Supplemental methods for: Geographic range dynamics drove hybridization in a lineage of angiosperms 1 1 1 2 1 R.A. FOLK , C.J. VISGER , P.S. SOLTIS , D.E. SOLTIS , R. GURALNICK 1Florida Museum of Natural History 2Biology, University of Florida 3Author for correspondence:
[email protected] 1 Sequencing: Sequencing followed previously developed methods1 with the following modifications: library preparation was performed by RAPiD Genomics (Gainesville, FL; using TruSeq-like adapters as in Folk et al. 2015), the targeted insert size was > 200 bp, and sequencing used a 300-cyle (150 bp read) kit for a HiSeq 3000 instrument. The overall outgroup sampling (21 taxa total; Supplementary Table S1) was improved > 5 fold.2 This includes several representatives each of all lineages that have been hypothesized to undergo hybridization in the Heuchera group of genera. For the transcriptomes, reads were assembled against the low-copy nuclear loci from our targeted enrichment experiment, where the targets stripped of intronic sequence but assembly methods otherwise followed a previously developed BWA-based approach1. Transcriptomic reads were also mapped to a Heuchera parviflora var. saurensis chloroplast genome reference1 which was stripped of intronic and intergenic sequence. Assembly methods for target-enriched data followed the BWA-based approach1 directly. In practice, intronic sequence can be recovered from RNAseq data,3 but has consistently lower coverage (pers. obs.); moreover non-coding read dropout can be expected to be high for more divergent outgroups added here. For this reason, only coding reference sequences were used to assemble transcriptomic taxa. For nuclear analyses, reads were assembled with 277 references comprising the gene sequences used for bait design, with intronic sequences stripped.