4.5 What additional information did genomic analysis provide?
The present results are consistent with patterns detected using only a
few allozymes over 40 years ago. However, several new insights have been
gained from the whole-genome analyses applied here. First, the results
suggest that the divergence between the two demes results primarily from
genetic drift, but that selection might also play a role, particularly
including polygenic traits of metabolic and growth processes. Second,
the pattern of divergence and the allele occurrence over the SNP array
indicate that Deme II is reproductively isolated, whereas Deme I appears
to be in at least some contact with Lake Ånnsjön, possibly by downstream
migration. Third, the level of genome-wide diversity and inbreeding is
strikingly different between the two demes and appears large also in
relation to brown trout of other lakes. Deme I shows the highest degree
of nucleotide diversity and lowest measures of runs of homozygosity
compared to all other samples studied here, whereas Deme II shows
radically lower levels of nucleotide diversity than any of the other
samples, and the highest measures of ROH (cf. Table 2, Figure 6 vs.
Tables S7, S12, Figures S12, S13). Further, we find that the genomic
background behind the LDH-1 allozyme expressions is complex and
likely involves regulatory mechanisms and possibly interactions between
several genes.
This study has not addressed what causes the reproductive isolation
between these demes and if this structuring has evolved sympatrically or
allopatrically, if it reflects natural evolution or if human induced
release has played a role. Preliminary analysis of the mitochondrial DNA
sequences of these demes do not lend support for separate lineages
reflecting colonization from different glaciation refugia (unpublished
data). Further, we cannot exclude human translocation. For example, such
translocation could imply that Deme I was translocated from one place
(e.g. Lake Ånnsjön) and Deme II from another lake, and that the
populations did not, or only to a very limited degree, hybridize in the
new environment. There are lakes c 20 km away where the LDH-1 null
allele has been observed (Allendorf et al.,
1984). Further, we have not been able to address the potential temporal
stability of these structures which appears highly warranted, but
difficult in light of a current strict protection of these lakes.