Raw reads have been submitted to Short Read Archive (SRA) as BioProject PRJNA612548 (SRA accession SAMN14377002).

Extended methods and results for baseline testing are found in

• 01 Reference Construction.html (Reference_Construction.Rmd): Contains code and parameters used for de novo reference construction.
• 02 Genotyping.html (Genotyping.Rmd): Contains details for read mapping, SNP calling, VCF filtering, and haplotyping of genomic data set used for analysis (data/POPGEN/CLE_by_est_genepop.gen)
• scr/QDFA_script.R and scr/M_ANOVA_script contain reproducible code for analyzing microchemistry data (data/POPGEN/Cleucas_cemistry_data.csv)
• TinHan_et_al2019_SuppMat.html (TinHan_et_al2019_SuppMat.Rmd) contains extended methods & results (including fully reproducible code) for baseline testing of genomic and microchemistry data.