1
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Ólafsdóttir GÁ, Turnbull S, Jónsdóttir IG, Nickel A, Karlsson H, Henke T, Nielsen EE, Pálsson S. Genetic assignment predicts depth of benthic settlement for 0-group Atlantic cod. PLoS One 2023; 18:e0292495. [PMID: 37792752 PMCID: PMC10550133 DOI: 10.1371/journal.pone.0292495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Atlantic cod is a keystone species that remains among the most economically important demersal fish in the North Atlantic. Throughout its distribution range, Atlantic cod is composed of populations with varying environmental preferences and migratory propensities. This life-history variation is likely to have contributed to the niche width and large population sizes of Atlantic cod, and its relative resilience to environmental change and exploitation. The Icelandic cod stock is currently managed as a single unit, but early research indicates population variation by depth and temperature and distinct offshore and inshore spawning components. Pelagic 0-group juveniles from different spawning grounds coexist in nursery areas around Iceland, but their genetic composition or habitat partitioning had not been examined post benthic settlement. In the current study we examine the genetic composition of Atlantic cod juvenile aggregations at nearshore nursery grounds in NW-Iceland and report distinct segregation by the depth of offshore and inshore juvenile cod. The physiological mechanism of this segregation is not known, but the pattern demonstrates the need to consider population structure at nursery grounds in the application of marine spatial planning and other area-based conservation tools.
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Affiliation(s)
- Guðbjörg Ásta Ólafsdóttir
- University of Iceland, Research Centre of the Westfjords, Bolungarvík, Iceland
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | - Shaun Turnbull
- University of Iceland, Research Centre of the Westfjords, Bolungarvík, Iceland
| | | | - Anja Nickel
- University of Iceland, Research Centre of the Westfjords, Bolungarvík, Iceland
| | - Hjalti Karlsson
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | - Theresa Henke
- University of Iceland, Research Centre of the Westfjords, Bolungarvík, Iceland
| | - Einar Eg Nielsen
- DTU Aqua, National Institute of Aquatic Resources, Silkeborg, Denmark
| | - Snæbjörn Pálsson
- University of Iceland, Faculty of Life and Environmental Sciences, Reykjavík, Iceland
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2
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Morris CJ, Nguyen KQ, Green JM. Comparison of lethal and non-lethal age-based growth estimation methodologies to assess an endemic bay population of Atlantic cod (Gadus morhua). J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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3
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Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods. Heredity (Edinb) 2022; 129:356-365. [PMID: 36357776 PMCID: PMC9709158 DOI: 10.1038/s41437-022-00570-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/05/2022] [Accepted: 10/19/2022] [Indexed: 11/12/2022] Open
Abstract
Characterizing the role of different mutational effect sizes in the evolution of fitness-related traits has been a major goal in evolutionary biology for a century. Such characterization in a diversity of systems, both model and non-model, will help to understand the genetic processes underlying fitness variation. However, well-characterized genetic architectures of such traits in wild populations remain uncommon. In this study, we used haplotype-based and multi-SNP Bayesian association methods with sequencing data for 313 individuals from wild populations to test the mutational composition of known candidate regions for sea age at maturation in Atlantic salmon (Salmo salar). We detected an association at five loci out of 116 candidates previously identified in an aquaculture strain with maturation timing in wild Atlantic salmon. We found that at four of these five loci, variation explained by the locus was predominantly driven by a single SNP suggesting the genetic architecture of this trait includes multiple loci with simple, non-clustered alleles and a locus with potentially more complex alleles. This highlights the diversity of genetic architectures that can exist for fitness-related traits. Furthermore, this study provides a useful multi-SNP framework for future work using sequencing data to characterize genetic variation underlying phenotypes in wild populations.
