Table 1. Kokanee and anadromous sockeye salmon samples used for assignment to migratory form and reproductive ecotypes across historical drainages.

Location	Migratory Ecotype	Reproductive Ecotype	Historical Drainage	Reference Sample Size	Novel Sample Size
Wood Lake	Kokanee	Shore	Columbia River	34	4
	Kokanee	Stream	Columbia River	34	4
Kootenay Lake	Kokanee	Shore (West Arm)a	Columbia River	45	5
	Kokanee	Stream (West Arm) a	Columbia River	48	3
	Kokanee	Stream (North Arm)	Columbia River	22	3
Okanagan Lake	Kokanee	Shore	Columbia River	48	12
	Kokanee	Stream	Columbia River	48	8
Skaha Lake	Kokanee	Stream	Columbia River	20	9
Okanagan River	Sockeye	Stream	Columbia River	35	10
Portage Creek	Sockeye	Stream	Fraser River	23	3
Anderson Lake	Kokanee	Deepb	Fraser River	23	4
Seton Lake	Kokanee	Deepb	Fraser River	23	4
Tchesinkut Lake	Kokanee	Shorec	Skeena River	36	4
	Kokanee	Streamc	Skeena River	36	4

The following reference populations were pooled for assignment analysis due to lack of structure in these systems as found in [35]:

^a Kootenay Lake West Arm shore- and stream-spawning kokanee;

^b Anderson Lake and Seton Lake deep-spawning kokanee;

^c Tchesinkut Lake shore- and stream- spawning kokanee. ‘Reference Sample Size’ represents the number of individuals included in baseline reference populations from RADseq_kokanee. ‘Novel Sample Size’ represent novel individuals not included in the reference population.