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Zong SB, Li YL, Liu JX. Genomic Architecture of Rapid Parallel Adaptation to Fresh Water in a Wild Fish. Mol Biol Evol 2021; 38:1317-1329. [PMID: 33146383 PMCID: PMC8480189 DOI: 10.1093/molbev/msaa290] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. However, the genetic architecture underlying these adaptive changes is still poorly understood. Using population genomic approaches, we investigated the genomic architecture that underlies rapid parallel adaptation of Coilia nasus to fresh water by comparing four freshwater-resident populations with their ancestral anadromous population. Linkage disequilibrium network analysis and population genetic analyses revealed two putative large chromosome inversions on LG6 and LG22, which were enriched for outlier loci and exhibited parallel association with freshwater adaptation. Drastic frequency shifts and elevated genetic differentiation were observed for the two chromosome inversions among populations, suggesting that both inversions would undergo divergent selection between anadromous and resident ecotypes. Enrichment analysis of genes within chromosome inversions showed significant enrichment of genes involved in metabolic process, immunoregulation, growth, maturation, osmoregulation, and so forth, which probably underlay differences in morphology, physiology and behavior between the anadromous and freshwater-resident forms. The availability of beneficial standing genetic variation, large optimum shift between marine and freshwater habitats, and high efficiency of selection with large population size could lead to the observed rapid parallel adaptive genomic change. We propose that chromosomal inversions might have played an important role during the evolution of rapid parallel ecological divergence in the face of environmental heterogeneity in C. nasus. Our study provides insights into the genomic basis of rapid adaptation of complex traits in novel habitats and highlights the importance of structural genomic variants in analyses of ecological adaptation.
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Affiliation(s)
- Shao-Bing Zong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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52
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Distinct genetic clustering in the weakly differentiated polar cod, Boreogadus saida Lepechin, 1774 from East Siberian Sea to Svalbard. Polar Biol 2021. [DOI: 10.1007/s00300-021-02911-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractThe cold-adapted polar cod Boreogadus saida, a key species in Arctic ecosystems, is vulnerable to global warming and ice retreat. In this study, 1257 individuals sampled in 17 locations within the latitudinal range of 75–81°N from Svalbard to East Siberian Sea were genotyped with a dedicated suite of 116 single-nucleotide polymorphic loci (SNP). The overall pattern of isolation by distance (IBD) found was driven by the two easternmost samples (East Siberian Sea and Laptev Sea), whereas no differentiation was registered in the area between the Kara Sea and Svalbard. Eleven SNP under strong linkage disequilibrium, nine of which could be annotated to chromosome 2 in Atlantic cod, defined two genetic groups of distinct size, with the major cluster containing seven-fold larger number of individuals than the minor. No underlying geographic basis was evident, as both clusters were detected throughout all sampling sites in relatively similar proportions (i.e. individuals in the minor cluster ranging between 4 and 19% on the location basis). Similarly, females and males were also evenly distributed between clusters and age groups. A differentiation was, however, found regarding size at age: individuals belonging to the major cluster were significantly longer in the second year. This study contributes to increasing the population genetic knowledge of this species and suggests that an appropriate management should be ensured to safeguard its diversity.
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53
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The genomic basis of geographic differentiation and fiber improvement in cultivated cotton. Nat Genet 2021; 53:916-924. [PMID: 33859417 DOI: 10.1038/s41588-021-00844-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023]
Abstract
Large-scale genomic surveys of crop germplasm are important for understanding the genetic architecture of favorable traits. The genomic basis of geographic differentiation and fiber improvement in cultivated cotton is poorly understood. Here, we analyzed 3,248 tetraploid cotton genomes and confirmed that the extensive chromosome inversions on chromosomes A06 and A08 underlies the geographic differentiation in cultivated Gossypium hirsutum. We further revealed that the haplotypic diversity originated from landraces, which might be essential for understanding adaptative evolution in cultivated cotton. Introgression and association analyses identified new fiber quality-related loci and demonstrated that the introgressed alleles from two diploid cottons had a large effect on fiber quality improvement. These loci provided the potential power to overcome the bottleneck in fiber quality improvement. Our study uncovered several critical genomic signatures generated by historical breeding effects in cotton and a wealth of data that enrich genomic resources for the research community.
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54
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Villoutreix R, Ayala D, Joron M, Gompert Z, Feder JL, Nosil P. Inversion breakpoints and the evolution of supergenes. Mol Ecol 2021; 30:2738-2755. [PMID: 33786937 PMCID: PMC7614923 DOI: 10.1111/mec.15907] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/04/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The coexistence of discrete morphs that differ in multiple traits is common within natural populations of many taxa. Such morphs are often associated with chromosomal inversions, presumably because the recombination suppressing effects of inversions help maintain alternate adaptive combinations of alleles across the multiple loci affecting these traits. However, inversions can also harbour selected mutations at their breakpoints, leading to their rise in frequency in addition to (or independent from) their role in recombination suppression. In this review, we first describe the different ways that breakpoints can create mutations. We then critically examine the evidence for the breakpoint-mutation and recombination suppression hypotheses for explaining the existence of discrete morphs associated with chromosomal inversions. We find that the evidence that inversions are favoured due to recombination suppression is often indirect. The evidence that breakpoints harbour mutations that are adaptive is also largely indirect, with the characterization of inversion breakpoints at the sequence level being incomplete in most systems. Direct tests of the role of suppressed recombination and breakpoint mutations in inversion evolution are thus needed. Finally, we emphasize how the two hypotheses of recombination suppression and breakpoint mutation can act in conjunction, with implications for understanding the emergence of supergenes and their evolutionary dynamics. We conclude by discussing how breakpoint characterization could improve our understanding of complex, discrete phenotypic forms in nature.
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Affiliation(s)
- Romain Villoutreix
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| | - Diego Ayala
- UMR MIVEGEC, Univ. Montpellier, CNRS, IRD, 34934 Montpellier, France
| | - Mathieu Joron
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| | | | - Jeffrey L. Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame,
Indiana 46556, USA
| | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
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55
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Grummer JA, Whitlock MC, Schulte PM, Taylor EB. Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss). BMC Ecol Evol 2021; 21:63. [PMID: 33888062 PMCID: PMC8063319 DOI: 10.1186/s12862-021-01795-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
Background Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhynchus mykiss)—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence. Results Genomic divergence was high between sympatric insectivores and piscivores (\documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River (\documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.159) that are > 500 km apart. A window-based \documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST analysis did not reveal “islands” of genomic differentiation; however, the window with highest \documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs. Conclusion Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01795-9.
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Affiliation(s)
- Jared A Grummer
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.
| | - Michael C Whitlock
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Patricia M Schulte
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Eric B Taylor
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.,Beaty Biodiversity Museum, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
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56
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Le Moan A, Bekkevold D, Hemmer-Hansen J. Evolution at two time frames: ancient structural variants involved in post-glacial divergence of the European plaice (Pleuronectes platessa). Heredity (Edinb) 2021; 126:668-683. [PMID: 33531657 PMCID: PMC8115344 DOI: 10.1038/s41437-020-00389-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 01/30/2023] Open
Abstract
Changing environmental conditions can lead to population diversification through differential selection on standing genetic variation. Structural variant (SV) polymorphisms provide examples of ancient alleles that in time become associated with novel environmental gradients. The European plaice (Pleuronectes platessa) is a marine flatfish showing large allele-frequency differences at two putative SVs associated with environmental variation. In this study, we explored the contribution of these SVs to population structure across the North East Atlantic. We compared genome-wide population structure using sets of RAD-sequencing SNPs with the spatial structure of the SVs. We found that in contrast to the rest of the genome, the SVs were only weakly associated with an isolation-by-distance pattern. Indeed, both SVs showed important variation in haplogroup frequencies, with the same haplogroup increasing both along the salinity gradient of the Baltic Sea, and found in high frequency in the northern-range margin of the Atlantic. Phylogenetic analyses suggested that the SV alleles are much older than the age of the Baltic Sea itself. These results suggest that the SVs are older than the age of the environmental gradients with which they currently co-vary. Altogether, our results suggest that the plaice SVs were shaped by evolutionary processes occurring at two time frames, firstly following their origin, ancient spread and maintenance in the ancestral populations, and secondly related to their current association with more recently formed environmental gradients such as those found in the North Sea-Baltic Sea transition zone.
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Affiliation(s)
- Alan Le Moan
- grid.5170.30000 0001 2181 8870National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark ,grid.8761.80000 0000 9919 9582Department of Marine Sciences at Tjärnö, University of Gothenburg, Laboratorievägen 10, Strömstad, Sweden
| | - Dorte Bekkevold
- grid.5170.30000 0001 2181 8870National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - Jakob Hemmer-Hansen
- grid.5170.30000 0001 2181 8870National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
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57
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Puncher GN, Rowe S, Rose GA, Parent GJ, Wang Y, Pavey SA. Life-stage-dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod, Gadus morhua, from Canada's Northern cod stock region and adjacent areas. JOURNAL OF FISH BIOLOGY 2021; 98:817-828. [PMID: 33244791 DOI: 10.1111/jfb.14632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 06/11/2023]
Abstract
Among highly migratory fish species, nursery areas occupied by juveniles often differ from adult habitats. To better understand the spatial dynamics of Canada's Northern cod stock, juveniles caught off the east coast of Newfoundland and Labrador were compared to adults from the same region as well as individuals from other areas in Atlantic Canada using double-digest restriction site-associated DNA sequencing-derived single nucleotide polymorphisms. A reduced proportion of homozygotes with a chromosomal inversion located in linkage group 1 (LG1) was detected between juvenile and adult samples in the Northern cod stock region, potentially indicating age-dependent habitat use or ontogenetic selection for attributes associated with the many genes located in LG1. No selectively neutral genetic differences were found between samples from the Northern cod stock; nevertheless, significant differences were found between some of these samples and cod collected from St. Pierre Bank, Bay of Fundy, Browns Bank and the southern Scotian Shelf. Clustering analysis of variants at neutral loci provided evidence for three major genetic units: (a) the Newfoundland Atlantic Coast, (b) eastern and southern Gulf of St. Lawrence and Burgeo Bank and (c) the Bay of Fundy, Browns Bank and southern Scotian Shelf. Both adaptive and neutral population structure within the Northern cod stock should be considered by managers to promote demographic rebuilding of the stock.