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4
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Wang F, Zhang R, Sun X, Wang J, Liu H, Zhang K, Wang C. An intelligent recognition method of chromosome rearrangement patterns based on information entropy. Sci Rep 2022; 12:19707. [PMID: 36385139 PMCID: PMC9668828 DOI: 10.1038/s41598-022-22046-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
Chromosome rearrangements play an important role in the speciation of plants and animals, and the recognition of chromosome rearrangement patterns is helpful to elucidate the mechanism of species differentiation at the chromosome level. However, the existing chromosome rearrangement recognition methods have some major limitations, such as low quality, barriers to parental selection, and inability to identify specific rearrangement patterns. Based on the whole genome protein sequences, we constructed the combined figure according to the slope of the collinear fragment, the number of homologous genes, the coordinates in the top left and bottom right of the collinear fragment. The standardized combination figure is compared with the four standard pattern figures, and then combined with the information entropy analysis strategy to automatically classify the chromosome images and identify the chromosome rearrangement pattern. This paper proposes an automatic karyotype analysis method EntroCR (intelligent recognition method of chromosome rearrangement based on information entropy), which integrates rearrangement pattern recognition, result recommendation and related chromosome determination, so as to infer the evolution process of ancestral chromosomes to the existing chromosomes. Validation experiments were conducted using whole-genome data of Gossypium raimondii and Gossypium arboreum, Oryza sativa and Sorghum bicolor. The conclusions were consistent with previous results. EntroCR provides a reference for researchers in species evolution and molecular marker assisted breeding as well as new methods for analyzing karyotype evolution in other species.
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Affiliation(s)
- Fushun Wang
- grid.274504.00000 0001 2291 4530College of Information Science and Technology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530Hebei Key Laboratory of Agricultural Big Data, Baoding, 071000 People’s Republic of China
| | - Ruolan Zhang
- grid.274504.00000 0001 2291 4530College of Information Science and Technology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Xiaohua Sun
- grid.484109.00000 0004 1758 9755Department of Digital Media, Hebei Software Institute, Baoding, 071000 People’s Republic of China
| | - Junhao Wang
- grid.274504.00000 0001 2291 4530College of Information Science and Technology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Hongquan Liu
- grid.274504.00000 0001 2291 4530Department of Urban and Rural Construction, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Kang Zhang
- grid.274504.00000 0001 2291 4530College of Life Science, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Chunyang Wang
- grid.274504.00000 0001 2291 4530College of Life Science, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
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5
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Yasir M, Kanwal HH, Hussain Q, Riaz MW, Sajjad M, Rong J, Jiang Y. Status and prospects of genome-wide association studies in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:1019347. [PMID: 36330239 PMCID: PMC9623101 DOI: 10.3389/fpls.2022.1019347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Over the last two decades, the use of high-density SNP arrays and DNA sequencing have allowed scientists to uncover the majority of the genotypic space for various crops, including cotton. Genome-wide association study (GWAS) links the dots between a phenotype and its underlying genetics across the genomes of populations. It was first developed and applied in the field of human disease genetics. Many areas of crop research have incorporated GWAS in plants and considerable literature has been published in the recent decade. Here we will provide a comprehensive review of GWAS studies in cotton crop, which includes case studies on biotic resistance, abiotic tolerance, fiber yield and quality traits, current status, prospects, bottlenecks of GWAS and finally, thought-provoking question. This review will serve as a catalog of GWAS in cotton and suggest new frontiers of the cotton crop to be studied with this important tool.
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Affiliation(s)
- Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Hafiza Hamrah Kanwal
- School of Computer Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Muhammad Waheed Riaz
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Muhammad Sajjad
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
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6
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Peng Y, Yan H, Guo L, Deng C, Wang C, Wang Y, Kang L, Zhou P, Yu K, Dong X, Liu X, Sun Z, Peng Y, Zhao J, Deng D, Xu Y, Li Y, Jiang Q, Li Y, Wei L, Wang J, Ma J, Hao M, Li W, Kang H, Peng Z, Liu D, Jia J, Zheng Y, Ma T, Wei Y, Lu F, Ren C. Reference genome assemblies reveal the origin and evolution of allohexaploid oat. Nat Genet 2022; 54:1248-1258. [PMID: 35851189 PMCID: PMC9355876 DOI: 10.1038/s41588-022-01127-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022]
Abstract
Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76 Gb and contig N50 of 75.27 Mb. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. The origin of hexaploid oat is inferred from whole-genome sequencing, chloroplast genomes and transcriptome assemblies of different Avena species. These findings and the high-quality reference genomes presented here will facilitate the full use of crop genetic resources to accelerate oat improvement. A reference-quality genome assembly of hexaploid oat variety ‘Sanfensan’ and genome assemblies of its diploid and tetraploid Avena ancestors provide insights into the evolutionary history of allohexaploid oat.
