Genetic Sex identification
We used two complementary methods to sex individuals. One procedure involved polymerase chain reaction (PCR) using highly conserved primers 2550F and 2718R (Fridolfsson & Ellegren, 1999) to amplify the differently sized introns of Z- and W-linked chromohelicase-DNA binding protein 1 (CHD1) genes. PCR products were separated on a stained 1% or 2% agarose gel run in TAE buffer, revealing one band for male birds and two for females. The other method was a bioinformatics approach where we compared the ratio of average read depth of SNPs from ddRAD sequencing that were aligned with the zebra finch on the Z chromosome with read depths of SNPs on autosomes (see Toews et al., 2018). Because males have two copies and females one copy of the Z chromosome, we would expect a Z:autosome depth ratio of 1 in males and 0.5 in females. Using the two approaches was confirmatory of the accuracy of each method and allowed us to investigate and correct for any possible error if they produced conflicting results.