Results
Neutral genetic structure among Oregon junco forms A plot of PC1 against PC2 (11.5% and 8.7% of explained variance, respectively) revealed considerable differentiation among Oregon junco forms. Most UCSD birds formed a highly differentiated cluster from the rest of the groups, with levels of divergence comparable to those of the southern isolated forms in Baja California, pontilis andtownsendi . The form pinosus also formed a separate cluster, although distance with respect to the remaining forms was less pronounced. Northern forms oreganus , shufeldti andmontanus showed very limited levels of structure and grouped into a single genetic cluster, which also included some of the UCSD n.b.s. individuals (Fig. 3A, upper plot). The plot of PC1 against PC3 (4.0% of explained variance) also revealed thurberi birds from Laguna Mountains as a differentiated population (Fig. 3A, lower plot).
The STRUCTURE analysis was consistent with PCA results and provided additional information on genetic differentiation among localities (Fig. 3B). At K = 2, most UCSD birds separated from the rest, and three breeders showed a limited degree of admixture with non-UCSD birds. Most UCSD n.b.s. birds belonged to the resident population, but five of them were clearly identified as winter visitors from further north. The plot for K = 3 and 4 also revealed townsendi and pontilis as highly divergent groups with respect to other junco populations and with respect to each other, although they share a considerable amount of variance. The form pinosus formed a clearly differentiated cluster at K = 5. Birds from Laguna Mountains also appeared as a separate population at K = 6, again congruently with the PCA and ruling out this population as the source of UCSD n.b.s. birds, which instead cluster with birds at more northern latitudes (eitherthurberi -Tahoe, montanus , shufeldti ororeganus ; Fig. 3B).
F ST values among forms based on neutral loci were generally congruent with the PCA and STRUCTURE results, with forms from Baja California and UCSD showing the highest degree of differentiation. The remaining forms showed lower levels of pairwise differentiation, yetthurberi from Laguna Mountains and pinosus had values that were moderately higher than those from northern populations (Table 2). Both heterozygosity and nucleotide diversity indices revealed lower levels of genetic variability at UCSD and townsendi compared to other populations, especially those corresponding to thurberi and more boreal forms (Table 1).
Breeding latitude of UCSD juncos sampled in the non-breeding season The linear regression between STRUCTURE scores for K = 2 and δD values recovered a highly significant signal (P = 2.52x10-8), where the two control UCSD breeders and 17 other genetically close individuals showed high isotopic ratios (Fig. S1, Supporting Information). In turn, the five UCSD n.b.s. individuals that were genetically different from UCSD breeders showed evidence of having grown their feathers elsewhere, and thus represent wintering individuals that do not breed at UCSD.
Phylogenetic and co-ancestry analysesPhylogenetic reconstructions based on maximum likelihood and neighbor-joining algorithms were consistent with population structure analyses in showing marked differentiation of Baja California and UCSD, as well as for pinosus and southern thurberi . In the unrooted maximum likelihood tree, pinosus and UCSD individuals formed two reciprocally monophyletic sister clades with strong support (Fig. 4). In turn, relatively low structure among northern Oregon juncos was detected in the analysis, in contrast to forms in Baja California, which clustered together in a differentiated clade with close affinity to southern thurberi individuals from Laguna Mountains (as suggested by K = 4 and 5 in the STRUCTURE analysis, Fig. 3). In the neighbor-net, UCSD and pinosus also appear as sister groups, yet the degree of differentiation with respect other forms is considerably less pronounced (Fig. S2). Forms townsendi andpontilis appear as sister clades, highly divergent from the remaining junco forms. Southern thurberi individuals from Laguna Mountains cluster together as well in this analysis, while little differentiation is observed among northern forms.
The RADpainter genetic ancestry analysis consistently recovered high average values of intra-population co-ancestry in those forms showing marked differentiation and geographic isolation, namelytownsendi , pontilis , pinosus and the UCSD population. UCSD individuals showed highest co-ancestry values with respect to pinosus individuals (Fig. 5A), a pattern that was significant according to a bootstrap analysis (Fig. 5B).