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7
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Nguyen KQ, Morris CJ. Fishing for Atlantic cod (Gadus morhua) with pots and gillnets: A catch comparison study along the southeast coast of Labrador. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2021.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Jeffery NW, Lehnert SJ, Kess T, Layton KKS, Wringe BF, Stanley RR. Application of Omics Tools in Designing and Monitoring Marine Protected Areas For a Sustainable Blue Economy. Front Genet 2022; 13:886494. [PMID: 35812740 PMCID: PMC9257101 DOI: 10.3389/fgene.2022.886494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/16/2022] [Indexed: 11/15/2022] Open
Abstract
A key component of the global blue economy strategy is the sustainable extraction of marine resources and conservation of marine environments through networks of marine protected areas (MPAs). Connectivity and representativity are essential factors that underlie successful implementation of MPA networks, which can safeguard biological diversity and ecosystem function, and ultimately support the blue economy strategy by balancing ocean use with conservation. New “big data” omics approaches, including genomics and transcriptomics, are becoming essential tools for the development and maintenance of MPA networks. Current molecular omics techniques, including population-scale genome sequencing, have direct applications for assessing population connectivity and for evaluating how genetic variation is represented within and among MPAs. Effective baseline characterization and long-term, scalable, and comprehensive monitoring are essential for successful MPA management, and omics approaches hold great promise to characterize the full range of marine life, spanning the microbiome to megafauna across a range of environmental conditions (shallow sea to the deep ocean). Omics tools, such as eDNA metabarcoding can provide a cost-effective basis for biodiversity monitoring in large and remote conservation areas. Here we provide an overview of current omics applications for conservation planning and monitoring, with a focus on metabarcoding, metagenomics, and population genomics. Emerging approaches, including whole-genome sequencing, characterization of genomic architecture, epigenomics, and genomic vulnerability to climate change are also reviewed. We demonstrate that the operationalization of omics tools can enhance the design, monitoring, and management of MPAs and thus will play an important role in a modern and comprehensive blue economy strategy.
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Affiliation(s)
- Nicholas W. Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
- *Correspondence: Nicholas W. Jeffery,
| | - Sarah J. Lehnert
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, NL, Canada
| | - Tony Kess
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, NL, Canada
| | - Kara K. S. Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Brendan F. Wringe
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
| | - Ryan R.E. Stanley
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
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9
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Breistein B, Dahle G, Johansen T, Besnier F, Quintela M, Jorde PE, Knutsen H, Westgaard JI, Nedreaas K, Farestveit E, Glover KA. Geographic variation in gene‐flow from a genetically distinct migratory ecotype drives population genetic structure of coastal Atlantic cod (
Gadus morhua
L.). Evol Appl 2022; 15:1162-1176. [PMID: 35899259 PMCID: PMC9309456 DOI: 10.1111/eva.13422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- B. Breistein
- Institute of Marine Research Bergen Norway
- Department of Biology University of Bergen Bergen Norway
| | - G. Dahle
- Institute of Marine Research Bergen Norway
- Department of Biology University of Bergen Bergen Norway
| | | | - F. Besnier
- Institute of Marine Research Bergen Norway
| | | | - P. E. Jorde
- Institute of Marine Research Flødevigen Norway
| | - H. Knutsen
- Institute of Marine Research Flødevigen Norway
- Centre for Coastal Research, Department of Natural Sciences University of Agder Norway
| | | | | | | | - K. A. Glover
- Institute of Marine Research Bergen Norway
- Department of Biology University of Bergen Bergen Norway
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10
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Thorstensen MJ, Euclide PT, Jeffrey JD, Shi Y, Treberg JR, Watkinson DA, Enders EC, Larson WA, Kobayashi Y, Jeffries KM. A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish. Ecol Evol 2022; 12:e8898. [PMID: 35571758 PMCID: PMC9077824 DOI: 10.1002/ece3.8898] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Matt J. Thorstensen
- Department of Biological Sciences University of Manitoba Winnipeg Manitoba Canada
| | - Peter T. Euclide
- Wisconsin Cooperative Fishery Research Unit College of Natural Resources U.S. Geological Survey University of Wisconsin‐Stevens Point Stevens Point Wisconsin USA
| | - Jennifer D. Jeffrey
- Department of Biological Sciences University of Manitoba Winnipeg Manitoba Canada
- Department of Biology Richardson College University of Winnipeg Winnipeg Manitoba Canada
| | - Yue Shi
- Wisconsin Cooperative Fishery Research Unit College of Natural Resources U.S. Geological Survey University of Wisconsin‐Stevens Point Stevens Point Wisconsin USA
- College of Fisheries and Ocean Sciences University of Alaska Fairbanks Juneau Alaska USA
| | - Jason R. Treberg
- Department of Biological Sciences University of Manitoba Winnipeg Manitoba Canada
| | | | - Eva C. Enders
