Statement of authorship: NMS has been involved in running the BioBasis sampling program for more than twenty years. TR, NMS, DWY, and OO conceived the study and its design. TH led the work in generating all the DNA samples and YJ led the work in assembling and annotating the mitogenomes for the mitochondrial genome reference database. TH led the work in generating the mock communities and bulk samples, with contributions from YJ and JW. YJ and DWY developed the molecular and bioinformatic methods. OO led the modelling of the data. TR and OO wrote the first draft of the manuscript, and all authors contributed substantially to its further improvement. Data accessibility statement: Should the manuscript be accepted, the data supporting the results will be archived in an appropriate public repository (Dryad), and the data DOI will be included at the end of the article. The bioinformatic and R scripts and associated data tables will also be made available on github.com.

Pacific salmon are a keystone resource in Alaska, with an economic impact of well over