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Pettersson ME, Quintela M, Besnier F, Deng Q, Berg F, Kvamme C, Bekkevold D, Mosbech MB, Bunikis I, Lille-Langøy R, Leonori I, Wallberg A, Glover KA, Andersson L. Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring. Genome Biol Evol 2024; 16:evae133. [PMID: 38918882 PMCID: PMC11226789 DOI: 10.1093/gbe/evae133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/21/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.
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Affiliation(s)
- Mats E Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | | - Qiaoling Deng
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Florian Berg
- Institute of Marine Research, 5817 Bergen, Norway
| | | | - Dorte Bekkevold
- DTU-Aqua National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | | | | | - Iole Leonori
- CNR IRBIM, Italian National Research Council, Institute for Marine Biological Resources and Biotechnology, 60125 Ancona, Italy
| | - Andreas Wallberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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2
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Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. Diverse pathways to speciation revealed by marine snails. Trends Genet 2024; 40:337-351. [PMID: 38395682 DOI: 10.1016/j.tig.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024]
Abstract
Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Rui Faria
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Alan Le Moan
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; CNRS & Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Marina Rafajlović
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Department of Marine Sciences, University of Gothenburg, SE 41390 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Anja Marie Westram
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Roger K Butlin
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Sean Stankowski
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Institute of Science and Technology Austria, Klosterneuburg, Austria; Department of Ecology and Evolution, University of Sussex, Brighton, UK
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3
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Lecomte L, Árnyasi M, Ferchaud A, Kent M, Lien S, Stenløkk K, Sylvestre F, Bernatchez L, Mérot C. Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations. Evol Appl 2024; 17:e13653. [PMID: 38495945 PMCID: PMC10940791 DOI: 10.1111/eva.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/14/2023] [Accepted: 01/13/2024] [Indexed: 03/19/2024] Open
Abstract
Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short- (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of F ST and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large-scale SV characterization and highlights its relevance for salmonid population genomics.
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Affiliation(s)
- Laurie Lecomte
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Département de BiologieUniversité LavalQuébecCanada
| | - Mariann Árnyasi
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE)Norwegian University of Life Sciences (NMBU)ÅsNorway
| | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Département de BiologieUniversité LavalQuébecCanada
- Present address:
Parks Canada, Office of the Chief Ecosystem ScientistQuébecQCCanada
| | - 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)ÅsNorway
| | - 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)ÅsNorway
| | - Kristina Stenløkk
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE)Norwegian University of Life Sciences (NMBU)ÅsNorway
| | - Florent Sylvestre
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Département de BiologieUniversité LavalQuébecCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Département de BiologieUniversité LavalQuébecCanada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Département de BiologieUniversité LavalQuébecCanada
- Present address:
UMR 6553 Ecobio, OSUR, CNRSUniversité de RennesRennesFrance
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4
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Dean LL, Whiting JR, Jones FC, MacColl ADC. Reproductive isolation in a three-way contact zone. Mol Ecol 2024; 33:e17275. [PMID: 38235507 DOI: 10.1111/mec.17275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Contact zones between divergent forms within a species provide insight into the role of gene flow in adaptation and speciation. Previous work has focused on contact zones involving only two divergent forms, but in nature, many more than two populations may overlap simultaneously and experience gene flow. Patterns of introgression in wild populations are, therefore, likely much more complicated than is often assumed. We begin to address this gap in current knowledge by investigating patterns of divergence and introgression across a complex natural contact zone. We use phenotypic and genomic data to confirm the existence of a three-way contact zone among divergent freshwater resident, saltwater resident and saltwater migratory three-spined stickleback (Gasterosteus aculeatus) on the island of North Uist, Scottish Western Isles. We find evidence for hybridization, mostly between saltwater resident and saltwater migratory forms. Despite hybridization, genomic analyses reveal pairwise islands of divergence between all forms that are maintained across the contact zone. Genomic cline analyses also provide evidence for selection and/or hybrid incompatibilities in divergent regions. Divergent genomic regions occur across multiple chromosomes and involve many known adaptive loci and several chromosomal inversions. We also identify distinct immune gene expression profiles between forms, but no evidence for transgressive expression in hybrids. Our results suggest that reproductive isolation is maintained in this three-way contact zone, despite some hybridization, and that reduced recombination in chromosomal inversions may play an important role in maintaining this isolation.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - James R Whiting
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
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5
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Andersson L, Bekkevold D, Berg F, Farrell ED, Felkel S, Ferreira MS, Fuentes-Pardo AP, Goodall J, Pettersson M. How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map. Annu Rev Anim Biosci 2024; 12:1-20. [PMID: 37906837 DOI: 10.1146/annurev-animal-021122-102933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.
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Affiliation(s)
- Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Edward D Farrell
- Killybegs Fishermen's Organisation, Killybegs, County Donegal, Ireland
| | - Sabine Felkel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Mafalda S Ferreira
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Angela P Fuentes-Pardo
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Jake Goodall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
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6
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Ulmo‐Diaz G, Engman A, McLarney WO, Lasso Alcalá CA, Hendrickson D, Bezault E, Feunteun E, Prats‐Léon FL, Wiener J, Maxwell R, Mohammed RS, Kwak TJ, Benchetrit J, Bougas B, Babin C, Normandeau E, Djambazian HHV, Chen S, Reiling SJ, Ragoussis J, Bernatchez L. Panmixia in the American eel extends to its tropical range of distribution: Biological implications and policymaking challenges. Evol Appl 2023; 16:1872-1888. [PMID: 38143897 PMCID: PMC10739100 DOI: 10.1111/eva.13599] [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: 05/23/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 12/26/2023] Open
Abstract
The American eel (Anguilla rostrata) has long been regarded as a panmictic fish and has been confirmed as such in the northern part of its range. In this paper, we tested for the first time whether panmixia extends to the tropical range of the species. To do so, we first assembled a reference genome (975 Mbp, 19 chromosomes) combining long (PacBio and Nanopore and short (Illumina paired-end) reads technologies to support both this study and future research. To test for population structure, we estimated genotype likelihoods from low-coverage whole-genome sequencing of 460 American eels, collected at 21 sampling sites (in seven geographic regions) ranging from Canada to Trinidad and Tobago. We estimated genetic distance between regions, performed ADMIXTURE-like clustering analysis and multivariate analysis, and found no evidence of population structure, thus confirming that panmixia extends to the tropical range of the species. In addition, two genomic regions with putative inversions were observed, both geographically widespread and present at similar frequencies in all regions. We discuss the implications of lack of genetic population structure for the species. Our results are key for the future genomic research in the American eel and the implementation of conservation measures throughout its geographic range. Additionally, our results can be applied to fisheries management and aquaculture of the species.
