Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr

Salmonids have a remarkable ability to form sympatric morphs after postglacial colonisation of freshwater lakes. These morphs often differ in morphology, feeding and spawning behaviour. Here, we explored the genetic basis of morph differentiation in Arctic charr (n = 283) by first establishing a high-quality reference genome and then using this in whole genome sequencing of distinct morphs present in two Norwegian and two Icelandic lakes. The four lakes represent the spectrum of genetic differentiation between morphs from one lake with no genetic differentiation between morphs, implying phenotypic plasticity, to two lakes with locus-specific genetic differentiation, implying incomplete reproductive isolation, and one lake with strong genome-wide divergence consistent with complete reproductive isolation. As many as 12 putative inversions ranging from 0.45 to 3.25 Mbp in size segregated among the four morphs present in one lake, Thingvallavatn, and these contributed significantly to the genetic differentiation among morphs. None of the putative inversions were found in any of the other lakes, but there were cases of partial haplotype sharing in similar morph contrasts in other lakes. Our findings are consistent with a highly polygenic basis of morph differentiation with population-specific selection on alleles linked to the development of similar morph phenotypes. The results support a model where morph differentiation is first established through phenotypic plasticity, leading to niche expansion and separation. This may be followed by gradual development of reproductive isolation, locus-specific differentiation and eventually complete reproductive isolation and genome-wide divergence.

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Journal
Molecular Ecology
Published
2025-08-26
DOI
https://doi.org/10.1111/mec.70085
Primary Topic
Fish Ecology and Management Studies
Type
article
Field-Weighted Citation Impact
0.00

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article

Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr

Zophonı́as O. Jónsson, Claúdio Ciofi, Jonathan M. D. Wood, Linda Laikre et al.
Molecular Ecology
Fish Ecology and Management Studies
article

Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr

Zophonı́as O. Jónsson, Claúdio Ciofi, Jonathan M. D. Wood, Linda Laikre, Kjetil Hindar, Tom Barker, Arnar Pálsson, David Swarbreck, Genevieve Diedericks, Nils Ryman, Karim Gharbi, Seanna McTaggart, Alessio Iannucci, Mats E. Pettersson, Hannes Svardal, Kendall Baker, Leif Andersson, Robert Michael Waterhouse, Sigurður S. Snorrason, Khrystyna Kurta, Naomi Irish, Christopher B. Watkins, Mariano Olivera Fedi, Henrique G. Leitão, Leah Catchpole, Alex Durrant, Maria Angela Diroma, Vanda Knitlhoffer, Sacha Lucchini, Joanna Collins, Han Xiao
article en

Abstract

Salmonids have a remarkable ability to form sympatric morphs after postglacial colonisation of freshwater lakes. These morphs often differ in morphology, feeding and spawning behaviour. Here, we explored the genetic basis of morph differentiation in Arctic charr (n = 283) by first establishing a high-quality reference genome and then using this in whole genome sequencing of distinct morphs present in two Norwegian and two Icelandic lakes. The four lakes represent the spectrum of genetic differentiation between morphs from one lake with no genetic differentiation between morphs, implying phenotypic plasticity, to two lakes with locus-specific genetic differentiation, implying incomplete reproductive isolation, and one lake with strong genome-wide divergence consistent with complete reproductive isolation. As many as 12 putative inversions ranging from 0.45 to 3.25 Mbp in size segregated among the four morphs present in one lake, Thingvallavatn, and these contributed significantly to the genetic differentiation among morphs. None of the putative inversions were found in any of the other lakes, but there were cases of partial haplotype sharing in similar morph contrasts in other lakes. Our findings are consistent with a highly polygenic basis of morph differentiation with population-specific selection on alleles linked to the development of similar morph phenotypes. The results support a model where morph differentiation is first established through phenotypic plasticity, leading to niche expansion and separation. This may be followed by gradual development of reproductive isolation, locus-specific differentiation and eventually complete reproductive isolation and genome-wide divergence.

Molecular EcologyVol. 34(19)
Uppsala University (SE), SIB Swiss Institute of Bioinformatics (CH), University of Antwerp (BE), Stockholm University (SE), University of Iceland (IS), Wellcome Sanger Institute (GB), Swedish University of Agricultural Sciences (SE), Earlham Institute (GB), Norwegian Institute for Nature Research (NO), University of Florence (IT), Texas A&M University (US), University of Lausanne (CH)
National Science Foundation, Havs- och Vattenmyndigheten, UK Research and Innovation, European Commission, Environmental Protection Agency, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Svenska Forskningsrådet Formas, Knut och Alice Wallenbergs Stiftelse, Naturvårdsverket, Vetenskapsrådet, Háskóli Íslands, Stockholms Universitet, Science for Life Laboratory, Directorate for Biological Sciences, HORIZON EUROPE Framework Programme, Biotechnology and Biological Sciences Research Council, Staatssekretariat für Bildung, Forschung und Innovation
Openalex Percentile: Top 78%
Fish Ecology and Management Studies
DOIOpen Access PDFOpenAlex
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