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Affiliation(s)
- Gregory Neils Puncher
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, Canada
- Genomics Laboratory, Maurice-Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Canada
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St. John's, Canada
| | - Sherrylynn Rowe
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St. John's, Canada
| | - George A Rose
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, Canada
| | - Geneviève J Parent
- Genomics Laboratory, Maurice-Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Canada
| | - Yanjun Wang
- Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, Canada
| | - Scott A Pavey
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, Canada
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58
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Schneider K, White TJ, Mitchell S, Adams CE, Reeve R, Elmer KR. The pitfalls and virtues of population genetic summary statistics: Detecting selective sweeps in recent divergences. J Evol Biol 2020; 34:893-909. [DOI: 10.1111/jeb.13738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Kevin Schneider
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Tom J. White
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Sonia Mitchell
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Colin E. Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
- Scottish Centre for Ecology and the Natural Environment Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Richard Reeve
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
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59
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Longo GC, Lam L, Basnett B, Samhouri J, Hamilton S, Andrews K, Williams G, Goetz G, McClure M, Nichols KM. Strong population differentiation in lingcod ( Ophiodon elongatus) is driven by a small portion of the genome. Evol Appl 2020; 13:2536-2554. [PMID: 33294007 PMCID: PMC7691466 DOI: 10.1111/eva.13037] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
Delimiting intraspecific genetic variation in harvested species is crucial to the assessment of population status for natural resource management and conservation purposes. Here, we evaluated genetic population structure in lingcod (Ophiodon elongatus), a commercially and recreationally important fishery species along the west coast of North America. We used 16,749 restriction site-associated DNA sequencing (RADseq) markers, in 611 individuals collected from across the bulk of the species range from Southeast Alaska to Baja California, Mexico. In contrast to previous population genetic work on this species, we found strong evidence for two distinct genetic clusters. These groups separated latitudinally with a break near Point Reyes off Northern California, and there was a high frequency of admixed individuals in close proximity to the break. F-statistics corroborate this genetic break between northern and southern sampling sites, although most loci are characterized by low FST values, suggesting high gene flow throughout most of the genome. Outlier analyses identified 182 loci putatively under divergent selection, most of which mapped to a single genomic region. When individuals were grouped by cluster assignment (northern, southern, and admixed), 71 loci were fixed between the northern and southern cluster, all of which were identified in the outlier scans. All individuals identified as admixed exhibited near 50:50 assignment to northern and southern clusters and were heterozygous for most fixed loci. Alignments of RADseq loci to a draft lingcod genome assembly and three other teleost genomes with chromosome-level assemblies suggest that outlier and fixed loci are concentrated on a single chromosome. Similar genomic patterns have been attributed to chromosomal inversions in diverse taxonomic groups. Regardless of the evolutionary mechanism, these results represent novel observations of genetic structure in lingcod and designate clear evolutionary units that could be used to inform fisheries management.
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Affiliation(s)
- Gary C. Longo
- NRC Research Associateship ProgramNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Laurel Lam
- Pacific States Marine Fisheries CommissionUnder contract to Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
- Moss Landing Marine LaboratoriesMoss LandingCAUSA
| | | | - Jameal Samhouri
- Conservation Biology DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | | | - Kelly Andrews
- Conservation Biology DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Greg Williams
- Pacific States Marine Fisheries CommissionUnder contract to Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Giles Goetz
- UWJISAOUnder contract to Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Michelle McClure
- Fisheries Resource Analysis and Monitoring DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
- Pacific Marine Environmental LaboratoryNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Krista M. Nichols
- Conservation Biology DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
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60
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Johansen T, Besnier F, Quintela M, Jorde PE, Glover KA, Westgaard J, Dahle G, Lien S, Kent MP. Genomic analysis reveals neutral and adaptive patterns that challenge the current management regime for East Atlantic cod Gadus morhua L. Evol Appl 2020; 13:2673-2688. [PMID: 33294016 PMCID: PMC7691467 DOI: 10.1111/eva.13070] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 01/03/2023] Open
Abstract
Challenging long-held perceptions of fish management units can help to protect vulnerable stocks. When a fishery consisting of multiple genetic stocks is managed as a single unit, overexploitation and depletion of minor genetic units can occur. Atlantic cod (Gadus morhua) is an economically and ecologically important marine species across the North Atlantic. The application of new genomic resources, including SNP arrays, allows us to detect and explore novel structure within specific cod management units. In Norwegian waters, coastal cod (i.e. those not undertaking extensive migrations) are divided into two arbitrary management units defined by ICES: one between 62° and 70°N (Norwegian coastal cod; NCC) and one between 58° and 62°N (Norwegian coastal south; NCS). Together, these capture a fishery area of >25,000 km2 containing many spawning grounds. To assess whether these geographic units correctly represent genetic stocks, we analysed spawning cod of NCC and NCS for more than 8,000 SNPs along with samples of Russian White Sea cod, north-east Arctic cod (NEAC: the largest Atlantic stock), and outgroup samples representing the Irish and Faroe Sea's. Our analyses revealed large differences in spatial patterns of genetic differentiation across the genome and revealed a complex biological structure within NCC and NCS. Haplotype maps from four chromosome sets show regional specific SNP indicating a complex genetic structure. The current management plan dividing the coastal cod into only two management units does not accurately reflect the genetic units and needs to be revised. Coastal cod in Norway, while highly heterogenous, is also genetically distinct from neighbouring stocks in the north (NEAC), west (Faroe Island) and the south. The White Sea cod are highly divergent from other cod, possibly yielding support to the earlier notion of subspecies rank.
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Affiliation(s)
| | | | | | | | - Kevin A. Glover
- Institute of Marine Research (IMR)BergenNorway
- Department of BiologyUniversity of BergenBergenNorway
| | | | - Geir Dahle
- Institute of Marine Research (IMR)BergenNorway
- Department of BiologyUniversity of BergenBergenNorway
| | - Sigbjørn Lien
- Department of Animal and Aquaculture SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Matthew P. Kent
- Department of Animal and Aquaculture SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
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61
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Tepolt CK, Palumbi SR. Rapid Adaptation to Temperature via a Potential Genomic Island of Divergence in the Invasive Green Crab, Carcinus maenas. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.580701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Widespread species often adapt easily to novel conditions – both those found in new habitats and those generated by climate change. However, rapid adaptation may be hindered in the marine realm, where long-distance dispersal and consequently high gene flow are predicted to limit potential for local adaptation. Here, we use a highly dispersive invasive marine crab to test the nature and speed of adaptation to temperature in the sea. Using single nucleotide polymorphisms (SNPs) generated from cardiac transcriptome sequencing, we characterized six populations of the European green crab (Carcinus maenas) located across parallel thermal gradients in their native and invasive ranges. We compared SNP frequencies with local temperatures and previously generated data on cardiac heat and cold tolerance to identify candidate markers associated with population-level differences in thermal physiology. Of 10,790 SNPs, 104 were identified as frequency outliers, a signal that was strongly driven by association with temperature and/or cold tolerance. Seventy-two of these outlier markers, representing 28 different genes, were in a cluster of SNPs identified as a potential inversion polymorphism using linkage disequilibrium network analysis. This SNP cluster was unique in the data set, which was otherwise characterized by low levels of linkage disequilibrium, and markers in this cluster showed a significant enrichment of coding substitutions relative to the full SNP set. These 72 outlier SNPs appear to be transmitted as a unit, and represent a putative genomic island of divergence which varied in frequency with organismal cold tolerance. This relationship was strikingly similar across both native and invasive populations, all of which showed a very strong correlation with cold tolerance (R2 = 0.96 over all six populations). Notably, three of these populations have diverged recently (<100 years) and show little to no neutral divergence, suggesting that this genomic region may be responding to temperature on a relatively short time scale. This relationship indicates adaptation to temperature based on the action of a putative genomic island of divergence, perhaps partially explaining the extraordinary invasive ability of this species.
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62
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Johannesson K, Le Moan A, Perini S, André C. A Darwinian Laboratory of Multiple Contact Zones. Trends Ecol Evol 2020; 35:1021-1036. [DOI: 10.1016/j.tree.2020.07.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
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63
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Jansson E, Besnier F, Malde K, André C, Dahle G, Glover KA. Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations. BMC Genet 2020; 21:118. [PMID: 33036553 PMCID: PMC7547435 DOI: 10.1186/s12863-020-00921-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
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Affiliation(s)
- Eeva Jansson
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Francois Besnier
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Ketil Malde
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Geir Dahle
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.,Institute of Biology, University of Bergen, P. O. Box 7803, 5020, Bergen, Norway
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64
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Otterå H, Johansen T, Folkvord A, Dahle G, Solvang Bingh MK, Westgaard JI, Glover KA. The pantophysin gene and its relationship with survival in early life stages of Atlantic cod. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191983. [PMID: 33204437 PMCID: PMC7657904 DOI: 10.1098/rsos.191983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Genetic markers are widely used in fisheries management around the world. While the genetic structure and markers selected are usually based on samples from the wild, very few controlled experiments have been carried out to investigate possible differences in influence on traits between markers. Here we examine the bi-allelic gene pantophysin (Pan I), widely used in the management of Atlantic cod, in a series of in vitro crosses under a range of temperatures. It has been proposed that this gene, or another tightly linked gene, may be under strong divergent selection. Resolving this issue is essential in order to interpret results when using this gene marker for stock management. We found no evidence of departure from the expected 1 : 2 : 1 Mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12°C temperature regimes in tank experiments favoured the survival of the Pan IAA genotype. No difference in genotype survival was, however, found in a more natural mesocosm environment. Collectively, these results suggest that for the early life stages of Atlantic cod, and under the current experimental conditions, there is no strong consistent influence of Pan I genotype on survival. The results also emphasize the importance of varied experimental studies to verify the importance of environmental factors influencing genotype selection.