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Affiliation(s)
- Gabriela Ulmo‐Diaz
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Augustin Engman
- University of Tennessee Institute of Agriculture, School of Natural ResourcesKnoxvilleTennesseeUSA
| | | | | | - Dean Hendrickson
- Department of Integrative Biology and Biodiversity CollectionsUniversity of Texas at AustinAustinTexasUSA
| | - Etienne Bezault
- UMR 8067 BOREA, Biologie Organismes Écosystèmes Aquatiques (MNHN, CNRS, SU, IRD, UCN, UA)Université des AntillesPointe‐à‐PitreGuadeloupe
- Caribaea Initiative, Département de BiologieUniversité Des Antilles‐Campus de FouillolePointe‐à‐PitreGuadeloupeFrance
| | - Eric Feunteun
- UMR 7208 BOREABiologie Organismes Écosystèmes Aquatiques (MNHN, CNRS, SU,IRD, UCN, UA)Station Marine de DinardRennesFrance
- EPHE‐PSLCGEL (Centre de Géoécologie Littorale)DinardFrance
| | | | - Jean Wiener
- Fondation pour la Protection de la Biodiversité Marine (FoProBiM)CaracolHaiti
| | - Robert Maxwell
- Inland Fisheries SectionLouisiana Department of Wildlife and FisheriesLouisianaUSA
| | - Ryan S. Mohammed
- The University of the West Indies (UWI)St. AugustineTrinidad and Tobago
- Present address:
Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
| | - Thomas J. Kwak
- US Geological SurveyNorth Carolina Cooperative Fish and Wildlife Research UnitDepartment of Applied EcologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | | | - Bérénice Bougas
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Charles Babin
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Eric Normandeau
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Haig H. V. Djambazian
- McGIll Genome Centre, Department of Human GeneticsVictor Phillip Dahdaleh Institute of Genomic MedicineMcGill UniversityMontrealQuebecCanada
| | - Shu‐Huang Chen
- McGIll Genome Centre, Department of Human GeneticsVictor Phillip Dahdaleh Institute of Genomic MedicineMcGill UniversityMontrealQuebecCanada
| | - Sarah J. Reiling
- McGIll Genome Centre, Department of Human GeneticsVictor Phillip Dahdaleh Institute of Genomic MedicineMcGill UniversityMontrealQuebecCanada
| | - Jiannis Ragoussis
- McGIll Genome Centre, Department of Human GeneticsVictor Phillip Dahdaleh Institute of Genomic MedicineMcGill UniversityMontrealQuebecCanada
| | - Louis Bernatchez
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
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7
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Barr K, Bossu CM, Bay RA, Anderson EC, Belthoff J, Trulio LA, Chromczak D, Wisinski CL, Smith TB, Ruegg KC. Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management. Evol Appl 2023; 16:1889-1900. [PMID: 38143900 PMCID: PMC10739168 DOI: 10.1111/eva.13600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 12/26/2023] Open
Abstract
Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation-by-distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation-by-distance, and substantially lower inbreeding. Using genotype-environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl.
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Affiliation(s)
- Kelly Barr
- Center for Tropical ResearchInstitute of the Environment and Sustainability, University of California, Los AngelesLos AngelesCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Christen M. Bossu
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Rachael A. Bay
- Department of Evolution and EcologyUniversity of California, DavisDavisCaliforniaUSA
| | - Eric C. Anderson
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Jim Belthoff
- Raptor Research Center and Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Lynne A. Trulio
- Department of Environmental StudiesSan José State UniversitySan JoseCaliforniaUSA
| | - Debra Chromczak
- Burrowing Owl Researcher & ConsultantRiegelsvillePennsylvaniaUSA
| | | | - Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment and Sustainability, University of California, Los AngelesLos AngelesCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Kristen C. Ruegg
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
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8
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Johnson ZV, Hegarty BE, Gruenhagen GW, Lancaster TJ, McGrath PT, Streelman JT. Cellular profiling of a recently-evolved social behavior in cichlid fishes. Nat Commun 2023; 14:4891. [PMID: 37580322 PMCID: PMC10425353 DOI: 10.1038/s41467-023-40331-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/21/2023] [Indexed: 08/16/2023] Open
Abstract
Social behaviors are diverse in nature, but it is unclear how conserved genes, brain regions, and cell populations generate this diversity. Here we investigate bower-building, a recently-evolved social behavior in cichlid fishes. We use single nucleus RNA-sequencing in 38 individuals to show signatures of recent behavior in specific neuronal populations, and building-associated rebalancing of neuronal proportions in the putative homolog of the hippocampal formation. Using comparative genomics across 27 species, we trace bower-associated genome evolution to a subpopulation of glia lining the dorsal telencephalon. We show evidence that building-associated neural activity and a departure from quiescence in this glial subpopulation together regulate hippocampal-like neuronal rebalancing. Our work links behavior-associated genomic variation to specific brain cell types and their functions, and suggests a social behavior has evolved through changes in glia.
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Affiliation(s)
- Zachary V Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA.
- Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
| | - Brianna E Hegarty
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - George W Gruenhagen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Tucker J Lancaster
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Jeffrey T Streelman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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9
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Reid BN, Star B, Pinsky ML. Detecting parallel polygenic adaptation to novel evolutionary pressure in wild populations: a case study in Atlantic cod ( Gadus morhua). Philos Trans R Soc Lond B Biol Sci 2023; 378:20220190. [PMID: 37246382 DOI: 10.1098/rstb.2022.0190] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/13/2023] [Indexed: 05/30/2023] Open
Abstract
Populations can adapt to novel selection pressures through dramatic frequency changes in a few genes of large effect or subtle shifts in many genes of small effect. The latter (polygenic adaptation) is expected to be the primary mode of evolution for many life-history traits but tends to be more difficult to detect than changes in genes of large effect. Atlantic cod (Gadus morhua) were subjected to intense fishing pressure over the twentieth century, leading to abundance crashes and a phenotypic shift toward earlier maturation across many populations. Here, we use spatially replicated temporal genomic data to test for a shared polygenic adaptive response to fishing using methods previously applied to evolve-and-resequence experiments. Cod populations on either side of the Atlantic show covariance in allele frequency change across the genome that are characteristic of recent polygenic adaptation. Using simulations, we demonstrate that the degree of covariance in allele frequency change observed in cod is unlikely to be explained by neutral processes or background selection. As human pressures on wild populations continue to increase, understanding and attributing modes of adaptation using methods similar to those demonstrated here will be important in identifying the capacity for adaptive responses and evolutionary rescue. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.
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Affiliation(s)
- Brendan N Reid
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08540, USA
| | - Bastiaan Star
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Malin L Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08540, USA
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10
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Helmerson C, Weist P, Brieuc MSO, Maurstad MF, Schade FM, Dierking J, Petereit C, Knutsen H, Metcalfe J, Righton D, André C, Krumme U, Jentoft S, Hanel R. Evidence of hybridization between genetically distinct Baltic cod stocks during peak population abundance(s). Evol Appl 2023; 16:1359-1376. [PMID: 37492148 PMCID: PMC10363836 DOI: 10.1111/eva.13575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 07/27/2023] Open
Abstract
Range expansions can lead to increased contact of divergent populations, thus increasing the potential of hybridization events. Whether viable hybrids are produced will most likely depend on the level of genomic divergence and associated genomic incompatibilities between the different entities as well as environmental conditions. By taking advantage of historical Baltic cod (Gadus morhua) otolith samples combined with genotyping and whole genome sequencing, we here investigate the genetic impact of the increased spawning stock biomass of the eastern Baltic cod stock in the mid 1980s. The eastern Baltic cod is genetically highly differentiated from the adjacent western Baltic cod and locally adapted to the brackish environmental conditions in the deeper Eastern basins of the Baltic Sea unsuitable for its marine counterparts. Our genotyping results show an increased proportion of eastern Baltic cod in western Baltic areas (Mecklenburg Bay and Arkona Basin)-indicative of a range expansion westwards-during the peak population abundance in the 1980s. Additionally, we detect high frequencies of potential hybrids (including F1, F2 and backcrosses), verified by whole genome sequencing data for a subset of individuals. Analysis of mitochondrial genomes further indicates directional gene flow from eastern Baltic cod males to western Baltic cod females. Our findings unravel that increased overlap in distribution can promote hybridization between highly divergent populations and that the hybrids can be viable and survive under specific and favourable environmental conditions. However, the observed hybridization had seemingly no long-lasting impact on the continuous separation and genetic differentiation between the unique Baltic cod stocks.
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Affiliation(s)
- Cecilia Helmerson
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
| | - Peggy Weist
- Thünen Institute of Fisheries EcologyBremerhavenGermany
| | - Marine Servane Ono Brieuc
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
- Institute of Marine ResearchBergenNorway
| | - Marius F. Maurstad
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
| | | | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research KielGermany
| | | | - Halvor Knutsen
- Institute of Marine ResearchBergenNorway
- Centre for Coastal ResearchUniversity of AgderKristiansandNorway
| | - Julian Metcalfe
- Centre for Environment Fisheries and Aquaculture ScienceLowestoftUK
| | - David Righton
- Centre for Environment Fisheries and Aquaculture ScienceLowestoftUK
| | - Carl André
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | - Uwe Krumme
- Thünen Institute of Baltic Sea FisheriesRostockGermany
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
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11
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Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations. Animals (Basel) 2023; 13:ani13061089. [PMID: 36978629 PMCID: PMC10044284 DOI: 10.3390/ani13061089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Simple Summary In recent decades, societies, states and local authorities have become increasingly aware that for effective long-term management and protection of aquatic ecosystems and populations, it is necessary to take into account the genetic changes occurring in these populations. One type of high-resolution molecular marker suitable for studying the neutral and adaptive genetic diversity of populations is single nucleotide polymorphism (SNP). This review is an attempt to show the benefits of using SNPs to recognize natural populations of aquatic animals and detect the threats to them from accidentally or intentionally released farm animals, fishery and global climate changes. It is postulated that conservation actions should protect not only pristine natural populations that are endangered or overfished, but also protect populations of non-threatened species from unnecessarily released semi-domesticated animals. The enhancement of natural populations with farmed material usually reduces their genetic diversity. Experimental size-selective catches of artificially created populations have caused evolutionary changes in the life cycles of fishes. However, fishery-induced evolution in natural populations is difficult to observe. The negative measurable effects on populations can be expected when the number of breeding individuals is reduced below 100, which occurs very rarely in the sea and more often in fragmented freshwater streams, ponds and seasonal rivers. Abstract An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.
