Computational protocol: Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct

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[…] Analysis of molecular variance (AMOVA) and principal coordinates analysis (PCoA) were conducted in GenAlEx 6.5 [,]. We conducted AMOVA in order to characterize how genetic variation was partitioned within and among populations. PCoA was used to examine how genetic variation within the museum samples was distributed within the Truckee River watershed and to further examine the relationship between the Pilot Peak strain and the museum samples. [...] We constructed a number of phylogenetic trees using a Cavalli-Sforza distance metric and neighbour-joining tree building algorithm in the Populations 1.2.26 (1000 replications; []) and visualized in TreeView []. Populations were grouped by river for a range-wide analysis, by contemporary and museum samples within the Truckee River analysis, and by museum sampling locations within the Truckee River watershed. […]

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