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Affiliation(s)
- Håkon Otterå
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
| | - Torild Johansen
- Institute of Marine Research, Tromsø Division, Framsenteret 9296 Tromsø, Norway
| | - Arild Folkvord
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
- Department of Biological Sciences, University of Bergen, Thormøhlensgt. 53, 5020Bergen
| | - Geir Dahle
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
| | | | - Jon-Ivar Westgaard
- Institute of Marine Research, Tromsø Division, Framsenteret 9296 Tromsø, Norway
| | - Kevin A. Glover
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
- Department of Biological Sciences, University of Bergen, Thormøhlensgt. 53, 5020Bergen
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65
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A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea. G3-GENES GENOMES GENETICS 2020; 10:2903-2910. [PMID: 32641450 PMCID: PMC7466986 DOI: 10.1534/g3.120.401423] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. The genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig length of 686 Mb with an N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize, to an extent not previously reported large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a 'southern' cod population which is complementary to the existing 'northern' population based genome assemblies and represents the first step toward developing pan-genomic resources for Atlantic cod.
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66
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Quintela M, Kvamme C, Bekkevold D, Nash RDM, Jansson E, Sørvik AG, Taggart JB, Skaala Ø, Dahle G, Glover KA. Genetic analysis redraws the management boundaries for the European sprat. Evol Appl 2020; 13:1906-1922. [PMID: 32908594 PMCID: PMC7463317 DOI: 10.1111/eva.12942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 02/03/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
Sustainable fisheries management requires detailed knowledge of population genetic structure. The European sprat is an important commercial fish distributed from Morocco to the Arctic circle, Baltic, Mediterranean, and Black seas. Prior to 2018, annual catch advice on sprat from the International Council for the Exploration of the Sea (ICES) was based on five putative stocks: (a) North Sea, (b) Kattegat-Skagerrak and Norwegian fjords, (c) Baltic Sea, (d) West of Scotland-southern Celtic Seas, and (e) English Channel. However, there were concerns that the sprat advice on stock size estimates management plan inadequately reflected the underlying biological units. Here, we used ddRAD sequencing to develop 91 SNPs that were thereafter used to genotype approximately 2,500 fish from 40 locations. Three highly distinct and relatively homogenous genetic groups were identified: (a) Norwegian fjords; (b) Northeast Atlantic including the North Sea, Kattegat-Skagerrak, Celtic Sea, and Bay of Biscay; and (c) Baltic Sea. Evidence of genetic admixture and possibly physical mixing was detected in samples collected from the transition zone between the North and Baltic seas, but not between any of the other groups. These results have already been implemented by ICES with the decision to merge the North Sea and the Kattegat-Skagerrak sprat to be assessed as a single unit, thus demonstrating that genetic data can be rapidly absorbed to align harvest regimes and biological units.
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Affiliation(s)
| | | | - Dorte Bekkevold
- DTU-Aqua National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark
| | | | | | | | - John B Taggart
- Institute of Aquaculture School of Natural Sciences University of Stirling Stirling UK
| | | | - Geir Dahle
- Institute of Marine Research Bergen Norway
| | - Kevin A Glover
- Institute of Marine Research Bergen Norway
- Institute of Biology University of Bergen Bergen Norway
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67
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Arsenault SV, King JT, Kay S, Lacy KD, Ross KG, Hunt BG. Simple inheritance, complex regulation: Supergene-mediated fire ant queen polymorphism. Mol Ecol 2020; 29:3622-3636. [PMID: 32749006 DOI: 10.1111/mec.15581] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 07/03/2020] [Accepted: 07/18/2020] [Indexed: 12/17/2022]
Abstract
The fire ant Solenopsis invicta exists in two alternate social forms: monogyne nests contain a single reproductive queen and polygyne nests contain multiple reproductive queens. This colony-level social polymorphism corresponds with individual differences in queen physiology, queen dispersal patterns and worker discrimination behaviours, all evidently regulated by an inversion-based supergene that spans more than 13 Mb of a "social chromosome," contains over 400 protein-coding genes and rarely undergoes recombination. The specific mechanisms by which this supergene influences expression of the many distinctive features that characterize the alternate forms remain almost wholly unknown. To advance our understanding of these mechanisms, we explore the effects of social chromosome genotype and natal colony social form on gene expression in queens sampled as they embarked on nuptial flights, using RNA-sequencing of brains and ovaries. We observe a large effect of natal social form, that is, of the social/developmental environment, on gene expression profiles, with similarly substantial effects of genotype, including: (a) supergene-associated gene upregulation, (b) allele-specific expression and (c) pronounced extra-supergene trans-regulatory effects. These findings, along with observed spatial variation in differential and allele-specific expression within the supergene region, highlight the complex gene regulatory landscape that emerged following divergence of the inversion-mediated Sb haplotype from its homologue, which presumably largely retained the ancestral gene order. The distinctive supergene-associated gene expression trajectories we document at the onset of a queen's reproductive life expand the known record of relevant molecular correlates of a complex social polymorphism and point to putative genetic factors underpinning the alternate social syndromes.
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Affiliation(s)
| | - Joanie T King
- Department of Entomology, University of Georgia, Athens, GA, USA.,Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Sasha Kay
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Kip D Lacy
- Department of Entomology, University of Georgia, Athens, GA, USA.,Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - Kenneth G Ross
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Athens, GA, USA
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68
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Oomen RA, Kuparinen A, Hutchings JA. Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change. J Hered 2020; 111:319-332. [PMID: 32620014 PMCID: PMC7423069 DOI: 10.1093/jhered/esaa020] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/25/2020] [Indexed: 12/26/2022] Open
Abstract
Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modeling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multilocus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.
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Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
| | - Anna Kuparinen
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Jeffrey A Hutchings
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
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69
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Junker J, Rick JA, McIntyre PB, Kimirei I, Sweke EA, Mosille JB, Wehrli B, Dinkel C, Mwaiko S, Seehausen O, Wagner CE. Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines. Mol Ecol 2020; 29:3277-3298. [PMID: 32687665 DOI: 10.1111/mec.15559] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 01/03/2023]
Abstract
Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced-representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika's two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex-specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large chromosomal rearrangement in L. miodon, creating two homokaryotypes and one heterokaryotype. We found all karyotypes throughout Lake Tanganyika, but the frequencies vary along a north-south gradient and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation by distance, even over the hundreds of kilometres covered by our sampling, but we do find shallow population structure.
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Affiliation(s)
- Julian Junker
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
| | - Jessica A Rick
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Peter B McIntyre
- Department of Natural Resources, Cornell University, Ithaca, NY, USA
| | - Ismael Kimirei
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Emmanuel A Sweke
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania.,Deep Sea Fishing Authority (DSFA), Zanzibar, Tanzania
| | - Julieth B Mosille
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Bernhard Wehrli
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zürich, Switzerland
| | - Christian Dinkel
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Salome Mwaiko
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
| | - Catherine E Wagner
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, WY, USA
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70
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Wenne R, Bernaś R, Kijewska A, Poćwierz-Kotus A, Strand J, Petereit C, Plauška K, Sics I, Árnyasi M, Kent MP. SNP genotyping reveals substructuring in weakly differentiated populations of Atlantic cod (Gadus morhua) from diverse environments in the Baltic Sea. Sci Rep 2020; 10:9738. [PMID: 32546719 PMCID: PMC7298039 DOI: 10.1038/s41598-020-66518-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/11/2020] [Indexed: 01/02/2023] Open
Abstract
Atlantic cod (Gadus morhua) is one of the most important fish species in northern Europe for several reasons including its predator status in marine ecosystems, its historical role in fisheries, its potential in aquaculture and its strong public profile. However, due to over-exploitation in the North Atlantic and changes in the ecosystem, many cod populations have been reduced in size and genetic diversity. Cod populations in the Baltic Proper, Kattegat and North Sea have been analyzed using a species specific single nucleotide polymorphism (SNP) array. Using a subset of 8,706 SNPs, moderate genetic differences were found between subdivisions in three traditionally delineated cod management stocks: Kattegat, western and eastern Baltic. However, an FST measure of population differentiation based on allele frequencies from 588 outlier loci for 2 population groups, one including 5 western and the other 4 eastern Baltic populations, indicated high genetic differentiation. In this paper, differentiation has been demonstrated not only between, but also within western and eastern Baltic cod stocks for the first time, with salinity appearing to be the most important environmental factor influencing the maintenance of cod population divergence between the western and eastern Baltic Sea.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland.
| | - Rafał Bernaś
- Department of Migratory Fishes in Rutki, Inland Fisheries Institute, Olsztyn, 10-719, Poland
| | - Agnieszka Kijewska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Anita Poćwierz-Kotus
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Jakob Strand
- Arctic Research Centre, Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Christoph Petereit
- GEOMAR, Helmholtz Centre for Ocean Research Kiel, Research Division 3: Marine Ecology, Research Unit: Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105, Kiel, Germany
- Bruno-Lorenzen-Schule Schleswig, Spielkoppel 6, 24837, Schleswig, Germany
| | - Kęstas Plauška
- Fisheries Service under the Ministry of Agriculture Division of Fisheries Research & Science, Smiltynes 1, 91001, Klaipeda, Lithuania
| | - Ivo Sics
- Institute of Food Safety, Animal Health and Environment "BIOR", Riga, Latvia
| | - Mariann Árnyasi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Norwegian University of Life Sciences (NMBU), PO Box, 5003, Aas, Norway
| | - Matthew P Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Norwegian University of Life Sciences (NMBU), PO Box, 5003, Aas, Norway
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71
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Huang K, Andrew RL, Owens GL, Ostevik KL, Rieseberg LH. Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype. Mol Ecol 2020; 29:2535-2549. [PMID: 32246540 DOI: 10.1111/mec.15428] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022]
Abstract
Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencing data and newly developed population genomic approaches to identify putative inversions that differentiate a sand dune ecotype of the prairie sunflower (Helianthus petiolaris) from populations found on the adjacent sand sheet. We detected seven large genomic regions that exhibit a different population structure than the rest of the genome and that vary in frequency between dune and nondune populations. These regions also show high linkage disequilibrium and high heterozygosity between, but not within, arrangements, consistent with the behaviour of large inversions, an inference subsequently validated in part by comparative genetic mapping. Genome-environment association analyses show that key environmental variables, including vegetation cover and soil nitrogen, are significantly associated with inversions. The inversions colocate with previously described "islands of differentiation," and appear to play an important role in adaptive divergence and incipient speciation within H. petiolaris.
