3.1. Population-level patterns
Before quality filtering, a total of 266, 262 and 256 million sites were
retained for analyses of polymorphism levels, among which 8.7, 9.2 and
8.4 million were variable sites in G. tenella , G. pusillaand G. calmariensis , respectively (Raw data: Yang, Wheat, Slotte,
& Hambäck, 2022). Species were strongly separated (Fig. S2) and there
were some additional within-species separation between sites (Fig. S3).
After quality filtering, we retained 7.6 million variable sites out of
126.5 million sites in G. tenella , 8.6 million variable sites out
of 130.6 million sites in G. pusilla and 7.2 million variable
sites out of 122.6 million total sites in G. calmariensis . At the
whole genome level, G. pusilla populations harboured the highest
nucleotide diversity (0.0058), G. calmariensis (0.0051) had the
lowest, with G. tenella (0.0056) having an intermediate
nucleotide diversity. The posterior mean estimates of the relative
effective population sizes (Ne ) from HDMKPRF on
the 4154 genes were N2 =1.045 for G. pusilla and
N3 = 0.934 for G. calmariensis in units ofG. tenella (N1). Thus, the relative ranking of
population sizes among species was G. pusilla > G.
tenella > G. calmariensis .