Genotyping-by-sequencing
Genomic DNA was extracted from blood and tissue samples using a Qiagen
DNeasy kit (QiagenTM, Valencia, CA). We used
genotyping-by-sequencing (GBS; Elshire et al. 2011) to obtain individual
genotypes from a total of 174 juncos. Of these, 46 individuals were
sampled at UCSD, 18 of them corresponding to confirmed resident breeders
(referred to as ‘UCSD breeders’ hereafter), and 28 were sampled during
the non-breeding season (referred to as ‘UCSD n.b.s.’ hereafter). In
addition, we sequenced 128 Oregon juncos belonging to the following taxa
(with sample sizes in parentheses): townsendi (16),pontilis (13), pinosus (14), thurberi (41; 23 of
them from Laguna Mountains, and 18 from Tahoe), montanus (16),shufeldti (12) and oreganus (16) (Fig. 1, Table 1, Table
S1 from Supporting Information). GBS libraries were prepared and
sequenced at Cornell University’s Institute for Genomic Diversity, using
restriction enzyme PstI for digestion. Sequencing of the 174
individually-barcoded libraries was carried out in five different lanes
(along with another 301 junco samples intended for other analyses) of an
Illumina HiSeq 2000, resulting in an average of 243.2 million good
barcoded single-end reads 100 bp in length per lane.