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Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Rose L Andrew
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Gregory L Owens
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Kate L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Biology, Duke University, Durham, NC, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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72
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Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes. Appl Environ Microbiol 2020; 86:AEM.02788-19. [PMID: 31953333 PMCID: PMC7054092 DOI: 10.1128/aem.02788-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
Abstract
The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation. The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we used metagenomic shotgun sequencing of individual specimens to compare the levels of intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) that have distinct behavior and habitats and three Gadidae species that occupy a range of ecological niches. Interestingly, we found significantly diverged microbiomes among the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species’ comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet, or a combination thereof, comprise major drivers of the intestinal community composition of codfishes. IMPORTANCE The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.
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73
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Kess T, Bentzen P, Lehnert SJ, Sylvester EVA, Lien S, Kent MP, Sinclair‐Waters M, Morris C, Wringe B, Fairweather R, Bradbury IR. Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish. Ecol Evol 2020; 10:638-653. [PMID: 32015832 PMCID: PMC6988541 DOI: 10.1002/ece3.5828] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023] Open
Abstract
Genomic architecture and standing variation can play a key role in ecological adaptation and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behavior in regional analyses. However, the degree of parallelism, the extent of independent inheritance, and functional distinctiveness of these rearrangements remain poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangements with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures, has likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.
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Affiliation(s)
- Tony Kess
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Paul Bentzen
- Biology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Sarah J. Lehnert
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Emma V. A. Sylvester
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Sigbjørn Lien
- Department of Animal and Aquacultural SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Matthew P. Kent
- Department of Animal and Aquacultural SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Marion Sinclair‐Waters
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
| | - Corey Morris
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Brendan Wringe
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | | | - Ian R. Bradbury
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Biology DepartmentDalhousie UniversityHalifaxNSCanada
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74
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Clucas GV, Lou RN, Therkildsen NO, Kovach AI. Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole-genome sequencing. Evol Appl 2019; 12:1971-1987. [PMID: 31700539 PMCID: PMC6824067 DOI: 10.1111/eva.12861] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 06/14/2019] [Accepted: 07/12/2019] [Indexed: 12/21/2022] Open
Abstract
Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome-wide patterns of variation, we used low-coverage sequencing to perform a region-wide, whole-genome analysis of fine-scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole-genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter- and spring-spawning populations revealed highly elevated relative (FST ) and absolute (dxy ) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain-pituitary-gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high-resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome-scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.
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Affiliation(s)
- Gemma V. Clucas
- Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - R. Nicolas Lou
- Department of Natural ResourcesCornell UniversityIthacaNYUSA
| | | | - Adrienne I. Kovach
- Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
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75
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Rodríguez-Ramilo ST, Baranski M, Moghadam H, Grove H, Lien S, Goddard ME, Meuwissen THE, Sonesson AK. Strong selection pressures maintain divergence on genomic islands in Atlantic cod (Gadus morhua L.) populations. Genet Sel Evol 2019; 51:61. [PMID: 31664896 PMCID: PMC6819574 DOI: 10.1186/s12711-019-0503-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/16/2019] [Indexed: 11/15/2022] Open
Abstract
Background Two distinct populations have been extensively studied in Atlantic cod (Gadus morhua L.): the Northeast Arctic cod (NEAC) population and the coastal cod (CC) population. The objectives of the current study were to identify genomic islands of divergence and to propose an approach to quantify the strength of selection pressures using whole-genome single nucleotide polymorphism (SNP) data. After applying filtering criteria, information on 93 animals (9 CC individuals, 50 NEAC animals and 34 CC × NEAC crossbred individuals) and 3,123,434 autosomal SNPs were used. Results Four genomic islands of divergence were identified on chromosomes 1, 2, 7 and 12, which were mapped accurately based on SNP data and which extended in size from 11 to 18 Mb. These regions differed considerably between the two populations although the differences in the rest of the genome were small due to considerable gene flow between the populations. The estimates of selection pressures showed that natural selection was substantially more important than genetic drift in shaping these genomic islands. Our data confirmed results from earlier publications that suggested that genomic islands are due to chromosomal rearrangements that are under strong selection and reduce recombination between rearranged and non-rearranged segments. Conclusions Our findings further support the hypothesis that selection and reduced recombination in genomic islands may promote speciation between these two populations although their habitats overlap considerably and migrations occur between them.
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Affiliation(s)
- Silvia T Rodríguez-Ramilo
- GenPhySE, INRA, 24 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France. .,Departamento de Mejora Genética Animal, INIA, Crta. A Coruña Km. 7,5, Madrid, 28040, Spain.
| | - Matthew Baranski
- NOFIMA Marine, Osloveien 1, Ås, 1430, Norway.,Mowi ASA, Sandviksboder 77AB, Bergen, 5035, Norway
| | - Hooman Moghadam
- NOFIMA Marine, Osloveien 1, Ås, 1430, Norway.,Salmobreed, Sandviksboder 3A, Bergen, 5035, Norway
| | - Harald Grove
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Arboretveien 6, Ås, 1430, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Arboretveien 6, Ås, 1430, Norway
| | - Mike E Goddard
- Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia.,Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Theo H E Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Arboretveien 6, Ås, 1430, Norway
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76
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Refoyo-Martínez A, da Fonseca RR, Halldórsdóttir K, Árnason E, Mailund T, Racimo F. Identifying loci under positive selection in complex population histories. Genome Res 2019; 29:1506-1520. [PMID: 31362936 PMCID: PMC6724678 DOI: 10.1101/gr.246777.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 07/23/2019] [Indexed: 12/24/2022]
Abstract
Detailed modeling of a species' history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method-called graph-aware retrieval of selective sweeps (GRoSS)-has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.
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Affiliation(s)
- Alba Refoyo-Martínez
- Lundbeck GeoGenetics Centre, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1350, Denmark
| | - Rute R da Fonseca
- Centre for Macroecology, Evolution and Climate, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copehnagen 2100, Denmark
| | - Katrín Halldórsdóttir
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík 107, Iceland
| | - Einar Árnason
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík 107, Iceland
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1350, Denmark
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77
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Saenko SV, Chouteau M, Piron-Prunier F, Blugeon C, Joron M, Llaurens V. Unravelling the genes forming the wing pattern supergene in the polymorphic butterfly Heliconius numata. EvoDevo 2019; 10:16. [PMID: 31406559 PMCID: PMC6686539 DOI: 10.1186/s13227-019-0129-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/12/2019] [Indexed: 11/25/2022] Open
Abstract
Background Unravelling the genetic basis of polymorphic characters is central to our understanding of the origins and diversification of living organisms. Recently, supergenes have been implicated in a wide range of complex polymorphisms, from adaptive colouration in butterflies and fish to reproductive strategies in birds and plants. The concept of a supergene is now a hot topic in biology, and identification of its functional elements is needed to shed light on the evolution of highly divergent adaptive traits. Here, we apply different gene expression analyses to study the supergene P that controls polymorphism of mimetic wing colour patterns in the neotropical butterfly Heliconius numata. Results We performed de novo transcriptome assembly and differential expression analyses using high-throughput Illumina RNA sequencing on developing wing discs of different H. numata morphs. Within the P interval, 30 and 17 of the 191 transcripts were expressed differentially in prepupae and day-1 pupae, respectively. Among these is the gene cortex, known to play a role in wing pattern formation in Heliconius and other Lepidoptera. Our in situ hybridization experiments confirmed the relationship between cortex expression and adult wing patterns. Conclusions This study found the majority of genes in the P interval to be expressed in the developing wing discs during the critical stages of colour pattern formation, and detect drastic changes in expression patterns in multiple genes associated with structural variants. The patterns of expression of cortex only partially recapitulate the variation in adult phenotype, suggesting that the remaining phenotypic variation could be controlled by other genes within the P interval. Although functional studies on cortex are now needed to determine its exact developmental role, our results are in accordance with the classical supergene hypothesis, whereby several genes inherited together due to tight linkage control a major developmental switch. Electronic supplementary material The online version of this article (10.1186/s13227-019-0129-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suzanne V Saenko
- 1Institut de Systématique, Evolution et Biodiversité, UMR 7205 (CNRS, MNHN, Sorbonne Université, EPHE), Muséum National d'Histoire Naturelle CP50, 57 rue Cuvier, 75005 Paris, France
| | - Mathieu Chouteau
- 2Laboratoire Ecologie, Evolution, Interactions Des Systèmes Amazoniens (LEEISA), USR 3456, CNRS Guyane, Université De Guyane, 275 route de Montabo, 97334 Cayenne, French Guiana
| | - Florence Piron-Prunier
- 1Institut de Systématique, Evolution et Biodiversité, UMR 7205 (CNRS, MNHN, Sorbonne Université, EPHE), Muséum National d'Histoire Naturelle CP50, 57 rue Cuvier, 75005 Paris, France
| | - Corinne Blugeon
- Genomic Facility, Institut de Biologie de l'Ecole normale superieure (IBENS), École normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Mathieu Joron
- 4Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS-Université de Montpellier, École Pratique des Hautes Études, Université Paul Valéry, 34293 Montpellier 5, France
| | - Violaine Llaurens
- 1Institut de Systématique, Evolution et Biodiversité, UMR 7205 (CNRS, MNHN, Sorbonne Université, EPHE), Muséum National d'Histoire Naturelle CP50, 57 rue Cuvier, 75005 Paris, France
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78
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Weist P, Schade FM, Damerau M, Barth JMI, Dierking J, André C, Petereit C, Reusch T, Jentoft S, Hanel R, Krumme U. Assessing SNP-markers to study population mixing and ecological adaptation in Baltic cod. PLoS One 2019; 14:e0218127. [PMID: 31220098 PMCID: PMC6586271 DOI: 10.1371/journal.pone.0218127] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/27/2019] [Indexed: 02/01/2023] Open
Abstract
Atlantic cod (Gadus morhua) is a species of great ecological and economical importance in the Baltic Sea. Here, two genetically differentiated stocks, the western and the eastern Baltic cod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessments and management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Baltic cod stocks and to enable studies of local adaptation to the specific environment in the Baltic Sea, respectively. We tested both panels on cod sampled from the southern Baltic Sea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdańsk Deep, were exclusively composed of eastern Baltic cod, whereas catches from adjacent western areas (Belt Sea and Öresund) were composed of western Baltic cod. Interestingly, the two Baltic cod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species’ potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries management to further illuminate the mixing dynamics of cod in the Baltic Sea and to better understand Baltic cod ecology.
