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 .