- Freshwater Institute, Fisheries and Oceans Canada Winnipeg Manitoba Canada
| | - Wesley A. Larson
- Wisconsin Cooperative Fishery Research Unit College of Natural Resources U.S. Geological Survey University of Wisconsin‐Stevens Point Stevens Point Wisconsin USA
- National Oceanographic and Atmospheric Administration National Marine Fisheries Service Alaska Fisheries Science Center Auke Bay Laboratories Juneau Alaska USA
| | - Yasuhiro Kobayashi
- Department of Biological Sciences Fort Hays State University Hays Kansas USA
- Department of Biology The College of St. Scholastica Duluth Minnesota USA
| | - Ken M. Jeffries
- Department of Biological Sciences University of Manitoba Winnipeg Manitoba Canada
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11
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Stronen AV, Norman AJ, Vander Wal E, Paquet PC. The relevance of genetic structure in ecotype designation and conservation management. Evol Appl 2022; 15:185-202. [PMID: 35233242 PMCID: PMC8867706 DOI: 10.1111/eva.13339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
The concept of ecotypes is complex, partly because of its interdisciplinary nature, but the idea is intrinsically valuable for evolutionary biology and applied conservation. The complex nature of ecotypes has spurred some confusion and inconsistencies in the literature, thereby limiting broader theoretical development and practical application. We provide suggestions for how incorporating genetic analyses can ease confusion and help define ecotypes. We approach this by systematically reviewing 112 publications across taxa that simultaneously mention the terms ecotype, conservation and management, to examine the current use of the term in the context of conservation and management. We found that most ecotype studies involve fish, mammals and plants with a focus on habitat use, which at 60% was the most common criterion used for categorization of ecotypes. Only 53% of the studies incorporated genetic analyses, and major discrepancies in available genomic resources among taxa could have contributed to confusion about the role of genetic structure in delineating ecotypes. Our results show that the rapid advances in genetic methods, also for nonmodel organisms, can help clarify the spatiotemporal distribution of adaptive and neutral genetic variation and their relevance to ecotype designations. Genetic analyses can offer empirical support for the ecotype concept and provide a timely measure of evolutionary potential, especially in changing environmental conditions. Genetic variation that is often difficult to detect, including polygenic traits influenced by small contributions from several genes, can be vital for adaptation to rapidly changing environments. Emerging ecotypes may signal speciation in progress, and findings from genome‐enabled organisms can help clarify important selective factors driving ecotype development and persistence, and thereby improve preservation of interspecific genetic diversity. Incorporation of genetic analyses in ecotype studies will help connect evolutionary biology and applied conservation, including that of problematic groups such as natural hybrid organisms and urban or anthropogenic ecotypes.
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Affiliation(s)
- Astrid V. Stronen
- Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
- Department of Biotechnology and Life Sciences Insubria University Varese Italy
- Department of Chemistry and Bioscience Aalborg University Aalborg Denmark
| | - Anita J. Norman
- Department of Fish, Wildlife and Environmental Studies Swedish University of Agricultural Sciences Umeå Sweden
| | - Eric Vander Wal
- Department of Biology Memorial University of Newfoundland St. John’s NL Canada
| | - Paul C. Paquet
- Department of Geography University of Victoria Victoria BC Canada
- Raincoast Conservation Foundation Sidney BC Canada
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12
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Watson KB, Lehnert SJ, Bentzen P, Kess T, Einfeldt A, Duffy S, Perriman B, Lien S, Kent M, Bradbury IR. Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon (Salmo salar). Mol Ecol 2021; 31:1057-1075. [PMID: 34862998 DOI: 10.1111/mec.16307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/25/2021] [Accepted: 11/19/2021] [Indexed: 01/17/2023]
Abstract
Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non-model organisms. In Atlantic Salmon (Salmo salar), variations in chromosomal rearrangements exist across the species natural range, yet the role and importance of these structural variants in maintaining adaptive differences among wild populations remains poorly understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations within a highly genetically structured region of southern Newfoundland, Canada with a 220K SNP array. Multivariate analysis, across two independent years, consistently identified variation in a structural variant (translocation between chromosomes Ssa01 and Ssa23), previously associated with evidence of trans-Atlantic secondary contact, as the dominant factor influencing population structure in the region. Redundancy analysis suggested that variation in the Ssa01/Ssa23 chromosomal translocation is strongly correlated with temperature. Our analyses suggest environmentally mediated selection acting on standing genetic variation in genomic architecture introduced through secondary contact may underpin fine-scale local adaptation in Placentia Bay, Newfoundland, Canada, a large and deep embayment, highlighting the importance of chromosomal structural variation as a driver of contemporary adaptive divergence.
