4.3 Difficulties in identifying subpopulations within metapopulations
Two populations were only found in the 2010s samples and were not observed in samples from the 1970-80s. These “new” populations were found in Lakes Daimatjärn 1 Ö and Munsvattnet (Skåarnja 1 and Hotagen 1, respectively) and indicate that our data do not represent the entire metapopulations present in these systems. We also found that the relative frequencies at which populations were observed in the samples fluctuated over time (Table S2), most likely as an effect of sampling.
The finding of the “new” populations complicate inference about the genetic diversity status of the two metapopulations involved. In metapopulation Skåarnja 1, for example, we observed a decrease or no change in diversity measures in all the three populations that occurred at both points in time. Yet, when regarding the whole metapopulation we see an increase in diversity over time (Figure 7a-b). This is due to the appearance of the new genetic cluster in the present sample, and this new population displays the highest levels of diversity in all measures when compared to the other populations in the present sample. Excluding the new population from the analysis results in a decrease in heterozygosity and no change of allelic diversity (A R, N A,P L) in this metapopulation. Like diversity, the estimate of metapopulation effective size N eV is affected by the appearance of the new population; including it results in an N eV of 65, while excluding this cluster doubles the effective size of the metapopulation (N eV=135). The reduction is due to the larger allele frequency change resulting from the new cluster. Similar observations can be made in the metapopulation Hotagen 1 (where a new population appears in the 2010s sample), but the effects of including it in the estimates for the whole system are less striking. Thus, recognizing the population genetic structure and identifying existing genetically distinct populations is important for the interpretation of indicator values.