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).