Morphometric data

Morphometric traits for all Berthelot's pipits from 2005/2006. Individual codes as in the microsatellite file. Island codes as in the manuscript

Microsatellite data

Microsatellite genotypes for 371 individuals and 27 loci. Island abbreviations as in the manuscript

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

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

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

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

Climate data

Climate data for 13 Berthelot's pipits populations, used to make geographical and ecological distance matrices

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

Data (SRA SRP035472)

The postdemultiplexing quality filtered data (i.e. output of "Demultiplexing and dropbase" of this repository) is available at the Sequence Read Archive (SRA), accession SRP035472. Those files were used to run Stacks and the resulted matrices coverage and SNP matrices produced after running the Stacks script *export_sql.pl* along with the subsequent files used to perform the analyses on R. See contents of the [2R](./2R) directory. For the rest of the pipeline the scripts used and when available and output summary are presented inside each directory