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Affiliation(s)
- Peggy Weist
- Thünen-Institute of Fisheries Ecology, Bremerhaven, Germany
- * E-mail:
| | | | - Malte Damerau
- Thünen-Institute of Fisheries Ecology, Bremerhaven, Germany
| | - Julia M. I. Barth
- Zoological Institute, University of Basel, Basel, Switzerland
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | | | | | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Reinhold Hanel
- Thünen-Institute of Fisheries Ecology, Bremerhaven, Germany
| | - Uwe Krumme
- Thünen-Institute of Baltic Sea Fisheries, Rostock, Germany
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79
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Miller AD, Hoffmann AA, Tan MH, Young M, Ahrens C, Cocomazzo M, Rattray A, Ierodiaconou DA, Treml E, Sherman CDH. Local and regional scale habitat heterogeneity contribute to genetic adaptation in a commercially important marine mollusc (
Haliotis rubra
) from southeastern Australia. Mol Ecol 2019; 28:3053-3072. [DOI: 10.1111/mec.15128] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/17/2019] [Accepted: 05/01/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Adam D. Miller
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
- Deakin Genomics Centre Deakin University Geelong Victoria Australia
| | - Ary A. Hoffmann
- School of BioSciences Bio21 Institute, The University of Melbourne Parkville Victoria Australia
| | - Mun Hua Tan
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
- Deakin Genomics Centre Deakin University Geelong Victoria Australia
| | - Mary Young
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Collin Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University Penrith New South Wales Australia
| | - Michael Cocomazzo
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Alex Rattray
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Daniel A. Ierodiaconou
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Eric Treml
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Craig D. H. Sherman
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
- Deakin Genomics Centre Deakin University Geelong Victoria Australia
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80
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Kess T, Bentzen P, Lehnert SJ, Sylvester EVA, Lien S, Kent MP, Sinclair-Waters M, Morris CJ, Regular P, Fairweather R, Bradbury IR. A migration-associated supergene reveals loss of biocomplexity in Atlantic cod. SCIENCE ADVANCES 2019; 5:eaav2461. [PMID: 31249864 PMCID: PMC6594766 DOI: 10.1126/sciadv.aav2461] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Chromosome structural variation may underpin ecologically important intraspecific diversity by reducing recombination within supergenes containing linked, coadapted alleles. Here, we confirm that an ancient chromosomal rearrangement is strongly associated with migratory phenotype and individual genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. We reconstruct trends in effective population size over the last century and reveal declines in effective population size matching onset of industrialized harvest (after 1950). We find different demographic trajectories between individuals homozygous for the chromosomal rearrangement relative to heterozygous or homozygous individuals for the noninverted haplotype, suggesting different selective histories across the past 150 years. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic, phenotypic, and demographic variation in a highly connected marine species and show how overfishing may have led to loss of biocomplexity within Northern cod stock.
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Affiliation(s)
- Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John’s, Newfoundland, Canada
| | - Paul Bentzen
- Biology Department, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sarah J. Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John’s, Newfoundland, Canada
| | - Emma V. A. Sylvester
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John’s, Newfoundland, Canada
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew P. Kent
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Marion Sinclair-Waters
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Corey J. Morris
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John’s, Newfoundland, Canada
| | - Paul Regular
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John’s, Newfoundland, Canada
| | | | - Ian R. Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John’s, Newfoundland, Canada
- Biology Department, Dalhousie University, Halifax, Nova Scotia, Canada
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81
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Clucas GV, Kerr LA, Cadrin SX, Zemeckis DR, Sherwood GD, Goethel D, Whitener Z, Kovach A. Adaptive genetic variation underlies biocomplexity of Atlantic Cod in the Gulf of Maine and on Georges Bank. PLoS One 2019; 14:e0216992. [PMID: 31125344 PMCID: PMC6534298 DOI: 10.1371/journal.pone.0216992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 05/02/2019] [Indexed: 12/15/2022] Open
Abstract
Atlantic cod (Gadus morhua) populations in the Gulf of Maine (GoM) are at a fraction of their historical abundance, creating economic hardships for fishermen and putting at risk the genetic diversity of the remaining populations. An understanding of the biocomplexity among GoM populations will allow for adaptive genetic diversity to be conserved to maximize the evolutionary potential and resilience of the fishery in a rapidly changing environment. We used restriction-site-associated DNA sequencing (RADseq) to characterize the population structure and adaptive genetic diversity of five spawning aggregations from the western GoM and Georges Bank. We also analyzed cod caught in the eastern GoM, an under-sampled area where spawning aggregations have been extirpated. Using 3,128 single nucleotide polymorphisms (SNPs), we confirmed the existence of three genetically separable spawning groups: (1) winter spawning cod from the western GoM, (2) spring spawning cod, also from the western GoM, and (3) Georges Bank cod. Non-spawning cod from the eastern GoM could not be decisively linked to either of the three spawning groups and may represent a unique component of the resource, a mixed sample, or cod from other unsampled source populations. The genetic differentiation among the three major spawning groups was primarily driven by loci putatively under selection, particularly loci in regions known to contain genomic inversions on linkage groups (LG) 7 and 12. These LGs have been found to be linked to thermal regime in cod across the Atlantic, and so it is possible that variation in timing of spawning in western GoM cod has resulted in temperature-driven adaptive divergence. This complex population structure and adaptive genetic differentiation could be crucial to ensuring the long-term productivity and resilience of the cod fishery, and so it should be considered in future management plans.
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Affiliation(s)
- G. V. Clucas
- Department of Natural Resources, University of New Hampshire, Durham, NH, United States of America
| | - L. A. Kerr
- Gulf of Maine Research Institute, Portland, ME, United States of America
| | - S. X. Cadrin
- School for Marine Science & Technology, University of Massachusetts Dartmouth, New Bedford, MA, United States of America
| | - D. R. Zemeckis
- Department of Agriculture and Natural Resources, Rutgers University, Toms River, NJ, United States of America
| | - G. D. Sherwood
- Gulf of Maine Research Institute, Portland, ME, United States of America
| | - D. Goethel
- F/V Ellen Diane, Hampton, NH, United States of America
| | - Z. Whitener
- Gulf of Maine Research Institute, Portland, ME, United States of America
| | - A.I. Kovach
- Department of Natural Resources, University of New Hampshire, Durham, NH, United States of America
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82
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Sävilammi T, Primmer CR, Varadharajan S, Guyomard R, Guiguen Y, Sandve SR, Vøllestad LA, Papakostas S, Lien S. The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids. G3 (BETHESDA, MD.) 2019; 9:1283-1294. [PMID: 30833292 PMCID: PMC6505133 DOI: 10.1534/g3.118.200919] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/04/2019] [Indexed: 12/13/2022]
Abstract
Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one of the earliest diverged salmonid subfamilies. To achieve this, we first generated relatively long genomic scaffolds by using a previously published draft genome assembly along with long-read sequencing data and a linkage map. We then merged those scaffolds by applying synteny evidence from the Atlantic salmon (Salmo salar) genome. Comparisons of the European grayling genome assembly to the genomes of Atlantic salmon and Northern pike (Esox lucius), the latter used as a nonduplicated outgroup, detailed aspects of the characteristic chromosome evolution process that has taken place in European grayling. While Atlantic salmon and other salmonid genomes are portrayed by the typical occurrence of numerous chromosomal fusions, European grayling chromosomes were confirmed to be fusion-free and were characterized by a relatively large proportion of paracentric and pericentric inversions. We further reported on transposable elements specific to either the European grayling or Atlantic salmon genome, on the male-specific sdY gene in the European grayling chromosome 11A, and on regions under residual tetrasomy in the homeologous European grayling chromosome pairs 9A-9B and 25A-25B. The same chromosome pairs have been observed under residual tetrasomy in Atlantic salmon and in other salmonids, suggesting that this feature has been conserved since the subfamily split.