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12
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Bachmann L, Beermann J, Brey T, de Boer HJ, Dannheim J, Edvardsen B, Ericson PGP, Holston KC, Johansson VA, Kloss P, Konijnenberg R, Osborn KJ, Pappalardo P, Pehlke H, Piepenburg D, Struck TH, Sundberg P, Markussen SS, Teschke K, Vanhove MPM. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. ZOOL SCR 2023. [DOI: 10.1111/zsc.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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13
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Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
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14
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Lapègue S, Reisser C, Harrang E, Heurtebise S, Bierne N. Genetic parallelism between European flat oyster populations at the edge of their natural range. Evol Appl 2023; 16:393-407. [PMID: 36793680 PMCID: PMC9923475 DOI: 10.1111/eva.13449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
Although all marine ecosystems have experienced global-scale losses, oyster reefs have shown the greatest. Therefore, substantial efforts have been dedicated to restoration of such ecosystems during the last two decades. In Europe, several pilot projects for the restoration of the native European flat oyster, Ostrea edulis, recently begun and recommendations to preserve genetic diversity and to conduct monitoring protocols have been made. In particular, an initial step is to test for genetic differentiation against homogeneity among the oyster populations potentially involved in such programs. Therefore, we conducted a new sampling of wild populations at the European scale and a new genetic analysis with 203 markers to (1) confirm and study in more detail the pattern of genetic differentiation between Atlantic and Mediterranean populations, (2) identify potential translocations that could be due to aquaculture practices and (3) investigate the populations at the fringe of the geographical range, since they seemed related despite their geographic distance. Such information should be useful to enlighten the choice of the animals to be translocated or reproduced in hatcheries for further restocking. After the confirmation of the general geographical pattern of genetic structure and the identification of one potential case of aquaculture transfer at a large scale, we were able to detect genomic islands of differentiation mainly in the form of two groups of linked markers, which could indicate the presence of polymorphic chromosomal rearrangements. Furthermore, we observed a tendency for these two islands and the most differentiated loci to show a parallel pattern of differentiation, grouping the North Sea populations with the Eastern Mediterranean and Black Sea populations, against geography. We discussed the hypothesis that this genetic parallelism could be the sign of a shared evolutionary history of the two groups of populations despite them being at the border of the distribution nowadays.
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Affiliation(s)
- Sylvie Lapègue
- MARBEC, Univ Montpellier, CNRS Ifremer, IRD Montpellier France
| | - Céline Reisser
- MARBEC, Univ Montpellier, CNRS Ifremer, IRD Montpellier France
| | | | | | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD Montpellier France
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15
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Pampoulie C, Berg PR, Jentoft S. Hidden but revealed: After years of genetic studies behavioural monitoring combined with genomics uncover new insight into the population dynamics of Atlantic cod in Icelandic waters. Evol Appl 2023; 16:223-233. [PMID: 36793686 PMCID: PMC9923494 DOI: 10.1111/eva.13471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/29/2022] [Accepted: 08/18/2022] [Indexed: 11/27/2022] Open
Abstract
Stock structure is of paramount importance for sustainable management of exploited resources. In that context, genetic markers have been used for more than two decades to resolve spatial structure of marine exploited resources and to fully fathom stock dynamics and interactions. While genetic markers such as allozymes and RFLP dominated the debate in the early era of genetics, technology advances have provided scientists with new tools every decade to better assess stock discrimination and interactions (i.e. gene flow). Here, we provide a review of genetic studies performed to understand stock structure of Atlantic cod in Icelandic waters, from the early allozyme approaches to the genomic work currently carried out. We further highlight the importance of the generation of a chromosome-anchored genome assembly together with whole-genome population data, which drastically changed our perception of the possible management units to consider. After nearly 60 years of genetic investigation of Atlantic cod structure in Icelandic waters, genetic (and later genomic) data combined with behavioural monitoring using Data Storage Tags shifted the attention from geographical population structures to behavioural ecotypes. This review also demonstrates the need for future research to further disentangle the impact of these ecotypes (and gene flow among them) on the population structure of Atlantic cod in Icelandic waters. It also highlights the importance of whole-genome data to unravel unexpected within-species diversity related to chromosomal inversions and associated supergenes, which are important to consider for future development of sustainable management programmes of the species within the North Atlantic.
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Affiliation(s)
| | - Paul Ragnar Berg
- Norwegian Institute for Water Research Oslo Norway.,Department of Natural Sciences, Centre for Coastal Research (CCR) University of Agder Kristiansand Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis Oslo Norway
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16
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Coughlan JM, Dagilis AJ, Serrato-Capuchina A, Elias H, Peede D, Isbell K, Castillo DM, Cooper BS, Matute DR. Patterns of Population Structure and Introgression Among Recently Differentiated Drosophila melanogaster Populations. Mol Biol Evol 2022; 39:msac223. [PMID: 36251862 PMCID: PMC9641974 DOI: 10.1093/molbev/msac223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Despite a century of genetic analysis, the evolutionary processes that have generated the patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. In particular, how genetic variation is partitioned within its putative ancestral range in Southern Africa remains unresolved. Here, we study patterns of population genetic structure, admixture, and the spatial structuring of candidate incompatibility alleles across a global sample, including 223 new accessions, predominantly from remote regions in Southern Africa. We identify nine major ancestries, six that primarily occur in Africa and one that has not been previously described. We find evidence for both contemporary and historical admixture between ancestries, with admixture rates varying both within and between continents. For example, while previous work has highlighted an admixture zone between broadly defined African and European ancestries in the Caribbean and southeastern USA, we identify West African ancestry as the most likely African contributor. Moreover, loci showing the strongest signal of introgression between West Africa and the Caribbean/southeastern USA include several genes relating to neurological development and male courtship behavior, in line with previous work showing shared mating behaviors between these regions. Finally, while we hypothesized that potential incompatibility loci may contribute to population genetic structure across the range of D. melanogaster; these loci are, on average, not highly differentiated between ancestries. This work contributes to our understanding of the evolutionary history of a key model system, and provides insight into the partitioning of diversity across its range.
