Comprehensive Puma Genetic Sampling in California

We obtained 354 tissue samples collected by the California Department of Fish and Wildlife between 2011–2017 from pumas either hit by car (~6%), found dead (~2%), poached (<1%), or through depredation permits (>90%), which had never been used in any previous genetic survey. Samples were well‐distributed throughout the state, except for smaller populations in smaller mountain ranges. To bolster our sample size in the Los Angeles region of southern California, we added the only remaining DNA extracts (N = 144) from pumas collected between 2002–2015 (Riley et al., 2014 (link); Vickers et al., 2015 (link)). After genomic and bioinformatic filtering (described below), we retained 401 out of 498 samples in the final dataset, which spanned the majority of puma habitat in California, excluding desert regions (Figure 1). For samples that lacked a precise GPS location, we used the nearest address or town where they were collected as their GPS point. Samples were stored at −80°C until DNA was extracted using Omega Bio‐tek Mag‐Bind Blood & Tissue DNA HDQ Kits (Omega Bio‐tek, #M6399‐01), with a manufacturer‐designed protocol for the Kingfisher Duo Prime (ThermoFisher Scientific, #5400110) automated DNA purification system. We measured the concentration of DNA from each sample using a Qubit 3.0 fluorometer (Invitrogen, #Q33216) with Qubit dsDNA high‐sensitivity kits (Invitrogen, #Q32854).