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Affiliation(s)
- Tiina Sävilammi
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program, Faculty of Biological & Environmental Sciences
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | - René Guyomard
- INRA, UMR1313 GABI Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352, Jouy-en-Josas Cedex, France
| | - Yann Guiguen
- INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France
| | - Simen R Sandve
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | | | | | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
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83
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Mérot C, Berdan EL, Babin C, Normandeau E, Wellenreuther M, Bernatchez L. Intercontinental karyotype-environment parallelism supports a role for a chromosomal inversion in local adaptation in a seaweed fly. Proc Biol Sci 2019; 285:rspb.2018.0519. [PMID: 29925615 PMCID: PMC6030540 DOI: 10.1098/rspb.2018.0519] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Large chromosomal rearrangements are thought to facilitate adaptation to heterogeneous environments by limiting genomic recombination. Indeed, inversions have been implicated in adaptation along environmental clines and in ecotype specialization. Here, we combine classical ecological studies and population genetics to investigate an inversion polymorphism previously documented in Europe among natural populations of the seaweed fly Coelopa frigida along a latitudinal cline in North America. We test if the inversion is present in North America and polymorphic, assess which environmental conditions modulate the inversion karyotype frequencies, and document the relationship between inversion karyotype and adult size. We sampled nearly 2000 flies from 20 populations along several environmental gradients to quantify associations of inversion frequencies to heterogeneous environmental variables. Genotyping and phenotyping showed a widespread and conserved inversion polymorphism between Europe and America. Variation in inversion frequency was significantly associated with environmental factors, with parallel patterns between continents, indicating that the inversion may play a role in local adaptation. The three karyotypes of the inversion are differently favoured across micro-habitats and represent life-history strategies likely to be maintained by the collective action of several mechanisms of balancing selection. Our study adds to the mounting evidence that inversions are facilitators of adaptation and enhance within-species diversity.
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Affiliation(s)
- Claire Mérot
- Département de biologie, Université Laval, Quebec, Canada
| | - Emma L Berdan
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Charles Babin
- Département de biologie, Université Laval, Quebec, Canada
| | | | - Maren Wellenreuther
- School of Biological Sciences, University of Auckland, New Zealand.,Seafood Research Unit, Port Nelson, Nelson, New Zealand
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84
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Arostegui MC, Quinn TP, Seeb LW, Seeb JE, McKinney GJ. Retention of a chromosomal inversion from an anadromous ancestor provides the genetic basis for alternative freshwater ecotypes in rainbow trout. Mol Ecol 2019; 28:1412-1427. [DOI: 10.1111/mec.15037] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Martin C. Arostegui
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Thomas P. Quinn
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - James E. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Garrett J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
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85
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Hemmer‐Hansen J, Hüssy K, Baktoft H, Huwer B, Bekkevold D, Haslob H, Herrmann J, Hinrichsen H, Krumme U, Mosegaard H, Nielsen EE, Reusch TBH, Storr‐Paulsen M, Velasco A, von Dewitz B, Dierking J, Eero M. Genetic analyses reveal complex dynamics within a marine fish management area. Evol Appl 2019; 12:830-844. [PMID: 30976313 PMCID: PMC6439499 DOI: 10.1111/eva.12760] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 11/20/2018] [Accepted: 11/29/2018] [Indexed: 01/01/2023] Open
Abstract
Genetic data have great potential for improving fisheries management by identifying the fundamental management units-that is, the biological populations-and their mixing. However, so far, the number of practical cases of marine fisheries management using genetics has been limited. Here, we used Atlantic cod in the Baltic Sea to demonstrate the applicability of genetics to a complex management scenario involving mixing of two genetically divergent populations. Specifically, we addressed several assumptions used in the current assessment of the two populations. Through analysis of 483 single nucleotide polymorphisms (SNPs) distributed across the Atlantic cod genome, we confirmed that a model of mechanical mixing, rather than hybridization and introgression, best explained the pattern of genetic differentiation. Thus, the fishery is best monitored as a mixed-stock fishery. Next, we developed a targeted panel of 39 SNPs with high statistical power for identifying population of origin and analyzed more than 2,000 tissue samples collected between 2011 and 2015 as well as 260 otoliths collected in 2003/2004. These data provided high spatial resolution and allowed us to investigate geographical trends in mixing, to compare patterns for different life stages and to investigate temporal trends in mixing. We found similar geographical trends for the two time points represented by tissue and otolith samples and that a recently implemented geographical management separation of the two populations provided a relatively close match to their distributions. In contrast to the current assumption, we found that patterns of mixing differed between juveniles and adults, a signal likely linked to the different reproductive dynamics of the two populations. Collectively, our data confirm that genetics is an operational tool for complex fisheries management applications. We recommend focussing on developing population assessment models and fisheries management frameworks to capitalize fully on the additional information offered by genetically assisted fisheries monitoring.
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Affiliation(s)
- Jakob Hemmer‐Hansen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Karin Hüssy
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | - Henrik Baktoft
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Bastian Huwer
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | - Dorte Bekkevold
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Jens‐Peter Herrmann
- Institute of Marine Ecosystem and Fishery ScienceUniversity of HamburgHamburgGermany
| | - Hans‐Harald Hinrichsen
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Uwe Krumme
- Thünen Institute of Baltic Sea FisheriesRostockGermany
| | - Henrik Mosegaard
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Thorsten B. H. Reusch
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Marie Storr‐Paulsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | | | - Burkhard von Dewitz
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Jan Dierking
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Margit Eero
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
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86
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Lamichhaney S, Andersson L. A comparison of the association between large haplotype blocks under selection and the presence/absence of inversions. Ecol Evol 2019; 9:4888-4896. [PMID: 31031951 PMCID: PMC6476765 DOI: 10.1002/ece3.5094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 12/31/2022] Open
Abstract
Inversions may contribute to ecological adaptation and phenotypic diversity, and with the advent of "second" and "third" generation sequencing technologies, the ability to detect inversion polymorphisms has been enhanced dramatically. A key molecular consequence of an inversion is the suppression of recombination allowing independent accumulation of genetic changes between alleles over time. This may lead to the development of divergent haplotype blocks maintained by balancing selection. Thus, divergent haplotype blocks are often considered as indicating the presence of an inversion. In this paper, we first review the features of a 7.7 Mb inversion causing the Rose-comb phenotype in chicken, as a model for how inversions evolve and directly affect phenotypes. Second, we compare the genetic basis for alternative mating strategies in ruff and timing of reproduction in Atlantic herring, both associated with divergent haplotype blocks. Alternative male mating strategies in ruff are associated with a 4.5 Mb inversion that occurred about 4 million years ago. In fact, the ruff inversion shares some striking features with the Rose-comb inversion such as disruption of a gene at one of the inversion breakpoints and generation of a new allele by recombination between the inverted and noninverted alleles. In contrast, inversions do not appear to be a major reason for the fairly large haplotype blocks (range 10-200 kb) associated with ecological adaptation in the herring. Thus, it is important to note that divergent haplotypes may also be maintained by natural selection in the absence of structural variation.
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Affiliation(s)
- Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard UniversityCambridgeMassachusetts
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexas
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
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87
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Barth JMI, Villegas-Ríos D, Freitas C, Moland E, Star B, André C, Knutsen H, Bradbury I, Dierking J, Petereit C, Righton D, Metcalfe J, Jakobsen KS, Olsen EM, Jentoft S. Disentangling structural genomic and behavioural barriers in a sea of connectivity. Mol Ecol 2019; 28:1394-1411. [PMID: 30633410 PMCID: PMC6518941 DOI: 10.1111/mec.15010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/21/2018] [Accepted: 12/27/2018] [Indexed: 12/17/2022]
Abstract
Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole‐genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord‐type cod. Continuous behavioural tracking over 4 year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord‐type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.
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Affiliation(s)
- Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - David Villegas-Ríos
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, IMEDEA CSIC-UIB, Esporles, Spain.,Department of Ecology and Marine Resources, Institute of Marine Research, (IIM CSIC), Vigo, Spain
| | - Carla Freitas
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway.,Oceanic Observatory of Madeira, Funchal, Portugal
| | - Even Moland
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, Gothenburg, Sweden
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Ian Bradbury
- Science Branch, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | | | - David Righton
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Julian Metcalfe
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Esben M Olsen
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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88
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Árnason E, Halldórsdóttir K. Codweb: Whole-genome sequencing uncovers extensive reticulations fueling adaptation among Atlantic, Arctic, and Pacific gadids. SCIENCE ADVANCES 2019; 5:eaat8788. [PMID: 30906856 PMCID: PMC6426462 DOI: 10.1126/sciadv.aat8788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 02/04/2019] [Indexed: 05/11/2023]
Abstract
Introgressive hybridization creates networks of genetic relationships across species. Among marine fish of the Gadidae family, Pacific cod and walleye pollock are separate invasions of an Atlantic cod ancestor into the Pacific. Cods are ecological success stories, and their ecologies allow them to support the largest fisheries of the world. The enigmatic walleye pollock differs morphologically, behaviorally, and ecologically from its relatives, representing a niche shift. Here, we apply whole-genome sequencing to Pacific, Arctic, and Atlantic gadids and reveal extensive introgression among them with the ABBA-BABA test and pseudolikelihood phylogenetic network analysis. We propose that walleye pollock resulted from extensive adaptive introgression or homoploid hybrid speciation. The path of evolution of these taxa is more web than a tree. Their ability to invade and expand into new habitats and become ecologically successful may depend on genes acquired through adaptive introgression or hybrid speciation.
