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.