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Affiliation(s)
- Jenn M Coughlan
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Andrius J Dagilis
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | | | - Hope Elias
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - David Peede
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Kristin Isbell
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Dean M Castillo
- Institute of Agriculture and Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
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17
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Martínez-García L, Ferrari G, Cuevas A, Atmore LM, López-Arias B, Culling M, Llorente-Rodríguez L, Morales-Muñiz A, Roselló-Izquierdo E, Quirós JA, Marlasca-Martín R, Hänfling B, Hutchinson WF, Jakobsen KS, Jentoft S, Orton D, Star B, Barrett JH. Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe. Proc Biol Sci 2022; 289:20221107. [PMID: 36259206 DOI: 10.1098/rspb.2022.1107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050-1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times.
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Affiliation(s)
- Lourdes Martínez-García
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway.,Royal Botanic Garden Edinburgh, Edinburgh EH3 5NZ, UK
| | - Angélica Cuevas
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Begoña López-Arias
- Laboratorio de Arqueozoología LAZ-UAM, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Mark Culling
- Evolutionary Biology Group, Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
| | - Laura Llorente-Rodríguez
- Laboratory for Archaezoological Studies, Faculty of Archaeology, University of Leiden, Leiden 2311 EZ, The Netherlands
| | - Arturo Morales-Muñiz
- Laboratorio de Arqueozoología LAZ-UAM, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | - Juan Antonio Quirós
- Department of Geography, Prehistory and Archaeology, University of the Basque Country, Vitoria-Gasteiz 48940, Spain
| | | | - Bernd Hänfling
- Institute for Biodiversity and Freshwater Conservation, UHI-Inverness, Inverness, UK
| | - William F Hutchinson
- Evolutionary Biology Group, Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - James H Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim 7012, Norway
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18
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Spies I, Tarpey C, Kristiansen T, Fisher M, Rohan S, Hauser L. Genomic differentiation in Pacific cod using
P
ool‐
S
eq. Evol Appl 2022; 15:1907-1924. [PMID: 36426128 PMCID: PMC9679252 DOI: 10.1111/eva.13488] [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: 03/15/2022] [Revised: 09/05/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022] Open
Abstract
Patterns of genetic differentiation across the genome can provide insight into selective forces driving adaptation. We used pooled whole genome sequencing, gene annotation, and environmental covariates to evaluate patterns of genomic differentiation and to investigate mechanisms responsible for divergence among proximate Pacific cod (Gadus macrocephalus) populations from the Bering Sea and Aleutian Islands and more distant Washington Coast cod. Samples were taken from eight spawning locations, three of which were replicated to estimate consistency in allele frequency estimation. A kernel smoothing moving weighted average of relative divergence (FST) identified 11 genomic islands of differentiation between the Aleutian Islands and Bering Sea samples. In some islands of differentiation, there was also elevated absolute divergence (dXY) and evidence for selection, despite proximity and potential for gene flow. Similar levels of absolute divergence (dXY) but roughly double the relative divergence (FST) were observed between the distant Bering Sea and Washington Coast samples. Islands of differentiation were much smaller than the four large inversions among Atlantic cod ecotypes. Islands of differentiation between the Bering Sea and Aleutian Island were associated with SNPs from five vision system genes, which can be associated with feeding, predator avoidance, orientation, and socialization. We hypothesize that islands of differentiation between Pacific cod from the Bering Sea and Aleutian Islands provide evidence for adaptive differentiation despite gene flow in this commercially important marine species.
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Affiliation(s)
- Ingrid Spies
- Resource Ecology and Fisheries Management Division Alaska Fisheries Science Center Seattle Washington USA
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | | | - Mary Fisher
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Sean Rohan
- Resource Assessment and Conservation Engineering Division Alaska Fisheries Science Center Seattle Washington USA
| | - Lorenz Hauser
- Resource Ecology and Fisheries Management Division Alaska Fisheries Science Center Seattle Washington USA
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19
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Kvistad L, Falk S, Austin L. Widespread genomic signatures of reproductive isolation and sex-specific selection in the Eastern Yellow Robin, Eopsaltria australis. G3 GENES|GENOMES|GENETICS 2022; 12:6605223. [PMID: 35686912 PMCID: PMC9438485 DOI: 10.1093/g3journal/jkac145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 05/31/2022] [Indexed: 11/16/2022]
Abstract
How new species evolve is one of the most fundamental questions in biology. Population divergence, which may lead to speciation, may be occurring in the Eastern Yellow Robin, a common passerine that lives along the eastern coast of Australia. This species is composed of 2 parapatric lineages that have highly divergent mitochondrial DNA; however, similar levels of divergence have not been observed in the nuclear genome. Here we re-examine the nuclear genomes of these mitolineages to test potential mechanisms underlying the discordance between nuclear and mitochondrial divergence. We find that nuclear admixture occurs in a narrow hybrid zone, although the majority of markers across the genome show evidence of reproductive isolation between populations of opposing mitolineages. There is an 8 MB section of a previously identified putative neo-sex chromosome that is highly diverged between allopatric but not parapatric populations, which may be the result of a chromosomal inversion. The neo-sex chromosomal nature of this region, as well as the geographic patterns in which it exhibits divergence, suggest it is unlikely to be contributing to reproductive isolation through mitonuclear incompatibilities as reported in earlier studies. In addition, there are sex differences in the number of markers that are differentiated between populations of opposite mitolineages, with greater differentiation occurring in females, which are heterozygous, than males. These results suggest that, despite the absence of previously observed assortative mating, mitolineages of Eastern Yellow Robin experience at least some postzygotic isolation from each other, in a pattern consistent with Haldane’s Rule.
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Affiliation(s)
- Lynna Kvistad
- Biological Sciences, Monash University , Clayton, VIC 3800, Australia
| | - Stephanie Falk
- Biological Sciences, Monash University , Clayton, VIC 3800, Australia
- Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics , Freiburg D-79108, Germany
| | - Lana Austin
- Biological Sciences, Monash University , Clayton, VIC 3800, Australia
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20
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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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21
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Rick JA, Junker J, Kimirei IA, Sweke EA, Mosille JB, Dinkel C, Mwaiko S, Seehausen O, Wagner CE. The Genetic Population Structure of Lake Tanganyika's Lates Species Flock, an Endemic Radiation of Pelagic Top Predators. J Hered 2022; 113:145-159. [PMID: 35575081 PMCID: PMC9113442 DOI: 10.1093/jhered/esab072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemic Lates species of Lake Tanganyika (Lates stappersii, L. microlepis, L. mariae, and L. angustifrons) using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST = 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure within L. mariae, with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis, and L. angustifrons). Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species-particularly that of L. mariae-which may be important for conservation and management of this culturally and economically important clade of fishes.
