Data input and tree output for: Morphological evolution and phylogeny are unlinked in Hawaiian Doryopteris (Cheilanthoideae: Pteridaceae)

This repository complements the manuscript 'Morphological evolution and phylogeny are unlinked in Hawaiian Doryopteris (Cheilanthoideae: Pteridaceae)'. The directory `input_data` contains three datasets: (i) 316 loci from the GoFlag probe set (targeted regions only), (ii) SNP data from the GoFlag probe set (targeted + flanking regions), and (iii) matK. Dataset [i] was used to infer species tree using ASTRAL-II and wASTRAL, dataset [ii] was used for principle component analyses, dataset [iii] was used to infer a plastid gene tree. The resulting trees are deposited in the directory `output_trees`. Scripts for data processing and analyses can be found at github.com/prilau/hawaiian_doryopteris/.