Evolutionary value of marginal alpine plant populations: beyond the genetic depauperation paradigm

In this study, we used candidate-gene targeted sequencing on S. ciliata populations. We sequenced a total of 2,414 candidate genes with high-confidence annotations. We used the DNeasy Plant minikit (QIAGEN, Valencia, USA) to extract and isolate DNA from 96 plants, sixteen for each of the six studied populations. Library preparation covering the targeted sequences followed the manufacturers protocol for Nugen SeqCap Developer kit. Samples were sequenced as 96-plex on a HiSeq2500 lane with paired-reads of 125 bp. Demultiplexing of reads was carried out with CASAVA 1.8.2 (Illumina Inc., San Diego, CA). Reads were masked for adapter contamination with cutadapt and low-quality bases removed using erne-filter (erne v.1.4.5). Alignment was carried out with BWA MEM v.0.7.10