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Venney CJ, Mérot C, Normandeau E, Rougeux C, Laporte M, Bernatchez L. Epigenetic and Genetic Differentiation Between Coregonus Species Pairs. Genome Biol Evol 2024; 16:evae013. [PMID: 38271269 PMCID: PMC10849188 DOI: 10.1093/gbe/evae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation. Whitefish, freshwater members of the salmonid family, are excellent systems to study phenotypic diversification and speciation due to the repeated divergence of benthic-limnetic species pairs serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between sympatric benthic-limnetic species pairs in lake and European whitefish (Coregonus clupeaformis and Coregonus lavaretus) from four lakes (N = 64). We found considerable, albeit variable, genetic and epigenetic differences between species pairs. All SNP types were enriched at CpG sites supporting the mutagenic nature of DNA methylation, though C>T SNPs were most common. We also found an enrichment of overlaps between outlier SNPs with the 5% highest FST between species and differentially methylated loci. This could possibly represent differentially methylated sites that have caused divergent genetic mutations between species, or divergent selection leading to both genetic and epigenetic variation at these sites. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence and mutagenesis during whitefish speciation.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Clément Rougeux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Ministère des Forêts, de la Faune et des Parcs (MFFP), Québec, Québec, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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2
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Mérot C, Stenløkk KSR, Venney C, Laporte M, Moser M, Normandeau E, Árnyasi M, Kent M, Rougeux C, Flynn JM, Lien S, Bernatchez L. Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads. Mol Ecol 2023; 32:1458-1477. [PMID: 35416336 DOI: 10.1111/mec.16468] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 11/26/2022]
Abstract
Nascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) such as insertions, deletions and other rearrangements, allowing further insights into the genetic architecture of speciation and how different types of variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the lake whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both C. clupeaformis sp. Normal and C. clupeaformis sp. Dwarf, annotated the transposable elements and analysed the genomes in the light of related coregonid species. Next, we used a combination of long- and short-read sequencing to characterize SVs and genotype them at the population scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species correspond to insertions or deletions of transposable elements (TEs), suggesting that TE accumulation may represent a key component of genetic divergence between the Dwarf and Normal species. Together, our results suggest that SVs may play an important role in speciation and that, by combining second- and third-generation sequencing, we now have the ability to integrate SVs into speciation genomics.
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Affiliation(s)
- Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Kristina S R Stenløkk
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Clare Venney
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Martin Laporte
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,Ministère des Forêts, de la Faune et des Parcs (MFFP) du Québec, Québec, Québec, Canada
| | - Michel Moser
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Mariann Árnyasi
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Matthew Kent
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Clément Rougeux
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Jullien M Flynn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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3
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Nikolic N, Devloo-Delva F, Bailleul D, Noskova E, Rougeux C, Delord C, Borsa P, Liautard-Haag C, Hassan M, Marie AD, Feutry P, Grewe P, Davies C, Farley J, Fernando D, Biton-Porsmoguer S, Poisson F, Parker D, Leone A, Aulich J, Lansdell M, Marsac F, Arnaud-Haond S. Stepping up to genome scan allows stock differentiation in the worldwide distributed blue shark Prionace glauca. Mol Ecol 2023; 32:1000-1019. [PMID: 36511846 DOI: 10.1111/mec.16822] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022]
Abstract
The blue shark Prionace glauca is a top predator with one of the widest geographical distributions of any shark species. It is classified as Critically Endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population. The blue shark was proposed as a possible archetype of the "grey zone of population differentiation," coined to designate cases where population structure may be too recent or too faint to be detected using a limited set of markers. Here, blue shark samples collected throughout its global range were sequenced using a specific RAD method (DArTseq), which recovered 37,655 genome-wide single nucleotide polymorphisms (SNPs). Two main groups emerged, with Mediterranean Sea and northern Atlantic samples (Northern population) differentiated significantly from the Indo-west Pacific samples (Southern population). Significant pairwise FST values indicated further genetic differentiation within the Atlantic Ocean, and between the Atlantic Ocean and the Mediterranean Sea. Reconstruction of recent demographic history suggested divergence between Northern and Southern populations occurred about 500 generations ago and revealed a drastic reduction in effective population size from a large ancestral population. Our results illustrate the power of genome scans to detect population structure and reconstruct demographic history in highly migratory marine species. Given that the management plans of the blue shark (targeted or bycatch) fisheries currently assume panmictic regional stocks, we strongly recommend that the results presented here be considered in future stock assessments and conservation strategies.
