Acknowledgements
Pau Aleixandre, Elena Berg, Setefilla Buenavista, John McCormack, Adán Oliveras de Ita, Vicente Rodríguez, Kristen Ruegg, and Alvar Veiga provided help with field sampling. Funding was provided by grants CGL-2011-25866 and CGL-2015-66381 from Spain’s Ministerio de Ciencia e Innovación to BM, and USA National Science Foundation IOS-1257527 to TJG.
Data Accessibility Junco hyemalis reference genome deposited in NCBI (Accession number: QZWM00000000). SNP ‘Full Dataset’, isotopic and georeferenced datasets are deposited in Dryad, as well as the model files for the demographic analysis with fastSIMCOAL2 and the R script for the redundancy analysis. Link for reviewers: https://datadryad.org/stash/share/RAlwLVkcw2K4HudDCqjp455t2yWE6JmRFNvVu55yWY0
Table 1. Oregon junco forms, number of genotyped individuals and population genetic diversity indices per locality. Indices include observed (HO) and expected (HE) heterozygosity. Figures in the last column correspond to the number of samples included in the analyses after filtering those with a rate of missing data above 0.6. State abbreviations are the following: British Columbia (BC) in Canada; Oregon (OR) and California (CA) in the USA; and Baja California Norte (BCN) in Mexico. For additional locality information see Table S1 in the Supplementary Information. The abbreviation n.b.s denotes UCSD individuals sampled during the non-breeding season.