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). 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. pusillaand 7.2 million variable sites out of 122.6 million total sites inG. calmariensis . At the whole genome level, G. pusillapopulations 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 of G. tenella(N1). Thus, the relative ranking of population sizes
among species was G. pusilla > G. tenella
> G. calmariensis .