Conservation Genetics Resources

, Volume 10, Issue 2, pp 169–171 | Cite as

Novel RAD sequence data reveal a lack of genomic divergence between dietary ecotypes in a landlocked salmonid population

  • Morten T. Limborg
  • Wesley A. Larson
  • Kyle Shedd
  • Lisa W. Seeb
  • James E. Seeb
Technical Note


Preservation of heritable ecological diversity within species and populations is a key challenge for managing natural resources and wild populations. Salmonid fish are iconic and socio-economically important species for commercial, aquaculture, and recreational fisheries across the globe. Many salmonids are known to exhibit ecological divergence within species, including distinct feeding ecotypes within the same lakes. Here we used 5559 SNPs, derived from RAD sequencing, to perform population genetic comparisons between two dietary ecotypes of sockeye salmon (Oncorhynchus nerka) in Jo-Jo Lake, Alaska (USA). We tested the standing hypothesis that these two ecotypes are currently diverging as a result of adaptation to distinct dietary niches; results support earlier conclusions of a single panmictic population. The RAD sequence data revealed 40 new SNPs not previously detected in the species, and our sequence data can be used in future studies of ecotypic diversity in salmonid species.


Ecological speciation Kokanee salmon SNPs RAD sequencing 



We thank Jeff Olsen at the USFWS Alaska Conservation Genetics Laboratory for sharing archived Jo-Jo Lake tissue samples and Carita Pascal for laboratory assistance. MTL was supported by a fellowship from the Carlsberg Foundation CF15-0721. WAL was supported by the H. Mason Keeler Endowment for Excellence and a US National Science Foundation Graduate Research Fellowship (Grant No. DGE-0718124). Any use of trade, firm, for product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Supplementary material

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Supplementary material 1 (DOCX 39 KB)
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Supplementary material 1 (XLSX 48 KB)


  1. Bernatchez L, Renaut S, Whiteley AR et al (2010) On the origin of species: insights from the ecological genomics of lake whitefish. Philos Trans R Soc B 365:1783–1800CrossRefGoogle Scholar
  2. Ellegren H, Smeds L, Burri R et al (2012) The genomic landscape of species divergence in Ficedula flycatchers. Nature 491:756–760CrossRefPubMedGoogle Scholar
  3. Everett MV, Miller MR, Seeb JE (2012) Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing. BMC Genom 13:521CrossRefGoogle Scholar
  4. Foll M, Gaggiotti O (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180:977–993CrossRefPubMedPubMedCentralGoogle Scholar
  5. Funk WC, McKay JK, Hohenlohe PA, Allendorf FW (2012) Harnessing genomics for delineating conservation units. Trends Ecol Evol 27:489–496CrossRefPubMedPubMedCentralGoogle Scholar
  6. Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405CrossRefPubMedGoogle Scholar
  7. Jones FC, Grabherr MG, Chan YF et al (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484:55–61CrossRefPubMedPubMedCentralGoogle Scholar
  8. Larson WA, McKinney GJ, Limborg MT et al (2016) Identification of multiple QTL hotspots in sockeye salmon (Oncorhynchus nerka) using genotyping-by-sequencing and a dense linkage map. J Hered 107:122–133CrossRefPubMedGoogle Scholar
  9. Larson WA, Limborg MT, McKinney GJ et al (2017) Genomic islands of divergence linked to ecotypic variation in sockeye salmon. Mol Ecol 26:554–570CrossRefPubMedGoogle Scholar
  10. Lemay MA, Russello MA (2015) Genetic evidence for ecological divergence in kokanee salmon. Mol Ecol 24:798–811CrossRefPubMedGoogle Scholar
  11. Limborg MT, Waples RK, Allendorf FW, Seeb JE (2015) Linkage mapping reveals strong chiasma interference in sockeye salmon: Implications for interpreting genomic data. G3 5, 2463–2473.CrossRefPubMedPubMedCentralGoogle Scholar
  12. McKinney GJ, Larson WA, Seeb LW, Seeb JE (2017) RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al. (2016). Mol Ecol Resour 17:356–361CrossRefPubMedGoogle Scholar
  13. Miller JL, Hamon T, Jones T, West F (2007) Kokanee exploit large prey in the absence of limnetic predators. Am Fish Soc Symp 54:73–83Google Scholar
  14. Palmé A, Laikre L, Ryman N (2013) Monitoring reveals two genetically distinct brown trout populations remaining in stable sympatry over 20 years in tiny mountain lakes. Conserv Genet 14:795–808CrossRefGoogle Scholar
  15. Ryman N, Allendorf FW, Ståhl G (1979) Reproductive isolation with little genetic divergence in sympatric populations of brown trout (Salmo trutta). Genetics 92:247–262PubMedPubMedCentralGoogle Scholar
  16. Schluter D (2000) The ecology of adaptive radiation. Oxford University Press, OxfordGoogle Scholar
  17. Shedd KR, von Hippel FA, Willacker JJ et al (2015) Ecological release leads to novel ontogenetic diet shift in kokanee (Oncorhynchus nerka). Can J Fish Aquat Sci 72:1718–1730CrossRefGoogle Scholar
  18. Soria-Carrasco V, Gompert Z, Comeault AA et al (2014) Stick insect genomes reveal natural selection’s role in parallel speciation. Science 344:738–742CrossRefPubMedGoogle Scholar
  19. Stearns S, Hendry A (2004) Evolution illuminated: salmon and their relatives. Oxford University Press, New YorkGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • Morten T. Limborg
    • 1
    • 2
  • Wesley A. Larson
    • 1
    • 3
  • Kyle Shedd
    • 4
  • Lisa W. Seeb
    • 1
  • James E. Seeb
    • 1
  1. 1.School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleUSA
  2. 2.Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
  3. 3.U.S. Geological Survey, Wisconsin Cooperative Fishery Research UnitUniversity of Wisconsin-Stevens PointStevens PointUSA
  4. 4.Gene Conservation Laboratory, Division of Commercial FisheriesAlaska Department of Fish and GameAnchorageUSA

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