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Affiliation(s)
- Einar Árnason
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavík, Iceland
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Katrín Halldórsdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavík, Iceland
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89
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Singhal S, Gomez SM, Burch CL. Recombination drives the evolution of mutational robustness. ACTA ACUST UNITED AC 2019; 13:142-149. [PMID: 31572829 DOI: 10.1016/j.coisb.2018.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Recombination can impose fitness costs as beneficial parental combinations of alleles are broken apart, a phenomenon known as recombination load. Computational models suggest that populations may evolve a reduced recombination load by reducing either the likelihood of recombination events (bring interacting loci in physical proximity) or the strength of interactions between loci (make loci more independent of one another). We review evidence for each of these possibilities and their consequences for the genotype-fitness relationship. In particular, we expect that reducing interaction strengths between loci will lead to genomes that are also robust to mutational perturbations, but reducing recombination rates alone will not. We note that both mechanisms most likely played a role in the evolution of extant populations, and that both can result in the frequently-observed pattern of physical linkage between interacting loci.
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Affiliation(s)
- Sonia Singhal
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shawn M Gomez
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514.,Joint Department of Biomedical Engineering at University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, USA
| | - Christina L Burch
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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90
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Kerr Q, Fuentes‐Pardo AP, Kho J, McDermid JL, Ruzzante DE. Temporal stability and assignment power of adaptively divergent genomic regions between herring ( Clupea harengus) seasonal spawning aggregations. Ecol Evol 2019; 9:500-510. [PMID: 30680131 PMCID: PMC6342187 DOI: 10.1002/ece3.4768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/07/2018] [Accepted: 11/12/2018] [Indexed: 11/07/2022] Open
Abstract
Atlantic herring (Clupea harengus), a vital ecosystem component and target of the largest Northwest Atlantic pelagic fishery, undergo seasonal spawning migrations that result in elusive sympatric population structure. Herring spawn mostly in fall or spring, and genomic differentiation was recently detected between these groups. Here we used a subset of this differentiation, 66 single nucleotide polymorphisms (SNPs) to analyze the temporal dynamics of this local adaptation and the applicability of SNP subsets in stock assessment. We showed remarkable temporal stability of genomic differentiation corresponding to spawning season, between samples taken a decade apart (2005 N = 90 vs. 2014 N = 71) in the Gulf of St. Lawrence, and new evidence of limited interbreeding between spawning components. We also examined an understudied and overexploited herring population in Bras d'Or lake (N = 97); using highly reduced SNP panels (N SNPs > 6), we verified little-known sympatric spawning populations within this unique inland sea. These results describe consistent local adaptation, arising from asynchronous reproduction in a migratory and dynamic marine species. Our research demonstrates the efficiency and precision of SNP-based assessments of sympatric subpopulations; and indeed, this temporally stable local adaptation underlines the importance of such fine-scale management practices.
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Affiliation(s)
- Quentin Kerr
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | | | - James Kho
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Jenni L. McDermid
- Marine Fish and Mammals Section, Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
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91
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Langangen Ø, Färber L, Stige LC, Diekert FK, Barth JMI, Matschiner M, Berg PR, Star B, Stenseth NC, Jentoft S, Durant JM. Ticket to spawn: Combining economic and genetic data to evaluate the effect of climate and demographic structure on spawning distribution in Atlantic cod. GLOBAL CHANGE BIOLOGY 2019; 25:134-143. [PMID: 30300937 PMCID: PMC7379705 DOI: 10.1111/gcb.14474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 09/05/2018] [Indexed: 05/15/2023]
Abstract
Climate warming and harvesting affect the dynamics of species across the globe through a multitude of mechanisms, including distribution changes. In fish, migrations to and distribution on spawning grounds are likely influenced by both climate warming and harvesting. The Northeast Arctic (NEA) cod (Gadus morhua) performs seasonal migrations from its feeding grounds in the Barents Sea to spawning grounds along the Norwegian coast. The distribution of cod between the spawning grounds has historically changed at decadal scales, mainly due to variable use of the northern and southern margins of the spawning area. Based on historical landing records, two major hypotheses have been put forward to explain these changes: climate and harvesting. Climate could affect the distribution through, for example, spatial habitat shifts. Harvesting could affect the distribution through impacting the demographic structure. If demographic structure is important, theory predicts increasing spawner size with migration distance. Here, we evaluate these hypotheses with modern data from a period (2000-2016) of increasing temperature and recovering stock structure. We first analyze economic data from the Norwegian fisheries to investigate geographical differences in size of spawning fish among spawning grounds, as well as interannual differences in mean latitude of spawning in relation to changes in temperature and demographic parameters. Second, we analyze genetically determined fish sampled at the spawning grounds to unambiguously separate between migratory NEA cod and potentially smaller sized coastal cod of local origin. Our results indicate smaller spawners farther away from the feeding grounds, hence not supporting the hypothesis that harvesting is a main driver for the contemporary spawning ground distribution. We find a positive correlation between annual mean spawning latitude and temperature. In conclusion, based on contemporary data, there is more support for climate compared to harvesting in shaping spawning ground distribution in this major fish stock in the North Atlantic Ocean.
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Affiliation(s)
- Øystein Langangen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
| | - Leonie Färber
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
| | - Leif C. Stige
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
| | - Florian K. Diekert
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
- Department of EconomicsHeidelberg UniversityHeidelbergGermany
| | - Julia M. I. Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
| | - Michael Matschiner
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
- Zoological InstituteUniversity of BaselBaselSwitzerland
| | - Paul R. Berg
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
- Centre for Coastal Research (CCR), Department of Natural SciencesUniversity of AgderKristiansandNorway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
| | - Nils Chr. Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
- Centre for Coastal Research (CCR), Department of Natural SciencesUniversity of AgderKristiansandNorway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
| | - Joël M. Durant
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
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92
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Population Genomics Applied to Fishery Management and Conservation. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2019_66] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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93
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Christmas MJ, Wallberg A, Bunikis I, Olsson A, Wallerman O, Webster MT. Chromosomal inversions associated with environmental adaptation in honeybees. Mol Ecol 2018; 28:1358-1374. [DOI: 10.1111/mec.14944] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/07/2018] [Accepted: 11/07/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Matthew T. Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala University Uppsala Sweden
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94
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Fairweather R, Bradbury IR, Helyar SJ, de Bruyn M, Therkildsen NO, Bentzen P, Hemmer‐Hansen J, Carvalho GR. Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod. Ecol Evol 2018; 8:12140-12152. [PMID: 30598806 PMCID: PMC6303715 DOI: 10.1002/ece3.4672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 11/11/2022] Open
Abstract
Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range-wide examinations suggest significant transatlantic divergence, although the fine-scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data-synthesis approach, integrating multiple genome-wide single-nucleotide polymorphism (SNP) datasets representative of different regions to create a single range-wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post-glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.
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Affiliation(s)
- Robert Fairweather
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- School of Biological SciencesBangor UniversityBangorUK
| | - Ian R. Bradbury
- Science Branch, Department of FisheriesSt John’s, Newfoundland and LabradorCanada
| | - Sarah J. Helyar
- Institute of Global Food SecurityQueen’s University BelfastBelfastUK
| | - Mark de Bruyn
- School of Biological SciencesBangor UniversityBangorUK
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | | | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Jakob Hemmer‐Hansen
- Section for Marine Living Resources, National Institute for Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
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95
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Jorde PE, Synnes A, Espeland SH, Sodeland M, Knutsen H. Can we rely on selected genetic markers for population identification? Evidence from coastal Atlantic cod. Ecol Evol 2018; 8:12547-12558. [PMID: 30619564 PMCID: PMC6308871 DOI: 10.1002/ece3.4648] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/30/2018] [Accepted: 10/03/2018] [Indexed: 01/03/2023] Open
Abstract
The use of genetic markers under putative selection in population studies carries the potential for erroneous identification of populations and misassignment of individuals to population of origin. Selected markers are nevertheless attractive, especially in marine organisms that are characterized by weak population structure at neutral loci. Highly fecund species may tolerate the cost of strong selective mortality during early life stages, potentially leading to a shift in offspring genotypes away from the parental proportions. In Atlantic cod, recent genetic studies have uncovered different genotype clusters apparently representing phenotypically cryptic populations that coexist in coastal waters. Here, we tested if a high-graded SNP panel specifically designed to classify individual cod to population of origin may be unreliable because of natural selection acting on the SNPs or their linked background. Temporal samples of cod were collected from two fjords, starting at the earliest life stage (pelagic eggs) and carried on until late autumn (bottom-settled juveniles), covering the period during summer of high natural mortality. Despite the potential for selective mortality during the study period, we found no evidence for selection, as both cod types occurred throughout the season, already in the earliest egg samples, and there was no evidence for a shift during the season in the proportions of one or the other type. We conclude that high-graded marker panels under putative natural selection represent a valid and useful tool for identifying biological population structure in this highly fecund species and presumably in others.
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Affiliation(s)
- Per Erik Jorde
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
- Institute of Marine ResearchHisNorway
| | - Ann‐Elin Synnes
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | - Sigurd Heiberg Espeland
- Institute of Marine ResearchHisNorway
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | - Marte Sodeland
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | - Halvor Knutsen
- Institute of Marine ResearchHisNorway
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
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96
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Hooper DM, Griffith SC, Price TD. Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone. Mol Ecol 2018; 28:1246-1262. [PMID: 30230092 DOI: 10.1111/mec.14874] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/23/2018] [Accepted: 08/27/2018] [Indexed: 12/11/2022]
Abstract
Across hybrid zones, the sex chromosomes are often more strongly differentiated than the autosomes. This is regularly attributed to the greater frequency of reproductive incompatibilities accumulating on sex chromosomes and their exposure in the heterogametic sex. Working within an avian hybrid zone, we explore the possibility that chromosome inversions differentially accumulate on the Z chromosome compared to the autosomes and thereby contribute to Z chromosome differentiation. We analyse the northern Australian hybrid zone between two subspecies of the long-tailed finch (Poephila acuticauda), first described based on differences in bill colour, using reduced-representation genomic sequencing for 293 individuals over a 1,530-km transect. Autosomal differentiation between subspecies is minimal. In contrast, 75% of the Z chromosome is highly differentiated and shows a steep genomic cline, which is displaced 350 km to the west of the cline in bill colour. Differentiation is associated with two or more putative chromosomal inversions, each predominating in one subspecies. If inversions reduce recombination between hybrid incompatibilities, they are selectively favoured and should therefore accumulate in hybrid zones. We argue that this predisposes inversions to differentially accumulate on the Z chromosome. One genomic region affecting bill colour is on the Z, but the main candidates are on chromosome 8. This and the displacement of the bill colour and Z chromosome cline centres suggest that bill colour has not strongly contributed to inversion accumulation. Based on cline width, however, the Z chromosome and bill colour both contribute to reproductive isolation established between this pair of subspecies.
