Mitogenome Sequencing Reveals Shallow Evolutionary Histories and Recent Splitting Times Between Morphologically and Ecologically Divergent European Lake Whitefish Coregonus spp. Morphs

The Danish European lake whitefish (Coregonus lavaretus, ELW) and the North Sea houting (Coregonus oxyrhincus, NSH) are closely related species within the North European whitefish complex. Like many other European whitefish species they are characterized by showing differences in biology and morphology, but only little differentiation at the nuclear DNA level, suggesting a recent divergence. So far, studies based on mtDNA have not shown evidence for a separate evolutionary history of the two species. However, these conclusions have been based using relatively small (<1000bp) fragments of the mitochondrial genome. Using next-generation sequencing techniques we sequenced 106 complete mitogenomes, including 16 ELW originating from the Baltic Sea, 63 ELW from Denmark, 21 NSH samples from Denmark and 6 samples from American lake whitefish (Coregonus clupeaformis). Phylogenetic analysis of the total dataset revealed two main clades of ELW, consistent with findings from the previous studies based on partial sequences. The NSH had, like other Danish ELW populations, been introgressed historically with Baltic migrants and did not constitute a monophyletic group. Using mutation rate estimates obtained from the literature as well as calculated from the dataset itself, the MRCA of all main clades was estimated. Using skyline plots implemented in BEAST to analyze past changes in effective population size showed no significant differences from a model assuming constant population size. Data simulations supported, however, an expansion in the combined Danish dataset and provided a reliable estimate of intra-specific mutation rate. Analyses of divergence times showed that the NSH diverged from the Danish ELW at a similar time as other Danish ELW populations diverged from each other, after the end of the last ice-age. The NSH did, however, only show small values of effective number of migrants compared to the other Danish ELW populations, and did not share any haplotypes with other sampled ELW. This indicates recent reproductive isolation from the Danish ELW populations, and that the NSH follow a separate evolutionary trajectory. In conclusion this study provides evidence for recent reproductive isolation (within the past ~10,000 years) between the NSH and ELW which supports the NSH status as a separate unit of conservation. It also illustrates the significantly added information content obtained by sequencing whole mitogenomes.