RESULTS
Patterns of genetic diversity and differentiation
We identified 15,038 SNPs at a mean of 27X sequencing depth across 17
sampling locations. Using a dataset filtered by a minor allele frequency
of 0.1, we find that genome-wide FST is extremely low
(0.0085), and measures of genetic diversity do not vary substantially
among sampling locations (Table 1). Across all of these wintering
starling populations, the highest pairwise FST was
0.0106 between birds from the adjacent states of Arizona and New Mexico.
Using a haplotype-based statistic of differentiation,
φST among populations shows an absence of genetic
structure (φST = 0.0002). Hierarchical AMOVAs reveal
that 94% of the observed genetic variance is explained by variation
within individuals, and the remaining variance reflects differences
among individuals in the same population, with negligible variation
explained at the between-population level (Figure 1C-D). Across the
genome, FST and nucleotide diversity are exceptionally
low (Table 1,2). Genome-wide heterozygosity is moderate at 0.339, and
across loci observed heterozygosity differs significantly from expected
(t = 66.6, df = 3569, P<0.001, Table 1).
Population structure
FST among populations is relatively low overall (Table
2): starlings sampled in Arizona show the highest differentiation from
other sampling locations (FST = 0.008-0.011), and only a
few other pairwise comparisons (NM-IL, NM-CO, and CO-WI) show an
FST of 0.009 or higher. However, we do not recover clear
population structure. The first two principal components each explain
about 1% of variation among individuals (Figure 1A), and although
STRUCTURE identified three populations at the best-supported value of K,
these predicted populations do not show obvious differences in ancestry
proportions (Figure 1B, Figure S1). Controlling for shared ancestry does
not resolve population structure, and instead provides support for
uniform gene flow among individuals (Figure S2). K-means clustering
within DAPC also does not identify biologically relevant clusters.
Starling populations follow a clear pattern of isolation-by-distance
(Mantel r = 0.139, P < 0.0001). Spatially explicit
models of isolation-by-distance suggest a fairly uniform rate of
migration range-wide, where local increases in migration rate are likely
a model artifact (Supplementary Information). However, models of
isolation by environment (IBE) show that the relationship between
environmental and genetic distances is stronger than the simple
geographic-genetic distance model. After controlling for geographic
distance, we find that all bioclimatic variables tested show non-zero
correlations between environmental and genetic distances (Supplementary
Information). There is a strong positive relationship between genetic
distance and both precipitation in the wettest quarter (BIO16, Mantelr = 0.282, P = 0.001) and elevation (Mantel r = 0.146, P =
0.001).