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Affiliation(s)
- K Beth Watson
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Sarah J Lehnert
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Tony Kess
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Antony Einfeldt
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Steven Duffy
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Ben Perriman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Matthew Kent
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ian R Bradbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
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13
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Sinclair-Waters M, Piavchenko N, Ruokolainen A, Aykanat T, Erkinaro J, Primmer CR. Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus. Mol Ecol 2021; 31:562-570. [PMID: 34716945 DOI: 10.1111/mec.16256] [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: 06/05/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/14/2022]
Abstract
Efforts to understand the genetic underpinnings of phenotypic variation are becoming more and more frequent in molecular ecology. Such efforts often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore validation of which genes are actually responsible for the signal is required. In Atlantic salmon (Salmo salar), a large-effect locus for maturation timing, an ecologically important trait, occurs in a genomic region including two genes, vgll3 and akap11, but data for clearly determining which of the genes (or both) contribute to the association have been lacking. Here, we take advantage of natural recombination events detected between the two candidate genes in a salmon broodstock to reduce linkage disequilibrium at the locus, thus enabling delineation of the influence of variation at these two genes on early maturation. By rearing 5,895 males to maturation age, of which 81% had recombinant vgll3/akap11 allelic combinations, we found that vgll3 single nucleotide polymorphism (SNP) variation was strongly associated with early maturation, whereas there was little or no association between akap11 SNP variation and early maturation. These findings provide strong evidence supporting vgll3 as the primary candidate gene in the chromosome 25 locus for influencing early maturation. This will help guide future research for understanding the genetic processes controlling early maturation. This also exemplifies the utility of natural recombinants to more precisely map causal variation underlying ecologically important phenotypic diversity.
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Affiliation(s)
- Marion Sinclair-Waters
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Nikolai Piavchenko
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Annukka Ruokolainen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | | | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
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14
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Layton KKS, Bradbury IR. Harnessing the power of multi-omics data for predicting climate change response. J Anim Ecol 2021; 91:1064-1072. [PMID: 34679193 DOI: 10.1111/1365-2656.13619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/11/2021] [Indexed: 01/19/2023]
Abstract
Predicting how species will respond to future climate change is of central importance in the midst of the global biodiversity crisis, and recent work has demonstrated the utility of population genomics for improving these predictions. Here, we suggest a broadening of the approach to include other types of genomic variants that play an important role in adaptation, like structural (e.g. copy number variants) and epigenetic variants (e.g. DNA methylation). These data could provide additional power for forecasting response, especially in weakly structured or panmictic species. Incorporating structural and epigenetic variation into estimates of climate change vulnerability, or maladaptation, may not only improve prediction power but also provide insight into the molecular mechanisms underpinning species' response to climate change.
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Affiliation(s)
- Kara K S Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Ian R Bradbury
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Canada
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15
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Meisner J, Albrechtsen A, Hanghøj K. Detecting selection in low-coverage high-throughput sequencing data using principal component analysis. BMC Bioinformatics 2021; 22:470. [PMID: 34587903 PMCID: PMC8480091 DOI: 10.1186/s12859-021-04375-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/10/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Identification of selection signatures between populations is often an important part of a population genetic study. Leveraging high-throughput DNA sequencing larger sample sizes of populations with similar ancestries has become increasingly common. This has led to the need of methods capable of identifying signals of selection in populations with a continuous cline of genetic differentiation. Individuals from continuous populations are inherently challenging to group into meaningful units which is why existing methods rely on principal components analysis for inference of the selection signals. These existing methods require called genotypes as input which is problematic for studies based on low-coverage sequencing data. MATERIALS AND METHODS We have extended two principal component analysis based selection statistics to genotype likelihood data and applied them to low-coverage sequencing data from the 1000 Genomes Project for populations with European and East Asian ancestry to detect signals of selection in samples with continuous population structure. RESULTS Here, we present two selections statistics which we have implemented in the PCAngsd framework. These methods account for genotype uncertainty, opening for the opportunity to conduct selection scans in continuous populations from low and/or variable coverage sequencing data. To illustrate their use, we applied the methods to low-coverage sequencing data from human populations of East Asian and European ancestries and show that the implemented selection statistics can control the false positive rate and that they identify the same signatures of selection from low-coverage sequencing data as state-of-the-art software using high quality called genotypes. CONCLUSION We show that selection scans of low-coverage sequencing data of populations with similar ancestry perform on par with that obtained from high quality genotype data. Moreover, we demonstrate that PCAngsd outperform selection statistics obtained from called genotypes from low-coverage sequencing data without the need for ad-hoc filtering.
