High gene flow across the range
We found no evidence of barriers to gene flow across the native and
expanded range of C. anna . Overall, genetic divergence was low
species-wide, with pairwise county divergence (FST)
ranging from 0–0.01 (Fig. S2). We detected no pattern of isolation by
distance in pairwise FST between counties (Fig. 1B;
Mantel Test P = 0.53). The admixture analyses showed that the
ancestral groups were dispersed relatively evenly across all
populations. Although the optimal number of ancestral groups was K=2
(Fig. 1C), there was no clear geographic structuring at either K=2 or
higher values of K (Fig. S3), suggesting only one major genetic group
with no barriers to gene flow. We found no geographic signal based on
the first three principal components axes although none of the PC axes
explained much more than 1% of the variance (Fig. 1D). There was a
correlation between sequencing pool and PC1 (Fig. S4A), although it
explained only a small amount of the variance similar to the other PC
axes, potentially highlighting the absence of other factors structuring
genetic variation across the range but also reinforcing the need for
consideration of sequencing artifacts in next-generation sequencing. To
investigate if a larger SNP dataset would clarify any population
structure, we reran the PCA with more permissive filtering (-minInd 49,
instead of -minInd 241 (all individuals)), which resulted in 9.5 million
SNPs. After identifying eight more pairs of potentially related
individuals (rab = 0.30–0.56), one individual from each pair was
excluded from the PCA (TL016, ANHU_323, ANHU_267, AN86237, UW113545,
UW119089, UCK89810), except for the pair UCK89662 and UCP71084 in which
both were excluded as they were outliers in an initial PCA. The
resulting PCA did not indicate spatial structuring, consistent with the
result from the PCA with fewer SNPs (Fig. S4B). We also conducted a PCA
with only females collected between February and April (N = 72, after
PCA outliers were removed) to ensure only breeding birds were examined,
which also showed no genetic structure (Fig. S4C).