Methods:
Field Collection
XXX leaf samples were collected from apple trees in Boulder County. The range of collection spanned from Valmont Road (?) to (southern border?), and trees were located using maps of historic homesteads in the county. At the time of sampling, tree height, width at breast height and GPS location were catalogued using the "Epicollect5" app. Height was calculated after the fact using the angles to the top and bottom of the tree from a set distance and height. Leaves were kept in separate manila envelops while en route to the lab where they were stored over desiccant until DNA was extracted.
DNA Extraction and Processing
Genomic DNA was extracted from XXX leaf samples from a subset of the sampled trees using a DNeasy 96 plant kit (QIAGEN). Genotyping-by-sequencing was done by XXX . This form of DNA sequencing allows for the comparison of species with high genetic diversity in determining population structure. Using 20 references from the National Center for Biotechnology Information’s Sequence Read Archive (SRA), we compared our samples to raw sequences of known species. Utilizing Samtools, BCFtools, and XXX, a filtered VCF table was created to include data from both our 94 samples and the 20 references from SRA. The table was filtered to contain only positions that were SNPs, had a sequencing depth of XXX, and XXX. From the filtered table we interpreted historical population structure, relation of apple samples, and signatures of selection on the varieties of apple species present.