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Affiliation(s)
- Jonas Meisner
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.
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16
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O’Donnell TP, Sullivan TJ. Low-coverage whole-genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod ( Gadus morhua, Linnaeus 1758). Ecol Evol 2021; 11:10659-10671. [PMID: 34367604 PMCID: PMC8328444 DOI: 10.1002/ece3.7878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 11/28/2022] Open
Abstract
Atlantic cod (Gadus morhua, Linnaeus 1758) in the western Gulf of Maine are managed as a single stock despite several lines of evidence supporting two spawning groups (spring and winter) that overlap spatially, while exhibiting seasonal spawning isolation. Low-coverage whole-genome sequencing was used to evaluate the genomic population structure of Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank using 222 individuals collected over multiple years. Results indicated low total genomic differentiation, while also showing strong differentiation between spring and winter-spawning groups at specific regions of the genome. Guided regularized random forest and ranked F ST methods were used to select panels of single nucleotide polymorphisms (SNPs) that could reliably distinguish spring and winter-spawning Atlantic cod (88.5% assignment rate), as well as males and females (95.0% assignment rate) collected in the western Gulf of Maine. These SNP panels represent a valuable tool for fisheries research and management of Atlantic cod in the western Gulf of Maine that will aid investigations of stock production and support accuracy of future assessments.
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Affiliation(s)
| | - Timothy J. Sullivan
- Gloucester Marine Genomics InstituteGloucesterMAUSA
- USDA – National Institute of Food and AgricultureKansas CityMOUSA
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17
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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: 7] [Impact Index Per Article: 2.3] [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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18
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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: 17] [Impact Index Per Article: 5.7] [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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19
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Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evol Lett 2021; 5:196-213. [PMID: 34136269 PMCID: PMC8190449 DOI: 10.1002/evl3.227] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/06/2021] [Accepted: 03/29/2021] [Indexed: 01/11/2023] Open
Abstract
Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.
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Affiliation(s)
- Eva L Koch
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Hernán E Morales
- Evolutionary Genetics Section Globe Institute University of Copenhagen Copenhagen Denmark.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Jenny Larsson
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Anja M Westram
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,IST Austria Klosterneuburg Austria
| | - Rui Faria
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee Florida FL 32306-4120
| | - E Moriarty Lemmon
- Department of Biological Science Florida State University Tallahassee Florida FL 32306-4295
| | - Kerstin Johannesson
- Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Roger K Butlin
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
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20
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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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21
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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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22
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Dai P, Sun G, Jia Y, Pan Z, Tian Y, Peng Z, Li H, He S, Du X. Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3273-3285. [PMID: 32844253 DOI: 10.1007/s00122-020-03668-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/08/2020] [Indexed: 05/06/2023]
Abstract
Three extensive eco-haplotypes associated with population differentiation and environmental adaptability in Upland cotton were identified, with A06_85658585, A08_43734499 and A06_113104285 considered the eco-loci for environmental adaptability. Population divergence is suggested to be the primary force driving the evolution of environmental adaptability in various species. Chromosome inversion increases reproductive isolation between subspecies and accelerates population divergence to adapt to new environments. Although modern cultivated Upland cotton (Gossypium hirsutum L.) has spread worldwide, the noticeable phenotypic differences still existed among cultivars grown in different areas. In recent years, the long-distance migration of cotton cultivation areas throughout China has demanded that breeders better understand the genetic basis of environmental adaptability in Upland cotton. Here, we integrated the genotypes of 419 diverse accessions, long-term environment-associated variables (EAVs) and environment-associated traits (EATs) to evaluate subgroup differentiation and identify adaptive loci in Upland cotton. Two highly divergent genomic regions were found on chromosomes A06 and A08, which likely caused by extensive chromosome inversions. The subgroups could be geographically classified based on distinct haplotypes in the divergent regions. A genome-wide association study (GWAS) also confirmed that loci located in these regions were significantly associated with environmental adaptability in Upland cotton. Our study first revealed the cause of population divergence in Upland cotton, as well as the consequences of variation in its environmental adaptability. These findings provide new insights into the genetic basis of environmental adaptability in Upland cotton, which could accelerate the development of molecular markers for adaptation to climate change in future cotton breeding.
