Our findings of extensive genomic re-arrangements of a substantial fraction of the 45S rDNA unit in the C. fontanae genome when compared with the situation in C. albula are in strong contrast with previously reported low genetic differentiation between these two species [6, 18].
Our results indicate that in the genome of C. fontanae next to the complete 6–10 NOR loci corresponding to similar number of NOR-bearing chromosomes in C. albula, up to 30 supernumerary and incomplete NOR loci occur. This is supported by results of the sequential fluorescent staining (CMA3 and DAPI), showing about 6–8 signals in karyotypes of both species, although on chromosomes of C. fontanae the signals were slightly weaker. However, these supernumerary sites in C. fontanae were not represented by repeating of the complete 45S rDNA unit (i.e. 18S rDNA, ITS1, 5.8S rDNA, ITS2, 28S rDNA)n but only by a part including probably complete ITS1 and ITS2 and a part of the 28S rDNA adjacent to the ITS2, i.e. the 5′ end of the 28S rDNA gene (the region of 5.8S rDNA was not investigated separately).
Most of the supernumerary signals of the 45S rDNA in chromosomes of C. fontanae were localized in the AT rich pericentromeric regions as well as the major accumulation of the Rex1 retrotransposon on both C. albula and C. fontanae chromosomes. This is in accordance with findings of other authors describing accumulations of transposable elements in centromeric heterochromatin e.g. in genome of humans  and in a cichlid fish Cichla kelberi[27, 28]. TEs in fishes generally tend to insert to heterochromatic areas of chromosomes (; reviewed by ). There are also records of specific integration of some non-LTR retrotransposons at the rRNA genes found in most animal phyla (summarized by ), in insects Drosophila melanogaster and Bombyx mori or in the fish Erythrinus erythrinus, where Rex3 retrotransposons were found in the 5S rRNA genes .
In the above-mentioned E. erythrinus fish, a similar multiplication of rRNA genes was described . In that case, four karyomorphs of E. erythrinus differ in their chromosomal number, karyotype, presence or absence of heteromorphic sex chromosomes and numbers of 5S rDNA loci. The karyomorph A in E. erythrinus showed only two 5S rDNA loci, while in the karyomorph D, 21–22 5S rDNA loci could be observed. All 5S rDNA sites co-localized with the Rex3 retrotransposon. On the other hand, no changes in the heterochromatin and 18S rDNA patterns were found between these two karyomorphs . Such two karyomorphs within a single species E. erythrinus may be seen as an incipient stage of a speciation event. This situation can thus represent an initial stage, later resulting in the condition observed in morphologically , ecologically and physiologically [33, 34] diverged species pair C. fontanae and C. albula described in this study. A similar observation of extremely multiplied NOR sites (46 and 49 countable FISH signals), however, without any further detailed analysis, were reported in brook char Salvelinus fontinalis (Salmonidae) .
In salmonid fishes, TEs have been studied intensively [30, 36, 37]. Microarray studies showed that transcription of rainbow trout transposons is activated by external stimuli, such as toxicity, stress and bacterial antigens . In the oligotrophic Lake Stechlin, the food availability for coregonines was extremely limited and the size at maturity and the maximal size of C. albula are far behind the other populations of this species in adjacent lakes in northern Germany . C. fontanae is the smallest species of the genus Coregonus in Europe . Raising both species in the laboratory demonstrated that both grew much larger if supported with unlimited food (unpublished obs., Freyhof). Therefore, it can be speculated that both species, especially C. fontanae, live in an extreme permanent starvation in the Lake Stechlin. It can be also hypothesized that the spring-spawning habit of C. fontanae might have originated simply by the shift of sexual maturity in the part of the population that has not been able to attain sexual maturity in autumn due to the lower food intake and hence environmental starvation stress.
Link between environmental stress and chromatin modification/regulation
Effects of stress on the genome can result in important perturbations creating new combinations better compatible with survival (summarized by ; more recently reviewed by ). After the discovery of transposable elements (TE) more than 50 years ago, their mutagenic effect had been increasingly viewed in association with rapid genome reorganizations by the creation of new regulation patterns and chromosome restructuring during last years . Stress activated mobilization of these elements by failure of epigenetic silencing (the host defence model of repressing the movement of mobile elements; [42, 43]) can lead to (re)activation of mobile elements and consequently to major and rapid genome alterations [40, 41, 44, 45].
Barbara McClintock  already considered TE as a source of hypermutagenicity creating viable and fertile individuals from a stressed population under risk of extinction. Moreover, she originally named TE “controlling elements” due to their ability to alter gene activity and genome structure .
TE-mediated genome rearrangements as a factor in speciation
With growing evidence for the importance of TEs in the genome evolution, the role of TE-mediated genome changes in the speciation by their possible contribution to pre- and post-mating reproductive isolation formation has been increasingly taken into account and discussed generally in eukaryotes [48, 49], Drosophila, fishes , mammals , and plants . However, lack of experimental data makes it difficult to prove this possibility (reviewed by [51, 54, 55]). On the other hand,  provides an overview of TE transposition bursts concomitant with radiation periods in seven cases. The same authors also discuss TE-induced rapid speciation associated with the ability of TEs to induce chromosomal rearrangements. Therefore, the sympatric species pair C. albula and C. fontanae in the context of other congeneric coregonine species and their variable evolutionary history in the Eurasian post-glacial lakes appears to be a suitable model system for exploring mechanisms of genomic differentiation and speciation with or without TE contribution.
In a very similar, but North American study system (lake whitefish species pairs, Coregonus spp.),  next generation sequencing (NGS) showed that TEs appeared to be highly expressed in hybrids between two recently diverged species. This may be potentially the mechanism responsible for post-zygotic reproductive isolation. Moreover, NGS can be viewed as a useful tool complementary with molecular cytogenetic approach presented in this study enabling confirmation of here documented results and search for other candidate groups of TEs involved in the genome re-arrangements and accelerated speciation.