3.1 Genetic structuring and occurrence of sympatric populations
Altogether, structure analyses identified 31 separate clusters (populations) in the 27 lakes included in the present study, with 13-199 fish assigned to each cluster (Table S2; Figure 4). 29 of these 31 clusters occurred at both points in time and we refer to them synonymously as populations, clusters, and subpopulations (if they occur within the same metapopulation). Two populations were not present in the 1970-80s (past) sample but appeared in the recent 2010s (present) sample (in Skåarnja 1 and Hotagen 1; Figure 4). No population was lost over the c. 40 years between sampling, although the relative frequencies at which populations occurred in the samples differed significantly between time points in five metapopulations (Figure S1a-d, f; χ2=6.16-47.60; p=0.000-0.046).
Although all 29 populations identified in the 1970-80s samples remained over time, allele frequency changes occurred in many of them.F ST between time points within populations varied between 0 and 3 percent (Table S3a). In 15 of the 29 populations, genetic divergence between time points was significantly different from zero (p=0-0.02; Table S3a).
Sympatric populations (i.e. genetically divergent clusters coexisting within the same lake) were observed at both time points in 12 lakes (Figure 4; Table S2; Figure S1). These lakes were distributed across five metapopulations, and the “independent” lake Ånnsjön. In the remaining two metapopulations and the two independent lakes, we observed only one population per lake. The occurrence of sympatric populations does not appear to correlate with the number of creeks/streams connected to the lake (i.e. potential spawning sites; r =0.29.; p=0.14), lake area (r =0.27; p=0.18), or average lake depth (r =-0.31; p=0.20).
The genetic relationships among the identified populations reflect the geographic location of the lakes and systems. Overall, the branching of the phylogenetic tree (Figure S2) corresponds to the main river drainages (Figure 1, 4). Lake Ånnsjön was found to harbor three subpopulations and is thus viewed as a metapopulation. The other two separate lakes (Saxvattnet and Rörvattnet) only harbored one population per lake. Thus, we have a total of eight metapopulations (Figure 4).