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Affiliation(s)
- Natacha Nikolic
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France.,INRAE, Ecobiop, AQUA, Saint-Pée-sur-Nivelle, France.,ARBRE, Agence de Recherche pour la Biodiversité à la Réunion, Saint-Gilles, France
| | - Floriaan Devloo-Delva
- CSIRO Environment, Hobart, Tasmania, Australia.,School of Natural Sciences-Quantitative Marine Science, University of Tasmania, Hobart, Tasmania, Australia
| | - Diane Bailleul
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | - Ekaterina Noskova
- Computer Technologies Laboratory, ITMO University, St Petersburg, Russia
| | | | - Chrystelle Delord
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | - Philippe Borsa
- Institut de recherche pour le développement, UMR ENTROPIE, Montpellier, France
| | | | - Mohamad Hassan
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France.,Animal Production Department, Tishreen University, Latakia, Syria
| | - Amandine D Marie
- ARBRE, Agence de Recherche pour la Biodiversité à la Réunion, Saint-Gilles, France
| | | | - Peter Grewe
- CSIRO Environment, Hobart, Tasmania, Australia
| | | | | | | | | | - François Poisson
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | - Denham Parker
- Department of Forestry, Fisheries and the Environment, (DFFE), Cape Town, South Africa.,Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Agostino Leone
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | | | | | - Francis Marsac
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
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4
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Venney CJ, Cayuela H, Rougeux C, Laporte M, Mérot C, Normandeau E, Leitwein M, Dorant Y, Præbel K, Kenchington E, Clément M, Sirois P, Bernatchez L. Genome-wide DNA methylation predicts environmentally driven life history variation in a marine fish. Evolution 2023; 77:186-198. [PMID: 36622671 DOI: 10.1093/evolut/qpac028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/21/2022] [Accepted: 11/16/2022] [Indexed: 01/10/2023]
Abstract
Epigenetic modifications are thought to be one of the molecular mechanisms involved in plastic adaptive responses to environmental variation. However, studies reporting associations between genome-wide epigenetic changes and habitat-specific variations in life history traits (e.g., lifespan, reproduction) are still scarce, likely due to the recent application of methylome resequencing methods to non-model species. In this study, we examined associations between whole genome DNA methylation and environmentally driven life history variation in 2 lineages of a marine fish, the capelin (Mallotus villosus), from North America and Europe. In both lineages, capelin harbor 2 contrasting life history tactics (demersal vs. beach-spawning). Performing whole genome and methylome sequencing, we showed that life history tactics are associated with epigenetic changes in both lineages, though the effect was stronger in European capelin. Genetic differentiation between the capelin harboring different life history tactics was negligible, but we found genome-wide methylation changes in both lineages. We identified 9,125 European and 199 North American differentially methylated regions (DMRs) due to life history. Gene ontology (GO) enrichment analysis for both lineages revealed an excess of terms related to neural function. Our results suggest that environmental variation causes important epigenetic changes that are associated with contrasting life history tactics in lineages with divergent genetic backgrounds, with variable importance of genetic variation in driving epigenetic variation. Our study emphasizes the potential role of genome-wide epigenetic variation in adaptation to environmental variation.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,University of Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Clément Rougeux
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Maëva Leitwein
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Kim Præbel
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ellen Kenchington
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial University of Newfoundland, St. John's, NL, Canada.,Labrador Institute, Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Pascal Sirois