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Affiliation(s)
- Daniel M Hooper
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York.,Committe on Evolutionary Biology, University of Chicago, Chicago, Illinois
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Trevor D Price
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois
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97
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Knutsen H, Jorde PE, Hutchings JA, Hemmer‐Hansen J, Grønkjær P, Jørgensen KM, André C, Sodeland M, Albretsen J, Olsen EM. Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales. Evol Appl 2018; 11:1527-1539. [PMID: 30344625 PMCID: PMC6183466 DOI: 10.1111/eva.12640] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/09/2018] [Indexed: 12/15/2022] Open
Abstract
Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analysed genetic origin of 6,483 individual cod sampled annually over 14 years from 125 locations along the Norwegian Skagerrak coast and document stable coexistence of two genetically divergent Atlantic cod ecotypes throughout the study area and study period. A "fjord" ecotype dominated in numbers deep inside fjords while a "North Sea" ecotype was the only type found in offshore North Sea. Both ecotypes coexisted in similar proportions throughout coastal habitats at all spatial scales. The size-at-age of the North Sea ecotype on average exceeded that of the fjord ecotype by 20% in length and 80% in weight across all habitats. Different growth and size among individuals of the two types might be one of several ecologically significant variables that allow for stable coexistence of closely related populations within the same habitat. Management plans, biodiversity initiatives and other mitigation strategies that do not account for the mixture of species ecotypes are unlikely to meet objectives related to the sustainability of fish and fisheries.
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Affiliation(s)
- Halvor Knutsen
- Institute of Marine ResearchFlødevigenHisNorway
- Department of BiosciencesCentre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernOsloNorway
- Centre for Coastal ResearchUniversity of AgderKristiansandNorway
| | - Per Erik Jorde
- Institute of Marine ResearchFlødevigenHisNorway
- Department of BiosciencesCentre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernOsloNorway
| | - Jeffrey A. Hutchings
- Institute of Marine ResearchFlødevigenHisNorway
- Department of BiosciencesCentre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernOsloNorway
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - Jakob Hemmer‐Hansen
- Section for Marine Living ResourcesNational Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Peter Grønkjær
- Department for BioscienceAarhus UniversityAquatic BiologyAarhusDenmark
| | | | - Carl André
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | - Marte Sodeland
- Centre for Coastal ResearchUniversity of AgderKristiansandNorway
| | | | - Esben M. Olsen
- Institute of Marine ResearchFlødevigenHisNorway
- Centre for Coastal ResearchUniversity of AgderKristiansandNorway
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98
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Dahle G, Quintela M, Johansen T, Westgaard JI, Besnier F, Aglen A, Jørstad KE, Glover KA. Analysis of coastal cod (Gadus morhua L.) sampled on spawning sites reveals a genetic gradient throughout Norway's coastline. BMC Genet 2018; 19:42. [PMID: 29986643 PMCID: PMC6036686 DOI: 10.1186/s12863-018-0625-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/18/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Atlantic cod (Gadus morhua L.) has formed the basis of many economically significant fisheries in the North Atlantic, and is one of the best studied marine fishes, but a legacy of overexploitation has depleted populations and collapsed fisheries in several regions. Previous studies have identified considerable population genetic structure for Atlantic cod. However, within Norway, which is the country with the largest remaining catch in the Atlantic, the population genetic structure of coastal cod (NCC) along the entire coastline has not yet been investigated. We sampled > 4000 cod from 55 spawning sites. All fish were genotyped with 6 microsatellite markers and Pan I (Dataset 1). A sub-set of the samples (1295 fish from 17 locations) were also genotyped with an additional 9 microsatellites (Dataset 2). Otoliths were read in order to exclude North East Arctic Cod (NEAC) from the analyses, as and where appropriate. RESULTS We found no difference in genetic diversity, measured as number of alleles, allelic richness, heterozygosity nor effective population sizes, in the north-south gradient. In both data sets, weak but significant population genetic structure was revealed (Dataset 1: global FST = 0.008, P < 0.0001. Dataset 2: global FST = 0.004, P < 0.0001). While no clear genetic groups were identified, genetic differentiation increased among geographically-distinct samples. Although the locus Gmo132 was identified as a candidate for positive selection, possibly through linkage with a genomic region under selection, overall trends remained when this locus was excluded from the analyses. The most common allele in loci Gmo132 and Gmo34 showed a marked frequency change in the north-south gradient, increasing towards the frequency observed in NEAC in the north. CONCLUSION We conclude that Norwegian coastal cod displays significant population genetic structure throughout its entire range, that follows a trend of isolation by distance. Furthermore, we suggest that a gradient of genetic introgression between NEAC and NCC contributes to the observed population genetic structure. The current management regime for coastal cod in Norway, dividing it into two stocks at 62°N, represents a simplification of the level of genetic connectivity among coastal cod in Norway, and needs revision.
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Affiliation(s)
- Geir Dahle
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - María Quintela
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Torild Johansen
- Institute of Marine Research (IMR), Postbox 6404, N-9019 Tromsø, Norway
| | | | - François Besnier
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Asgeir Aglen
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Knut E. Jørstad
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Kevin A. Glover
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
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99
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Jørgensen TE, Karlsen BO, Emblem Å, Breines R, Andreassen M, Rounge TB, Nederbragt AJ, Jakobsen KS, Nymark M, Ursvik A, Coucheron DH, Jakt LM, Nordeide JT, Moum T, Johansen SD. Mitochondrial genome variation of Atlantic cod. BMC Res Notes 2018; 11:397. [PMID: 29921324 PMCID: PMC6009815 DOI: 10.1186/s13104-018-3506-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/15/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The objective of this study was to analyse intraspecific sequence variation of Atlantic cod mitochondrial DNA, based on a comprehensive collection of completely sequenced mitochondrial genomes. RESULTS We determined the complete mitochondrial DNA sequence of 124 cod specimens from the eastern and western part of the species' distribution range in the North Atlantic Ocean. All specimens harboured a unique mitochondrial DNA haplotype. Nine hundred and fifty-two polymorphic sites were identified, including 109 non-synonymous sites within protein coding regions. Eighteen variable sites were identified as indels, exclusively distributed in structural RNA genes and non-coding regions. Phylogeographic analyses based on 156 available cod mitochondrial genomes did not reveal a clear structure. There was a lack of mitochondrial genetic differentiation between two ecotypes of cod in the eastern North Atlantic, but eastern and western cod were differentiated and mitochondrial genome diversity was higher in the eastern than the western Atlantic, suggesting deviating population histories. The geographic distribution of mitochondrial genome variation seems to be governed by demographic processes and gene flow among ecotypes that are otherwise characterized by localized genomic divergence associated with chromosomal inversions.
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Affiliation(s)
- Tor Erik Jørgensen
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Bård Ove Karlsen
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital, Bodø, Norway
| | - Åse Emblem
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Ragna Breines
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Morten Andreassen
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Trine B Rounge
- Centre for Ecological and Evolutionary Syntheses (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Alexander J Nederbragt
- Centre for Ecological and Evolutionary Syntheses (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Syntheses (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marianne Nymark
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Anita Ursvik
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Dag H Coucheron
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Lars Martin Jakt
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Jarle T Nordeide
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Truls Moum
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Steinar D Johansen
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway.
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100
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Roesti M. Varied Genomic Responses to Maladaptive Gene Flow and Their Evidence. Genes (Basel) 2018; 9:E298. [PMID: 29899287 PMCID: PMC6027369 DOI: 10.3390/genes9060298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/17/2018] [Accepted: 05/30/2018] [Indexed: 12/02/2022] Open
Abstract
Adaptation to a local environment often occurs in the face of maladaptive gene flow. In this perspective, I discuss several ideas on how a genome may respond to maladaptive gene flow during adaptation. On the one hand, selection can build clusters of locally adaptive alleles at fortuitously co-localized loci within a genome, thereby facilitating local adaptation with gene flow ('allele-only clustering'). On the other hand, the selective pressure to link adaptive alleles may drive co-localization of the actual loci relevant for local adaptation within a genome through structural genome changes or an evolving intra-genomic crossover rate ('locus clustering'). While the expected outcome is, in both cases, a higher frequency of locally adaptive alleles in some genome regions than others, the molecular units evolving in response to gene flow differ (i.e., alleles versus loci). I argue that, although making this distinction is important, we commonly lack the critical empirical evidence to do so. This is mainly because many current approaches are biased towards detecting local adaptation in genome regions with low crossover rates. The importance of low-crossover genome regions for adaptation with gene flow, such as in co-localizing relevant loci within a genome, thus remains unclear. Future empirical investigations should address these questions by making use of comparative genomics, where multiple de novo genome assemblies from species evolved under different degrees of genetic exchange are compared. This research promises to advance our understanding of how a genome adapts to maladaptive gene flow, thereby promoting adaptive divergence and reproductive isolation.
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Affiliation(s)
- Marius Roesti
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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