Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (<i>Coregonus</i> sp.) with long and short reads

Mérot, Claire; Stenløkk, Kristina; Venney, Clare J; Laporte, Martin; Moser, Michel; Normandeau, Éric; Árnyasi, Mariann; Kent, Matthew; Rougeux, Clément; Flynn, Jullien M; Lien, Sigbjørn; Bernatchez, Louis

doi:10.1111/mec.16468

Cited by 27 publications

(59 citation statements)

References 169 publications

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“…We observed genetic differentiation between species in all four lakes, consistent with previous studies showing genetic differences between whitefish benthic-limnetic species Østbye et al 2006;Rogers and Bernatchez 2007;Bernatchez et al 2010;Siwertsson et al 2013;Dion-Côté et al 2017;Rougeux et al 2017;Feulner and Seehausen 2019;Rougeux, Gagnaire, Praebel, et al 2019;De-Kayne et al 2022;Mérot et al 2022). There was relatively high genetic differentiation between species and lakes in North America, though differentiation between lakes was greater in Europe than in North America.…”

Section: Considerable But Variable Genetic Divergence Between Species...supporting

confidence: 91%

“…There was relatively high genetic differentiation between species and lakes in North America, though differentiation between lakes was greater in Europe than in North America. There was greater differentiation between species in Cliff Lake than Indian Lake, as previously reported in our sister study (Mérot et al 2022). Genetic differentiation between lakes was greater than between species in Europe (Table 1B), likely due to the Zurich Lake and Langfjordvatn Lake populations having occupied two different glacial refugia during the last glaciation period .…”

Section: Considerable But Variable Genetic Divergence Between Species...supporting

confidence: 79%

“…The extent of genetic differentiation between the benthic and the limnetic species varied among lakes. FST estimates for Cliff Lake and Indian Lake in North America were previously published in Mérot et al (2022). In North America, moderate to high divergence between lakes both within and between species was observed (FST between lakes: 0.084 between Cliff Lake and Indian Lake limnetic species to 0.182 between Cliff Lake and Indian Lake benthic species), with greater FST between species in Cliff Lake than Indian Lake (0.098 for Indian Lake and 0.175 for Cliff Lake; Table 1A).…”

Section: Genetic Divergence Between Benthic-limnetic Species Pairsmentioning

confidence: 99%

“…WGS was performed using paired end 150 bp sequencing on an Illumina HiSeq4000 with estimated 5X coverage. The North American samples were previously used and sequenced in Mérot et al (2022). WGBS was performed using paired end 150 bp sequencing on the Illumina HiSeqXwith samples randomly distributed across 16 lanes (four individuals pooled per lane) with estimated 10X coverage.…”

Section: Sample Preparation and Sequencingmentioning

confidence: 99%

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Epigenetic and genetic differentiation betweenCoregonusspecies pairs

Venney

Mérot

Normandeau

et al. 2022

Preprint

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Phenotypic diversification and speciation are classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that epigenetic mechanisms like DNA methylation may contribute to species divergence due to their effects on transcription and phenotype. Methylation can also increase mutagenesis and could lead to genetic assimilation of plastic phenotypes into genetic variants when the environment remains stable over many generations, though there has been minimal empirical research on assimilation. Whitefish are excellent systems to study speciation and genetic assimilation due to the repeated independent divergence of benthic-limnetic species pairs that have coexisted in lakes for ~12 000 years serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between benthic-limnetic species pairs in lake whitefish (Coregonus clupeaformis) and European whitefish (C. lavaretus) from four lakes (N=64). We found considerable, albeit variable, genetic and epigenetic differences between benthic and limnetic species in all four lakes. Polymorphism was enriched at CpG sites confirming the mutagenic nature of DNA methylation; all SNP types were enriched in all lakes, though C > T SNPs were most common. We also identified a surplus of potential sites undergoing genetic assimilation putatively associated with speciation, defined as sites harbouring both a differentially methylated site and a highly divergent SNP. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence, influences mutagenesis, and drives genetic assimilation of phenotypes that are ultimately associated with ecological speciation in whitefish species complexes.

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Section: Considerable But Variable Genetic Divergence Between Species...supporting

confidence: 91%

Section: Considerable But Variable Genetic Divergence Between Species...supporting

confidence: 79%

Section: Genetic Divergence Between Benthic-limnetic Species Pairsmentioning

confidence: 99%

Section: Sample Preparation and Sequencingmentioning

confidence: 99%

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Epigenetic and genetic differentiation betweenCoregonusspecies pairs

Venney

Mérot

Normandeau

et al. 2022

Preprint

Self Cite

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“…It is important to note that our results only suggest a putative inversion. Future studies could take advantage of the recently released long‐read genome assemblies of lake whitefish (Mérot et al, 2022 ) to verify the existence of this putative chromosomal inversion.…”

Section: Discussionmentioning

confidence: 99%

High‐density genomic data reveal fine‐scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan

Shi

Homola

Euclide

et al. 2022

Evolutionary Applications

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Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (Coregonus clupeaformis) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform the management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management.

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Evolutionary loss of the β1-adrenergic receptor in salmonids

Joyce¹

2023

General and Comparative Endocrinology

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Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads

Cited by 27 publications

References 169 publications

Epigenetic and genetic differentiation betweenCoregonusspecies pairs

Epigenetic and genetic differentiation betweenCoregonusspecies pairs

High‐density genomic data reveal fine‐scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan

Evolutionary loss of the β1-adrenergic receptor in salmonids

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