5 CONCLUSIONS
We revisited the first reported case of cryptic sympatry in brown trout that was detected by contrasting homozygosity at an allozyme locus in the tiny Lakes Bunnersjöarna, central Sweden using a 96 SNP array and genomic tools. The present findings confirm reproductive isolation between the sympatric demes. Our genomic data show that divergence between these two demes is a genome-wide phenomenon governed by genetic drift but also by selective mechanisms. Our work demonstrates that populations from the same habitat may have large genome-wide divergence without obvious morphological distinction, which has important implications for management and conservation.
ACKNOWLEDGEMENTS
We thank Sigbjørn Lien and Matthew Peter Kent at CIGENE, Norwegian University of Life Sciences for providing SNP sequences and linkage map for development of the 96-SNP array on the EP1TMFluidigm genotyping platform. We acknowledge support from the National Genomics Infrastructure (NGI) in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research Council, SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. This research was supported by the Swedish Research Council Formas (L.L.), the Swedish Research Council (L.L.) the Swedish Agency for Marine and Water Management (L.L.), the Carl Trygger and the Erik Philip-Sörensen Foundations (L.L.), the SciLifeLab Bioinformatics Long‐term Support (L.L.) funded by the Knut and Alice Wallenberg foundation (grant no. 2014.0278). V.E.K. and D.E. are financially supported by the Knut and Alice Wallenberg Foundation as part of the National Bioinformatics Infrastructure Sweden at SciLifeLab.
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DATA ACCESSIBILITY
Illumina raw sequences from this study have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB41224 (https://www.ebi.ac.uk/ena/browser/view/PRJEB41224). Processed data are available at Dryad xxxx (to be completed after manuscript is accepted for publication).
AUTHOR CONTRIBUTION
L.L., A.A., Sa.Ku., N.R. designed the study; N.R., F.W.A., G.S., L.L. provided the material and allozyme data, St.Ka. provided 96 SNP array genotypes, A.A., A.S., N.R., L.L. analyzed SNP array data, A.S. analyzed genomics data initially instructed by Sa.Ku. and further supervised by V.E.K., D.E., and M.K. O.H and N.R. performed POWSIM theoretical evaluation and supervised simulations performed by A.S. N.L.P.K guided and located the 96 SNPs in the reference genome and performed theLDH-A analysis with allozyme guidance from F.W.A. and G.S. A.S. and L.L. led the writing with contribution from all authors. L.L. funded the study.