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Affiliation(s)
- Jessica A Rick
- Department of Botany and Program in Ecology, University of Wyoming, 1000 E University Dr., Laramie, WY 82072, USA
| | - Julian Junker
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Ismael A Kimirei
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Emmanuel A Sweke
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
- Deep Sea Fishing Authority (DSFA), Zanzibar, Tanzania
| | - Julieth B Mosille
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Christian Dinkel
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
| | - Salome Mwaiko
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Ole Seehausen
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Catherine E Wagner
- Department of Botany and Program in Ecology, University of Wyoming, 1000 E University Dr., Laramie, WY 82072, USA
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22
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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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23
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Martínez-García L, Ferrari G, Hufthammer AK, Jakobsen KS, Jentoft S, Barrett JH, Star B. Ancient DNA reveals a southern presence of the Northeast Arctic cod during the Holocene. Biol Lett 2022; 18:20220021. [PMID: 35506242 PMCID: PMC9065953 DOI: 10.1098/rsbl.2022.0021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Climate change has been implicated in an increased number of distributional shifts of marine species during the last century. Nonetheless, it is unclear whether earlier climatic fluctuations had similar impacts. We use ancient DNA to investigate the long-term spawning distribution of the Northeast Arctic cod (skrei) which performs yearly migrations from the Barents Sea towards spawning grounds along the Norwegian coast. The distribution of these spawning grounds has shifted northwards during the last century, which is thought to be associated with food availability and warming temperatures. We genetically identify skrei specimens from Ruskeneset in west Norway, an archaeological site located south of their current spawning range. Remarkably, 14C analyses date these specimens to the late Holocene, when temperatures were warmer than present-day conditions. Our results either suggest that temperature is not the only driver influencing the spawning distribution of Atlantic cod, or could be indicative of uncertainty in palaeoclimate reconstructions in this region. Regardless, our findings highlight the utility of aDNA to reconstruct the historical distribution of economically important fish populations and reveal the complexity of long-term ecological interactions in the marine environment.
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Affiliation(s)
- Lourdes Martínez-García
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| | - Giada Ferrari
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| | - Anne Karin Hufthammer
- Department of Natural HistoryThe University Museum, , University of Bergen, N-5020 Bergen, Norway
| | - Kjetill S Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| | - Sissel Jentoft
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| | - James H Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, Erling Skakkes 47b, Trondheim, Norway
| | - Bastiaan Star
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
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24
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Stabilizing selection on Atlantic cod supergenes through a millennium of extensive exploitation. Proc Natl Acad Sci U S A 2022; 119:2114904119. [PMID: 35165196 PMCID: PMC8872764 DOI: 10.1073/pnas.2114904119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 12/21/2022] Open
Abstract
Ecological disruption due to human impacts is evident worldwide, and a key to mitigation lies in characterizing the underlying mechanisms of species and ecosystem stability. Here we show that three extensive “supergenes” are maintained in Atlantic cod by stabilizing selection, tying these genes to the persistence of a keystone species distributed across the northern Atlantic Ocean. Removal of this species has caused severe ecosystem reshuffling in several areas of its range. Genomic inference of historic stock sizes further shows that cod has been under pressure in the North Sea system since the Viking period, in line with zooarchaeological records. Expansion of fisheries in Northern Europe through the past millennium is well documented and supports the inferred long-term declines. Life on Earth has been characterized by recurring cycles of ecological stasis and disruption, relating biological eras to geological and climatic transitions through the history of our planet. Due to the increasing degree of ecological abruption caused by human influences many advocate that we now have entered the geological era of the Anthropocene, or “the age of man.” Considering the ongoing mass extinction and ecosystem reshuffling observed worldwide, a better understanding of the drivers of ecological stasis will be a requisite for identifying routes of intervention and mitigation. Ecosystem stability may rely on one or a few keystone species, and the loss of such species could potentially have detrimental effects. The Atlantic cod (Gadus morhua) has historically been highly abundant and is considered a keystone species in ecosystems of the northern Atlantic Ocean. Collapses of cod stocks have been observed on both sides of the Atlantic and reported to have detrimental effects that include vast ecosystem reshuffling. By whole-genome resequencing we demonstrate that stabilizing selection maintains three extensive “supergenes” in Atlantic cod, linking these genes to species persistence and ecological stasis. Genomic inference of historic effective population sizes shows continued declines for cod in the North Sea–Skagerrak–Kattegat system through the past millennia, consistent with an early onset of the marine Anthropocene through industrialization and commercialization of fisheries throughout the medieval period.
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25
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Matschiner M, Barth JMI, Tørresen OK, Star B, Baalsrud HT, Brieuc MSO, Pampoulie C, Bradbury I, Jakobsen KS, Jentoft S. Supergene origin and maintenance in Atlantic cod. Nat Ecol Evol 2022; 6:469-481. [PMID: 35177802 PMCID: PMC8986531 DOI: 10.1038/s41559-022-01661-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
Abstract
Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation. Atlantic cod carries four supergenes linked to migratory lifestyle and environmental adaptations. Using whole-genome sequencing, the authors show that the genome inversions that underlie the supergenes originated at different times and show gene flux between supergene haplotypes.