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Affiliation(s)
- Panhong Dai
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Agricultural College, Yangtze University, Jingzhou, 434000, China
| | - Gaofei Sun
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- School of Computer Science & Information Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Yinhua Jia
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaoe Pan
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yingbing Tian
- Agricultural College, Yangtze University, Jingzhou, 434000, China
| | - Zhen Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Hongge Li
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Shoupu He
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| | - Xiongming Du
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
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23
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Nowling RJ, Manke KR, Emrich SJ. Detecting inversions with PCA in the presence of population structure. PLoS One 2020; 15:e0240429. [PMID: 33119626 PMCID: PMC7595445 DOI: 10.1371/journal.pone.0240429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Chromosomal inversions can lead to reproductive isolation and adaptation in insects such as Drosophila melanogaster and the non-model malaria vector Anopheles gambiae. Inversions can be detected and characterized using principal component analysis (PCA) of single nucleotide polymorphisms (SNPs). To aid in developing such methods, we formed a new benchmark derived from three publicly-available insect data. We then used this benchmark to perform an extended validation of our software for inversion analysis (Asaph). Through that process, we identified and characterized several problematic test cases liable to misinterpretation that can help guide PCA-based inversion detection. Lastly, we re-analyzed the 2R chromosome arm of 150 An. gambiae and coluzzii samples and observed two inversions (2Rc and 2Rd) that were previously known but not annotated in these particular individuals. The resulting benchmark data set and methods will be useful for future inversion detection based solely on SNP data.
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Affiliation(s)
- Ronald J. Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, WI
| | - Krystal R. Manke
- Physics and Chemistry, Milwaukee School of Engineering, Milwaukee, WI
| | - Scott J. Emrich
- Electrical Engineering and Computer Science, University of Tennessee–Knoxville, Knoxville, TN
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24
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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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25
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Perrier C, Rougemont Q, Charmantier A. Demographic history and genomics of local adaptation in blue tit populations. Evol Appl 2020; 13:1145-1165. [PMID: 32684952 PMCID: PMC7359843 DOI: 10.1111/eva.13035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 12/24/2022] Open
Abstract
Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio‐temporal variations in population demography and variations in recombination rate and in diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests, and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (FST = 0.003 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long‐lasting gene flow between populations inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (FST = 0.08 on average), in line with the inference of moderate ancestral migration, followed by isolation since the end of the last glaciation. Effective population sizes were large, yet smaller on the island than on the mainland. Weak and nonparallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds and were more often found in regions of low recombination, as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8 Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.
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Affiliation(s)
- Charles Perrier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 CNRS Univ Montpellier CNRS EPHE IRD Univ Paul Valéry Montpellier 3 Montpellier France.,Centre de Biologie pour la Gestion des Populations UMR CBGP INRAE CIRAD IRD Montpellier SupAgro Univ Montpellier Montpellier France
| | - Quentin Rougemont
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 CNRS Univ Montpellier CNRS EPHE IRD Univ Paul Valéry Montpellier 3 Montpellier France
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26
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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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27
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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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28
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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: 23] [Impact Index Per Article: 4.6] [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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29
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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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30
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Weinstein SY, Thrower FP, Nichols KM, Hale MC. A large-scale chromosomal inversion is not associated with life history development in rainbow trout from Southeast Alaska. PLoS One 2019; 14:e0223018. [PMID: 31539414 PMCID: PMC6754156 DOI: 10.1371/journal.pone.0223018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/11/2019] [Indexed: 01/12/2023] Open
Abstract
In studying the causative mechanisms behind migration and life history, the salmonids-salmon, trout, and charr-are an exemplary taxonomic group, as life history development is known to have a strong genetic component. A double inversion located on chromosome 5 in rainbow trout (Oncorhynchus mykiss) is associated with life history development in multiple populations, but the importance of this inversion has not been thoroughly tested in conjunction with other polymorphisms in the genome. To that end, we used a high-density SNP chip to genotype 192 F1 migratory and resident rainbow trout and focused our analyses to determine whether this inversion is important in life history development in a well-studied population of rainbow trout from Southeast Alaska. We identified 4,994 and 436 SNPs-predominantly outside of the inversion region-associated with life history development in the migrant and resident familial lines, respectively. Although F1 samples showed genomic patterns consistent with the double inversion on chromosome 5 (reduced observed and expected heterozygosity and an increase in linkage disequilibrium), we found no statistical association between the inversion and life history development. Progeny produced by crossing resident trout and progeny produced by crossing migrant trout both consisted of a mix of migrant and resident individuals, irrespective of the individuals' inversion haplotype on chromosome 5. This suggests that although the inversion is present at a low frequency, it is not strongly associated with migration as it is in populations of Oncorhynchus mykiss from lower latitudes.
