Nonbreeding assignment
Implicit in the assignment of the nonbreeding individuals to breeding
populations is that the breeding origin of these individuals is unknown.
Given that assignment to the ESSBPs had an accuracy of 99.4% (168 out
of 169 samples) for individuals with sequencing coverage of 0.6X –
2.0X, and accuracy of 97.9% (46 out of 47 individuals) for individuals
down sampled to sequencing coverage of 0.01X, we assumed that we could
correctly assign nonbreeding individuals (sequencing coverage range:
0.02X – 2.0X, mean 1.3X) with high confidence. Assignment of the 148
nonbreeding individuals resulted in the largest number of individuals
being assigned to the Northern Temperate population (n = 64) and the
least number of individuals being assigned to the Basin Rockies
population (n = 2; Table S5). Of the 148 individuals, 139 individuals
had assignment consistency of at least 0.8 for the 10 subsets of data,
and these individuals were used to infer migratory connectivity. Testing
consistency of assignment on the 47 breeding individuals identified
three individuals with assignment consistency of < 0.8. One of
these individuals from Minnesota was previously identified as an outlier
in the PCA, and the other two individuals were from Pennsylvania, which
is on the boundary of the Southern Temperate and Northern Temperate
populations.
Mapping of the nonbreeding assignment results revealed patterns of
strong migratory connectivity across the breeding range. Notably, the
Maritime Provinces breeding population has strong connectivity with
eastern Colombia, the Northern Temperate breeding population with the
Greater Antilles, the Southern Temperate breeding population with the
Lesser Antilles, and the Western Boreal breeding population with Central
America and Mexico.