Species identification
We used Sanger sequencing to identify C. anna from a set of 32 unknown nestlings and fledglings using 30 individuals of known species identity for comparison. We removed 14 of the 62 ND2 sequences due to low quality or short sequence length, including 10 samples of unknown species. Within known samples, C. anna samples formed a monophyletic group allowing us to reliably identify other C. annain our unknown samples (Fig. S1). Of the 22 remaining unknown hummingbird samples, 18 were identified as C. anna (Fig. S1) and nine of those had location data and were therefore used for whole genome sequencing.