Supermatrix phylogeny using species tree constraint
\nSupermatrix construction: We created a supermatrix that included all available published sequence data of Afrobatrachian frogs, using five nuclear loci included in our captures (FICD, KIAA2013, POMC, TYR, and RAG-1) and the mtDNA marker 16S. Nuclear loci were aligned using MUSCLE (Edgar 2004), and 16S sequences were aligned using MAFFT with the E-INS-i strategy (Katoh et al. 2002; Katoh et al. 2005). The final concatenated alignment consisted of 283 taxa and 3,991 bp, with 36% total missing data.
\nPhylogenetic methods: We reconstructed the phylogenetic relationships of Afrobatrachian frogs from the five nuclear gene and mtDNA data set using a maximum likelihood (ML) approach in RAXML v8 (Stamatakis 2014). To preserve the relationships inferred with our species tree analyses of sequence capture loci, the sequence capture hyperoliid species tree containing 153 taxa (143 ingroup and 10 outgroup taxa) was used as a partial constraint tree for the ML analysis of the 283-taxon alignment of six loci.
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