Testing sequence depth thresholds for assignment
To test whether lower coverage data would affect our ability to
accurately assign breeding individuals, we used the 47 individuals from
the breeding populations, that were not used in the ESSBPs, as a testing
set for further down sampling. We did not down sample individuals from
the ESSBPs because we did not want to lower the effective sample size of
the source populations, but rather test how well we could assign
individuals with lower coverage given the effective sample sizes of our
source populations (and the amount of genetic differentiation among
them). The testing set consisted of 22 individuals from the Southern
Temperate population, 14 individuals from the Northern Temperate
population, 6 individuals from Basin Rockies population, and 5
individuals from the Western Boreal population. The sequencing depth of
these 47 individuals ranged from 0.6X – 2.0X. Down sampling these
individuals to 0.1X resulted in 100% assignment accuracy, and further
down sampling to 0.01X resulted in 97.9% accuracy (one individual from
the Southern Temperate population assigned to the Northern Temperate
population; Table 1, Table S4). The individual incorrectly assigned from
the Southern Temperate population was from a sampling site in
Pennsylvania which is on the border of our boundary for the Southern
Temperate and Northern Temperate populations.