Population structure and genetic differentiation
The observed differences in flight performance may suggest strong
population differentiation, but our genomic analyses revealed that this
is not the case. The GATK genotyping pipeline resulted in a total of
32.2 million SNPs. A total of 25.9 million SNPs passed quality control
filtering to be used for further analysis. A total of 20.9 million SNPs
that were covered in all 43 samples were used for Principal Component
Analysis (PCA) and ADMIXTURE (Alexanderet al. , 2009) analysis to determine the genetic structure in the
dataset. The PCA generated using the SNPrealte
(Zheng et al. , 2012) package
showed no evidence for clustering of eastern and western monarchs (Fig.
3), and determined that all samples in the data set belong to one
population with K=1 showing the lowest error rate (Fig. 3; Table S2).
While eastern and western monarchs could not be separated, three samples
from Big Sur, California, seemed to cluster.
Genome-wide genetic differentiation (FST ) and
absolute divergence (DXY ) between eastern and
western monarchs, calculated in windows of 10kb, were extremely low
(Table 1, Fig. 4). Genetic differentiation between monarchs from the
three western overwintering sites was likewise low (Tables 2, S3; Fig.
S3). The genome-wide differentiation landscapes of eastern and western
monarch comparisons were highly correlated with the genome-wide
differentiation landscapes of the comparisons between western monarchs
from different overwintering sites (Fig. S4). The maximum values ofFS T in all comparisons were also
extremely low (Table S3), as was the genetic differentiation within
genes (eastern vs. western FST (Genes) = 0.0008 ± 0.0004).FSTZ window outliers were
calculated separately for autosomes, Z-chromosome and neo-Z-chromosome,
and were very low (Table 3). The extremely low maximum measures of
genetic differentiation and the top 1%FSTZ window outliers suggest
that there are no regions in the genome with reduced gene flow. This is
in contrast with many other species, where islands of differentiation
appear to be common (Jiggins, Naisbit, Coe
& Mallet, 2001; Martin et al. ,
2013; Cruickshank & Hahn, 2014;
Nadeau et al. , 2014;
Talla, Kalsoom, Shipilina, Marova &
Backström, 2017; Irwin et al. ,
2018). These results were not driven by window size, as low
differentiation was also found for window sizes of 100, 500 and 5,000bp
(Fig. S5, Table S4).
In line with these results we also did not identify any fixed nucleotide
differences between eastern and western monarchs (Fig. 5). The majority
of polymorphisms are shared between eastern and western monarchs, while
similar proportions of private polymorphisms are observed in both
eastern and western monarchs (Fig. 5). This supports the conclusion that
there are no regions in the genome with restricted gene flow or islands
of genetic differentiation.