DNA extraction methods
Two different DNA extraction methods were used: 1) an organic DNA
extraction using a phenol-chloroform based method that avoids pipetting
to maximize the integrity of the DNA (Ana Ramón-Laca et al., 2021) and
favors the isolation of DNA of high molecular weight; 2) and a
mitochondria isolation procedure (see below, Fig 1 and S1) followed by
the phenol-chloroform extraction. A chinook salmon (Oncorhynchus
tshawytscha ) from the NOAA Northwest Fisheries Science Center hatchery
was euthanized and approximately 0.125 cm3 of skeletal
muscle (fresh) and liver and heart (frozen at -80ºC) samples were
dissected (Table 2). These tissue samples in Longmire buffer were
macerated using a TissueRuptor (Qiagen) with disposable probes. DNA was
eluted in 100 and 50 µl of TlowE for either extraction method,
respectively. Additional methods discarded for the purposes of this
study are in File S3. Additional species (Table 2) were also extracted
with either one or the two methods and these were eluted in 200 and 100
µl of TlowE, respectively. Wide bore tips were used where required to
avoid fragmentation. All DNA extractions were performed in a dedicated
genetics laboratory.