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
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5
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Jasper RJ, McDonald TK, Singh P, Lu M, Rougeux C, Lind BM, Yeaman S. Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch. Mol Ecol Resour 2022; 22:2524-2533. [PMID: 35510784 PMCID: PMC9544674 DOI: 10.1111/1755-0998.13628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/11/2022] [Accepted: 03/29/2022] [Indexed: 11/28/2022]
Abstract
The use of next‐generation sequencing (NGS) data sets has increased dramatically over the last decade, but there have been few systematic analyses quantifying the accuracy of the commonly used variant caller programs. Here we used a familial design consisting of diploid tissue from a single lodgepole pine (Pinus contorta) parent and the maternally derived haploid tissue from 106 full‐sibling offspring, where mismatches could only arise due to mutation or bioinformatic error. Given the rarity of mutation, we used the rate of mismatches between parent and offspring genotype calls to infer the single nucleotide polymorphism (SNP) genotyping error rates of FreeBayes, HaplotypeCaller, SAMtools, UnifiedGenotyper, and VarScan. With baseline filtering HaplotypeCaller and UnifiedGenotyper yielded more SNPs and higher error rates by one to two orders of magnitude, whereas FreeBayes, SAMtools and VarScan yielded lower numbers of SNPs and more modest error rates. To facilitate comparison between variant callers we standardized each SNP set to the same number of SNPs using additional filtering, where UnifiedGenotyper consistently produced the smallest proportion of genotype errors, followed by HaplotypeCaller, VarScan, SAMtools, and FreeBayes. Additionally, we found that error rates were minimized for SNPs called by more than one variant caller. Finally, we evaluated the performance of various commonly used filtering metrics on SNP calling. Our analysis provides a quantitative assessment of the accuracy of five widely used variant calling programs and offers valuable insights into both the choice of variant caller program and the choice of filtering metrics, especially for researchers using non‐model study systems.
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Affiliation(s)
- Russ J Jasper
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | | | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,3EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Clément Rougeux
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Brandon M Lind
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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6
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Laporte M, Le Luyer J, Rougeux C, Dion-Côté AM, Krick M, Bernatchez L. DNA methylation reprogramming, TE derepression, and postzygotic isolation of nascent animal species. Sci Adv 2019; 5:eaaw1644. [PMID: 31663013 PMCID: PMC6795504 DOI: 10.1126/sciadv.aaw1644] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 09/19/2019] [Indexed: 05/05/2023]
Abstract
The genomic shock hypothesis stipulates that the stress associated with divergent genome admixture can cause transposable element (TE) derepression, which could act as a postzygotic isolation mechanism. TEs affect gene structure, expression patterns, and chromosome organization and may have deleterious consequences when released. For these reasons, they are silenced by heterochromatin formation, which includes DNA methylation. Here, we show that a significant proportion of TEs are differentially methylated between the "dwarf" (limnetic) and the "normal" (benthic) whitefish, two nascent species that diverged some 15,000 generations ago within the Coregonus clupeaformis species complex. Moreover, TEs are overrepresented among loci that were demethylated in hybrids, indicative of their transcriptional derepression. These results are consistent with earlier studies in this system that revealed TE transcriptional derepression causes abnormal embryonic development and death of hybrids. Hence, this supports a role of DNA methylation reprogramming and TE derepression in postzygotic isolation of nascent animal species.
