Sequences after initial processing in QIIME (seqs.fna, library 1)

Raw sequence data from the Roche 454 GS FLX sequencer, region 1 (split_library_output_1). These data are the output of the command: split_libraries.py -m 454_Map.txt -f 1.TCA.454Reads.fna -q 1.TCA.454Reads.qual -o split_library_output_1/ -l 100 -L 700 -H 9 -M 2 -b 1

Dryad_HDY-13-OR0304R_Survival_Growth_Data

Dryad_HDY-13-OR0304R_Survival_Growth_Dat

Lab protocol and sequencing report

Contains: i) a summary of the ddRAD labwork, description of final libraries and sequencing output, ii) modified ddRAD sequencing protocol and iii) sequencing quality control reports for each lane

Figures

Contains the R markdown files that were used to generate the Figures from the main text (Figures.Rmd) and the figures from the supporting information (SupportingInfomation_*). Needs the data and scripts from the *2.R analyses of Stacks outputs* section of this repositor

Datasets

This .zip files contains two folders. The folder "Control" contains the 15 raw 454 sequence files generated from the "Test Pools" analysis detailed in Table 2 of the manuscript, and a file of 27 Sanger sequences listed in Table S1. The folder "Tenerife" contains the 6 raw 454 sequence files associated generated from the "Tenerife Forest Samples" analysis detailed in Table 3 of the manuscript

0.Demultiplexing and dropbase

Contains the custom Perl scripts of the pipeline used to demultiplex raw reads and drop a base position that was causing a lane effect

2.R analyses of Stacks outputs

Contains the R scripts, input-output data and metainformation used to perform the analyses described in the *General processing of Stacks outputs* and *Error rates* of the manuscript

Sampling localities

Cointains and the geographic information of sampling sites. See tab "B.alpina B.moranensis" for Berberis alpina and B. moranensis populations and "Berberis outgroups" for B. trifolia and B. pallid

Primers, MIDs, sequence formats and consensus reference sequence used in this study.

<p>ColFol-for ColFol-rev are the Sanger primers. 454-ColFol-for and 454-Col307-rev are the primers for mass amplification. Adaptors A and B are used by the ‘454’ sequencer to attach individual DNA molecules to microscopic beads, for subsequent sequencing. MIDs (Multiplex Identifiers) are 7 bp sequences that allow different samples to be sequenced together on a single ‘454’ plate and then separated bioinformatically for downstream analysis. There is no MID with 454-Col307-rev because we only pyrosequenced from the forward direction. Row 5 is an example of a 454 read after demultiplexing with the Roche tools. The forward primer is underlined, and the reverse primer dashed underlined. The MID tag is removed during demultiplexing. Row 6 is an example of a sequence after processing of sequences to produce a file of unique sequences.</p

1.Running Stacks

Contains scripts and part of the output data of running *Stacks* with the demultiplexed-lane-effect-corrected data (see section **Demultiplexing and dropbase/0.1DropBase** of this repository) available at the Sequence Read Archive (SRA), accession SRP035472; to subsequently produce SNP (*.SNP) and coverage (*.COV) tsv matrices and to run the *populations* program of Stacks with the selected loci of the downstream analyses. The Stacks parameter values corresponds to the experiments defined as *1) Exploratory analysis of Stacks assembly key parameters and SNP calling model using replicates* and *2) Effect of using different parameters on the output information content and on the detection of genetic structuring