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Affiliation(s)
- Michael Matschiner
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. .,Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland. .,Natural History Museum, University of Oslo, Oslo, Norway.
| | - Julia Maria Isis Barth
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Ole Kristian Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Helle Tessand Baalsrud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marine Servane Ono Brieuc
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Ian Bradbury
- Fisheries and Oceans Canada, St John's, Newfoundland and Labrador, Canada
| | - Kjetill Sigurd Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
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26
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Spies I, Drinan DP, Petrou EL, Spurr R, Tarpey C, Hartinger T, Larson W, Hauser L. Evidence for selection and spatially distinct patterns found in a putative zona pellucida gene in Pacific cod, and implications for management. Ecol Evol 2021; 11:16661-16679. [PMID: 34938464 PMCID: PMC8668774 DOI: 10.1002/ece3.8284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 11/11/2022] Open
Abstract
Genetic differentiation has been observed in marine species even when no obvious barriers to gene flow exist, and understanding such differentiation is essential for effective fisheries management. Highly differentiated outlier loci can provide information on how genetic variation might not only contribute to local adaptation but may also be affected by historical demographic events. A locus which aligned to a predicted zona pellucida sperm-binding protein 3 gene (ZP3) in Atlantic cod (Gadus morhua) was previously identified as the highest outlier based on F ST in a RADseq study of Pacific cod (Gadus macrocephalus) across the West Coast of North America. However, because of the limited length of the RAD sequence and restricted geographic area of sampling, no conclusion on the functional significance of the observed variation was possible. In other marine species, ZP3 is involved in reproductive isolation, local adaptation, and has neofunctionalized as an antifreeze gene, and so it may provide important insights in functional population structure of Pacific cod. Here, we sequenced a 544-bp region of ZP3 in 230 Pacific cod collected from throughout their geographic range. We observed striking patterns of spatial structuring of ZP3 haplotypes, with a sharp break near Kodiak, Alaska, USA where populations within ~200 km of each other are nearly fixed for different haplotypes, contrasting a pattern of isolation by distance at other genetic markers in this region (F ST = 0.003). Phylogenetic analysis of ZP3 haplotypes revealed that the more southern haplotypes appear to be ancestral, with the northern haplotype evolving more recently, potentially in response to a novel selective pressure as Pacific cod recolonized northern latitudes after glaciation. The sharp break in haplotype frequencies suggests strong selective pressures are operating on small spatial scales and illustrates that selection can create high divergence even in marine species with ample opportunities for gene flow.
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Affiliation(s)
- Ingrid Spies
- Resource Ecology and Fisheries Management DivisionAlaska Fisheries Science CenterSeattleWashingtonUSA
| | - Daniel P. Drinan
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Eleni L. Petrou
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Rory Spurr
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Carolyn Tarpey
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Theodore Hartinger
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Wes Larson
- Ted Stevens Marine Research InstituteAlaska Fisheries Science Center/Auke Bay LaboratoryJuneauAlaskaUSA
| | - Lorenz Hauser
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
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27
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Ferrari G, Atmore LM, Jentoft S, Jakobsen KS, Makowiecki D, Barrett JH, Star B. An accurate assignment test for extremely low-coverage whole-genome sequence data. Mol Ecol Resour 2021; 22:1330-1344. [PMID: 34779123 DOI: 10.1111/1755-0998.13551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.
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Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Daniel Makowiecki
- Department of Environmental Archaeology and Human Paleoecology, Institute of Archaeology, Nicolaus Copernicus University, Torun, Poland
| | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK.,Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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28
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Kitada S, Nakamichi R, Kishino H. Understanding population structure in an evolutionary context: population-specific FST and pairwise FST. G3-GENES GENOMES GENETICS 2021; 11:6364900. [PMID: 34549777 PMCID: PMC8527463 DOI: 10.1093/g3journal/jkab316] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 08/27/2021] [Indexed: 01/04/2023]
Abstract
Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise FST measures population structure, whereas population-specific FST measures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specific FST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise FST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise FST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares estimate of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to coastal areas with abundant rainfall, and to the south where summers are dry. Genomic data highlight the power of the bias-corrected moment estimators of FST, whether global, pairwise, or population-specific, that provide unbiased estimates of FST. All FST moment estimators described in this paper have reasonable processing times and are useful in population genomics studies.
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Affiliation(s)
- Shuichi Kitada
- Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | | | - Hirohisa Kishino
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.,The Research Institute of Evolutionary Biology, Tokyo 138-0098, Japan
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29
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Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern. Mol Ecol 2021; 30:5949-5965. [PMID: 34424587 PMCID: PMC9290615 DOI: 10.1111/mec.16141] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
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Affiliation(s)
- Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, Virginia, USA.,Centre for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - David Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Marissa F Le Lec
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Joseph Guhlin
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand.,Genomics Aotearoa, Dunedin, Otago, New Zealand
| | - Anna W Santure
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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30
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da Silva SAS, de Lima-Filho PA, da Motta-Neto CC, da Costa GWWF, Cioffi MDB, Bertollo LAC, Molina WF. High chromosomal evolutionary dynamics in sleeper gobies (Eleotridae) and notes on disruptive biological factors in Gobiiformes karyotypes (Osteichthyes, Teleostei). MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:293-302. [PMID: 37073290 PMCID: PMC10077260 DOI: 10.1007/s42995-020-00084-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/15/2020] [Indexed: 05/03/2023]
Abstract
The order Gobiiformes is made up of more than 2200 species, representing one of the most diverse groups among teleost fishes. The biological causes for the tachytelic karyotype evolution of the gobies have not yet been fully studied. Here we expanded cytogenetic data for the Eleotridae family, analyzing the neotropical species Dormitator maculatus, Eleotris pisonis, Erotelis smaragdus, and Guavina guavina. In addition, a meta-analytical approach was followed for elucidating the karyotype diversification versus biological aspects (habitat and egg type) of the Gobiiformes. The species E. smaragdus and E. pisonis present 2n = 46 acrocentric chromosomes (NF = 46), D. maculatus 2n = 46 (36sm + 4st + 6a; NF = 86), and G. guavina, the most divergent karyotype, with 2n = 52 acrocentric chromosomes (NF = 52). Besides numeric and structural diversification in the karyotypes, the mapping of rDNAs and microsatellites also showed noticeable numerical and positional variation, supporting the high chromosomal evolutionary dynamism of these species. In Gobiiformes, karyotype patterns which are more divergent from the basal karyotype (2n = 46a) are associated with characteristics less effective to dispersion, such as the benthic habit. These adaptive characteristics, connected with the organization of the repetitive DNA content in the chromosomes, likely play a synergistic role in the remarkable karyotype diversification of this group.
