment length refers to the alignment length in the concatenated supermatrix; nuclear-encoded genes have been further trimmed for calculation of haplotype networks. Thermal cycling schemes start with temperature (in °C) of each step, followed by the time in seconds between parentheses; cycling repetitions are indicated within brackets. — Table S2. Substitution models and partitions applied for the multigene BI phylogenetic reconstruction. — Table S3. Minimum and maximum pairwise uncorrected distance for a fragment of the mitochondrial cytochrome b gene among the nine main mitochondrial lineages of the G. liber complex. — Table S4. Minimum and maximum pairwise uncorrected distance for a fragment of the 5’-end of the mitochondrial 16S rRNA gene among the nine main mitochondrial lineages of the G. liber complex. — Figure S1. Maximum likelihood trees calculated from DNA sequences of fragments of the mitochondrial gene for cytochrome b, and from the phased allele sequences for four nuclear-encoded genes, for samples from An’Ala where mitochondrial haplotypes corresponding to the genetic lineages NCE1 and NCE2 occur in syntopy (as obvious from the cytochrome b tree). The four nuclear genes do not show any evidence of concordant differentiation of these two lineages at this site. — Figure S2. Maximum likelihood trees calculated from DNA sequences of fragments of three nuclear-encoded genes, for lineages NE1 (red) and NE2 (magenta; within box delimited by dotted line). The trees illustrates that samples from Ambodivoangy (highlighted yellow) are assigned to NE2 by the nuclear-encoded markers, suggesting they probably belong to this lineage (= G. fotsitenda), in agreement with their occurrence at low elevation, but possess an introgressed mitochondrial genome from NE1 and therefore cluster within NE1 in the mitochondrial tree (Fig. 1). — Figure S3. Species tree obtained with ASTRAL from gene trees of 12,951 nuclear-encoded markers. Pie charts represent the quartet score frequency i.e., the proportion of gene trees that support the different topologies. The biggest slice is the current topology and indicates how many gene trees support that topology compared to the others. — Figure S4. Dorsal and ventral views of the designated lectotype of Gephyromantis variabilis Millot and Guibe, 1951 (MNHN 1953.117) from Itremo.

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