Abstract
The availability of diverse ecological niches can promote adaptation of trophic specializations and related traits, as has been repeatedly observed in evolutionary radiations of freshwater fish. The role of genetics, environment and history in ecologically driven divergence and adaptation, can be studied on adaptive radiations or populations showing ecological polymorphism. Salmonids, especially the Salvelinus genus, are renowned for both phenotypic diversity and polymorphism. Arctic charr (Salvelinus alpinus) invaded Icelandic streams during the glacial retreat (about 10,000 years ago) and exhibits many instances of sympatric polymorphism. Particularly well studied are the four morphs in Lake Þingvallavatn in Iceland. The small benthic (SB), large benthic (LB), planktivorous (PL) and piscivorous (PI) charr differ in many regards, including size, form and life history traits. To investigate relatedness and genomic differentiation between morphs we identified variable sites from RNA-sequencing data from three of those morphs, and verified 22 variants in population samples. The data reveal genetic differences between the morphs, with the two benthic morphs being more similar and the PL-charr more genetically different. The markers with high differentiation map to all linkage groups, suggesting ancient and pervasive genetic separation of these three morphs. Furthermore, GO analyses suggest differences in collagen metabolism, odontogenesis and sensory systems between PL-charr and the benthic morphs. Genotyping in population samples from all four morphs confirms the genetic separation and indicates that the PI-charr are less genetically distinct than the other three morphs. The genetic separation of the other three morphs indicates certain degree of reproductive isolation. The extent of gene flow between the morphs and the nature of reproductive barriers between them remain to be elucidated.
Footnotes
In this revised manuscript we trimmed the text, tried to provide a clearer focus for the study, modifying introduction, results and discussion and have taken into account the very helpful comments provided by the reviewers. For instance, we have added more details regarding generation of crosses and sampling and discuss them in the results. We also disclose that two errors were discovered in the genotyping-assay, that were corrected as follows: 1) A individual labeled as an SB-charr in previous version, was actually a PL-charr (based on a photograph). This was the stray SB that previously grouped with the PL-charr. 2) The peculiar "result" of strong LD between cdkn2a and gnl3l which mapped to different chromosomes was due to technical error. These two markers had been run at the same time and there was a primer mixup. Both primers were rerun that gave the same results for cdkn2a but quit different for gnl3l. These two errors led us to rewrite the results on genotyping (KASP-assay) and redo associated figures and tables. But these corrections did not affect the general conclusions, rather strengthened the correlation of allele frequencies in the transcriptome and the KASP data. Finally, we changed the format of references to a Harvard style and uploaded supplementary tables and files on figshare.