Data from: Population structure of sea-type and lake-type sockeye salmon and kokanee in the Fraser River and Columbia River drainages

Population structure of three ecotypes of Oncorhynchus nerka (sea-type
Sockeye Salmon, lake-type Sockeye Salmon, and Kokanee) in the Fraser River
and Columbia River drainages was examined with microsatellite variation,
with the main focus as to whether Kokanee population structure within the
Fraser River drainage suggested either a monophyletic or polyphyletic
origin of the ecotype within the drainage. Variation at 14 microsatellite
loci was surveyed for sea-type and lake-type Sockeye Salmon and Kokanee
sampled from 121 populations in the two river drainages. An index of
genetic differentiation, FST, over all populations and loci was 0.087,
with individual locus values ranging from 0.031 to 0.172. Standardized to
an ecotype sample size of 275 individuals, the least genetically diverse
ecotype was sea-type Sockeye Salmon with 203 alleles, whereas Kokanee
displayed the greatest number of alleles (260 alleles), with lake-type
Sockeye Salmon intermediate (241 alleles). Kokanee populations from the
Columbia River drainage (Okanagan Lake, Kootenay Lake), the South Thompson
River (a major Fraser River tributary) drainage populations, and the
mid-Fraser River populations all clustered together in a neighbor-joining
analysis, indicative of a monophyletic origin of the Kokanee ecotype in
these regions, likely reflecting the origin of salmon radiating from a
refuge after the last glaciation period. However, upstream of the
mid-Fraser River populations, there were closer relationships between the
lake-type Sockeye Salmon ecotype and the Kokanee ecotype, indicative of
the Kokanee ecotype evolving independently from the lake-type Sockeye
Salmon ecotype in parallel radiation. Kokanee population structure within
the entire Fraser River drainage suggested a polyphyletic origin of the
ecotype within the drainage. Studies employing geographically restricted
population sampling may not outline accurately the phylogenetic history of
salmonid ecotypes.