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Rougeux C, Gagnaire P, Praebel K, Seehausen O, Bernatchez L. Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex. Mol Ecol 2019; 28:4388-4403. [DOI: 10.1111/mec.15226] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Clément Rougeux
- Département de biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec City QC Canada
| | | | - Kim Praebel
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Ole Seehausen
- Aquatic Ecology and Evolution Institute of Ecology & Evolution University of Bern Bern Switzerland
| | - Louis Bernatchez
- Département de biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec City QC Canada
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8
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Rougeux C, Gagnaire PA, Bernatchez L. Model-based demographic inference of introgression history in European whitefish species pairs'. J Evol Biol 2019; 32:806-817. [PMID: 31038776 DOI: 10.1111/jeb.13482] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/27/2019] [Accepted: 04/22/2019] [Indexed: 12/25/2022]
Abstract
Parallel phenotypic differentiation is generally attributed to parallel adaptive divergence as an evolutionary response to similar environmental contrasts. Such parallelism may actually originate from several evolutionary scenarios ranging from repeated parallel divergence caused by divergent selection to a unique divergence event followed by gene flow. Reconstructing the evolutionary history underlying parallel phenotypic differentiation is thus fundamental to understand the relative contribution of demography and selection on genomic divergence during speciation. In this study, we investigate the divergence history of replicate European whitefish (Coregonus lavaretus), limnetic and benthic species pairs from two lakes in Norway and two lakes in Switzerland. Demographic models accounting for semi-permeability and linked selection were fitted to the unfolded joint allele frequency spectrum built from genome-wide SNPs and compared to each other in each species pair. We found strong support for a model of asymmetrical post-glacial secondary contact between glacial lineages in all four lakes. Moreover, our results suggest that heterogeneous genomic differentiation has been shaped by the joint action of linked selection accelerating lineage sorting during allopatry, and heterogeneous migration eroding divergence at different rates along the genome following secondary contact. Our analyses reveal how the interplay between demography, selection and historical contingency has influenced the levels of diversity observed in previous whitefish phylogeographic studies. This study thus provides new insights into the historical demographic and selective processes that shaped the divergence associated with ecological speciation in European whitefish.
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Affiliation(s)
- Clément Rougeux
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Québec, Canada
| | | | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Québec, Canada
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9
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Rougeux C, Bernatchez L, Gagnaire PA. Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis). Genome Biol Evol 2018; 9:2057-2074. [PMID: 28903535 PMCID: PMC5737413 DOI: 10.1093/gbe/evx150] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2017] [Indexed: 02/07/2023] Open
Abstract
Parallel divergence across replicated species pairs occurring in similar environmental contrasts may arise through distinct evolutionary scenarios. Deciphering whether such parallelism actually reflects repeated parallel divergence driven by divergent selection or a single divergence event with subsequent gene flow needs to be ascertained. Reconstructing historical gene flow is therefore of fundamental interest to understand how demography and selection jointly shaped genomic divergence during speciation. Here, we use an extended modeling framework to explore the multiple facets of speciation-with-gene-flow with demo-genetic divergence models that capture both temporal and genomic variation in effective population size and migration rate. We investigate the divergence history of replicate sympatric species pairs of Lake Whitefish (normal benthic and dwarf limnetic) characterized by variable degrees of ecological divergence and reproductive isolation. Genome-wide SNPs were used to document the extent of genetic differentiation in each species pair, and 26 divergence models were fitted and compared with the unfolded joint allele frequency spectrum of each pair. We found evidence that a recent (circa 3,000–4,000 generations) asymmetrical secondary contact between expanding postglacial populations has accompanied Whitefish diversification. Our results suggest that heterogeneous genomic differentiation has emerged through the combined effects of linked selection generating variable rates of lineage sorting across the genome during geographical isolation, and heterogeneous introgression eroding divergence at different rates across the genome upon secondary contact. This study thus provides a new retrospective insight into the historical demographic and selective processes that shaped a continuum of divergence associated with ecological speciation.
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Affiliation(s)
- Clément Rougeux
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Pierre-Alexandre Gagnaire
- Université de Montpellier, Place Eugène Bataillon, France.,Institut des Sciences de l'Évolution de Montpellier-UMR 5554 UM-CNRS-IRD-EPHE, Place Eugène Bataillon, Montpellier, France
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10
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Hashemzadeh Segherloo I, Normandeau E, Benestan L, Rougeux C, Coté G, Moore JS, Ghaedrahmati N, Abdoli A, Bernatchez L. Genetic and morphological support for possible sympatric origin of fish from subterranean habitats. Sci Rep 2018; 8:2909. [PMID: 29440653 PMCID: PMC5811452 DOI: 10.1038/s41598-018-20666-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 01/16/2018] [Indexed: 11/09/2022] Open
Abstract
Two blind Iran cave barbs, Garra typhlops and Garra lorestanensis, exist in sympatry in a single subterranean habitat, raising the hypothesis that they may represent a case of sympatric speciation following a colonization event. Their different mental disc forms have prompted some authors to propose the alternative hypothesis of two separate colonization events. In this study, we analysed a genome-wide panel of 11,257 SNPs genotyped by means of genotyping-by-sequencing combined with mitochondrial cytochrome c oxidase sub-unit I sequence data, field observations and morphological traits to test these two hypotheses. Field data suggest some degree of ecological divergence despite some possible niche overlap such that hybridization is possible. According to both nuclear and mtDNA data, the cave barb species are monophyletic with close phylogenetic relationships with Garra gymnothorax from the Karun-Dez and Karkheh river basins. The historical demography analysis revealed that a model of Isolation-with-Migration (IM) best fitted the data, therefore better supporting a scenario of sympatric origin than that of allopatric isolation followed by secondary contact. Overall, our results offer stronger support to the hypothesis that speciation in the subterranean habitat could have occurred in sympatry following a colonization event from the Karun-Dez-Karkheh basins in the Zagros Mountains of Iran.