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Affiliation(s)
- Spencer Y. Weinstein
- Department of Biology, Texas Christian University, Fort Worth, United States of America
| | - Frank P. Thrower
- Ted Stevens Marine Research Institute, Alaska Fisheries Center, NOAA, Juneau, AK, United States of America
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, Seattle, WA, United States of America
| | - Matthew C. Hale
- Department of Biology, Texas Christian University, Fort Worth, United States of America
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31
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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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32
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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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33
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Lehnert SJ, Bentzen P, Kess T, Lien S, Horne JB, Clément M, Bradbury IR. Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon. Mol Ecol 2019; 28:2074-2087. [DOI: 10.1111/mec.15065] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/12/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Sarah J. Lehnert
- Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada
| | - Paul Bentzen
- Biology Department Dalhousie University Halifax Nova Scotia Canada
| | - Tony Kess
- 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
| | - John B. Horne
- Gulf Coast Research Laboratory University of Southern Mississippi Ocean Springs Mississippi USA
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute Memorial University of Newfoundland St. John's Newfoundland Canada
- Labrador Institute Memorial University of Newfoundland Happy Valley‐Goose Bay 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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34
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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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35
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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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36
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Fuller ZL, Koury SA, Phadnis N, Schaeffer SW. How chromosomal rearrangements shape adaptation and speciation: Case studies in Drosophila pseudoobscura and its sibling species Drosophila persimilis. Mol Ecol 2019; 28:1283-1301. [PMID: 30402909 PMCID: PMC6475473 DOI: 10.1111/mec.14923] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/30/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023]
Abstract
The gene arrangements of Drosophila have played a prominent role in the history of evolutionary biology from the original quantification of genetic diversity to current studies of the mechanisms for the origin and establishment of new inversion mutations within populations and their subsequent fixation between species supporting reproductive barriers. This review examines the genetic causes and consequences of inversions as recombination suppressors and the role that recombination suppression plays in establishing inversions in populations as they are involved in adaptation within heterogeneous environments. This often results in the formation of clines of gene arrangement frequencies among populations. Recombination suppression leads to the differentiation of the gene arrangements which may accelerate the accumulation of fixed genetic differences among populations. If these fixed mutations cause incompatibilities, then inversions pose important reproductive barriers between species. This review uses the evolution of inversions in Drosophila pseudoobscura and D. persimilis as a case study for how inversions originate, establish and contribute to the evolution of reproductive isolation.
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Affiliation(s)
- Zachary L. Fuller
- Department of Biology, The Pennsylvania State University, 208 Erwin W. Mueller Laboratory, University Park, PA 16802-5301
| | - Spencer A. Koury
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Nitin Phadnis
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Stephen W. Schaeffer
- Department of Biology, The Pennsylvania State University, 208 Erwin W. Mueller Laboratory, University Park, PA 16802-5301
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37
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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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38
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Wellband K, Mérot C, Linnansaari T, Elliott JAK, Curry RA, Bernatchez L. Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon. Mol Ecol 2018; 28:1439-1459. [PMID: 30506831 DOI: 10.1111/mec.14965] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/30/2022]
Abstract
Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation, we genotyped 728 juvenile salmon using a 50 K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global FST = 0.004) and failed to support hierarchical structure between the river's two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (FST = 0.019), and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250-Kb region of chromosome 9, including the gene six6 that has previously been linked to age-at-maturity and run-timing for this species. Overall, our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.
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Affiliation(s)
- Kyle Wellband
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Tommi Linnansaari
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - J A K Elliott
- Cooke Aquaculture Inc, Oak Bay, New Brunswick, Canada
| | - R Allen Curry
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
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39
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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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40
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Campbell CR, Poelstra JW, Yoder AD. What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly063] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - J W Poelstra
- Department of Biology, Duke University, Durham, NC, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
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41
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Eco-Evolutionary Genomics of Chromosomal Inversions. Trends Ecol Evol 2018; 33:427-440. [DOI: 10.1016/j.tree.2018.04.002] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/17/2023]
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