SI_Fig1

Phylogeny of the gapCp "retained clones." Includes gapC, gapCp "short," and gapCp "long" sequences

nucleotide_all_data

Nexus file for nucleotide-model based analyes (including a block of recoded indels)

SI_Fig2

SI_Fig

SI Table 3

SI Table

Dryad_BASEML_results_summary

Outputs from BASEML runs (part of the PAML package)

SI_Table2

Voucher table and sequence data for the broad gapCp and gapC family sequences

codon_all_genes

Nexus file for the codon-based analyses

eupolypodsII_character_matrix

Includes 79 discrete morphological characters scored for 81 taxa and one tree file depicting relationships of eupolypod II fern

SI_Table1

Primers used in amplification and sequencing

Alignment_Nuclear_Loci

The alignments of the four nuclear loci