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Affiliation(s)
- Iraj Hashemzadeh Segherloo
- Department of Fisheries and Environmental Sciences, Faculty of Natural Resources and Earth Sciences, Shahr-e-Kord University, Shahr-e-Kord, P. B. 115, Iran.
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Laura Benestan
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Clément Rougeux
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Guillaume Coté
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Jean-Sébastien Moore
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| | | | - Asghar Abdoli
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research center, Shahid Beheshti University, Tehran, Iran
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
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11
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Benestan L, Moore JS, Sutherland BJG, Le Luyer J, Maaroufi H, Rougeux C, Normandeau E, Rycroft N, Atema J, Harris LN, Tallman RF, Greenwood SJ, Clark FK, Bernatchez L. Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems. Mol Ecol 2017; 26:6767-6783. [DOI: 10.1111/mec.14217] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/23/2017] [Accepted: 03/29/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Laura Benestan
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jean-Sébastien Moore
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Ben J. G. Sutherland
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jérémy Le Luyer
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Clément Rougeux
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Eric Normandeau
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | | | - Jelle Atema
- Department of Biology; Boston University; Boston MA USA
| | - Les N. Harris
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Ross F. Tallman
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Spencer J. Greenwood
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Fraser K. Clark
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Louis Bernatchez
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
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12
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Dalziel AC, Laporte M, Rougeux C, Guderley H, Bernatchez L. Convergence in organ size but not energy metabolism enzyme activities among wild Lake Whitefish (Coregonus clupeaformis) species pairs. Mol Ecol 2016; 26:225-244. [DOI: 10.1111/mec.13847] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/31/2016] [Accepted: 09/06/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Anne C. Dalziel
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
- Department of Biology; Saint Mary's University; 923 Robie Street Halifax Nova Scotia Canada B3H 3C3
| | - Martin Laporte
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
| | - Clément Rougeux
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
| | - Helga Guderley
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
| | - Louis Bernatchez
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
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13
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Laporte M, Pavey SA, Rougeux C, Pierron F, Lauzent M, Budzinski H, Labadie P, Geneste E, Couture P, Baudrimont M, Bernatchez L. RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels. Mol Ecol 2015; 25:219-37. [DOI: 10.1111/mec.13466] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 11/06/2015] [Accepted: 11/06/2015] [Indexed: 12/14/2022]
Affiliation(s)
- M. Laporte
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
| | - S. A. Pavey
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- Institut National de la Recherche Scientifique (INRS); Centre Eau Terre et Environnement; 490, rue de la Couronne Québec QC G1K 9A9 Canada
- Department of Biology; University of New Brunswick; PO Box 5050 Saint-John NB E2L 4L5 Canada
| | - C. Rougeux
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
| | - F. Pierron
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - M. Lauzent
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - H. Budzinski
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - P. Labadie
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - E. Geneste
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - P. Couture
- Institut National de la Recherche Scientifique (INRS); Centre Eau Terre et Environnement; 490, rue de la Couronne Québec QC G1K 9A9 Canada
| | - M. Baudrimont
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - L. Bernatchez
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
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