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.