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Affiliation(s)
- Simião Alefe Soares da Silva
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59.078-970 Brazil
| | | | - Clóvis Coutinho da Motta-Neto
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59.078-970 Brazil
| | | | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13.565-905 Brazil
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13.565-905 Brazil
| | - Wagner Franco Molina
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59.078-970 Brazil
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31
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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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32
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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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33
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Zivanovic G, Arenas C, Mestres F. Adaptation of Drosophila subobscura chromosomal inversions to climatic variables: the Balkan natural population of Avala. Genetica 2021; 149:155-169. [PMID: 34129131 DOI: 10.1007/s10709-021-00125-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/10/2021] [Indexed: 11/26/2022]
Abstract
The adaptive value of chromosomal inversions continues raising relevant questions in evolutionary biology. In many species of the Drosophila genus, different inversions have been recognized to be related to thermal adaptation, but it is necessary to determine to which specific climatic variables the inversions are adaptive. With this aim, the behavior of thermal adapted inversions of Drosophila subobscura regarding climatic variables was studied in the natural population of Avala (Serbia) during the 2014-2017 period. The results obtained were compared with those previously reported in the Font Groga (Barcelona, Spain) population, which presents different climatic and environmental conditions. In both populations, it was observed that most thermal adapted inversions were significantly associated with the first, second or both principal components, which were related with maximum, minimum and mean temperatures. Moreover, a significant increase over years (2004-2017) for the minimum temperature was detected. In parallel, a significant variation over time in Avala was only observed for the frequencies of 'warm' and 'non-thermal' adapted inversions of the U chromosome. However, stability in the chromosomal inversion polymorphism was observed for the 2014-2017 period which might result from the temporal span of the study and/or selective process acting on the population.
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Affiliation(s)
- Goran Zivanovic
- Department of Genetics, Institute for Biological Research "Sinisa Stankovic" - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Concepció Arenas
- Departament de Genètica, Microbiologia i Estadística, Secció d'Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Mestres
- Departament de Genètica, Microbiologia i Estadística, Secció de Genètica Biomèdica, Evolutiva i Desenvolupament - IRBio (Institut de Recerca per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain.
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.
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Martínez-García L, Ferrari G, Oosting T, Ballantyne R, van der Jagt I, Ystgaard I, Harland J, Nicholson R, Hamilton-Dyer S, Baalsrud HT, Brieuc MSO, Atmore LM, Burns F, Schmölcke U, Jakobsen KS, Jentoft S, Orton D, Hufthammer AK, Barrett JH, Star B. Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.671281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
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35
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The genomic basis of geographic differentiation and fiber improvement in cultivated cotton. Nat Genet 2021; 53:916-924. [PMID: 33859417 DOI: 10.1038/s41588-021-00844-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023]
Abstract
Large-scale genomic surveys of crop germplasm are important for understanding the genetic architecture of favorable traits. The genomic basis of geographic differentiation and fiber improvement in cultivated cotton is poorly understood. Here, we analyzed 3,248 tetraploid cotton genomes and confirmed that the extensive chromosome inversions on chromosomes A06 and A08 underlies the geographic differentiation in cultivated Gossypium hirsutum. We further revealed that the haplotypic diversity originated from landraces, which might be essential for understanding adaptative evolution in cultivated cotton. Introgression and association analyses identified new fiber quality-related loci and demonstrated that the introgressed alleles from two diploid cottons had a large effect on fiber quality improvement. These loci provided the potential power to overcome the bottleneck in fiber quality improvement. Our study uncovered several critical genomic signatures generated by historical breeding effects in cotton and a wealth of data that enrich genomic resources for the research community.
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Hierarchical genetic structure in an evolving species complex: Insights from genome wide ddRAD data in Sebastes mentella. PLoS One 2021; 16:e0251976. [PMID: 34043665 PMCID: PMC8158871 DOI: 10.1371/journal.pone.0251976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 05/06/2021] [Indexed: 11/22/2022] Open
Abstract
The diverse biology and ecology of marine organisms may lead to complex patterns of intraspecific diversity for both neutral and adaptive genetic variation. Sebastes mentella displays a particular life-history as livebearers, for which existence of multiple ecotypes has been suspected to complicate the genetic population structure of the species. Double digest restriction-site associated DNA was used to investigate genetic population structure in S. mentella and to scan for evidence of selection. In total, 42,288 SNPs were detected in 277 fish, and 1,943 neutral and 97 tentatively adaptive loci were selected following stringent filtration. Unprecedented levels of genetic differentiation were found among the previously defined ‘shallow pelagic’, ‘deep pelagic’ and ‘demersal slope’ ecotypes, with overall mean FST = 0.05 and 0.24 in neutral and outlier SNPs, respectively. Bayesian computation estimated a concurrent and historical divergence among these three ecotypes and evidence of local adaptation was found in the S. mentella genome. Overall, these findings imply that the depth-defined habitat divergence of S. mentella has led to reproductive isolation and possibly adaptive radiation among these ecotypes. Additional sub-structuring was detected within the ‘shallow’ and ‘deep’ pelagic ecotypes. Population assignment of individual fish showed more than 94% agreement between results based on SNP and previously generated microsatellite data, but the SNP data provided a lower estimate of hybridization among the ecotypes than that by microsatellite data. We identified a SNP panel with only 21 loci to discriminate populations in mixed samples based on a machine-learning algorithm. This first SNP based investigation clarifies the population structure of S. mentella, and provides novel and high-resolution genomic tools for future investigations. The insights and tools provided here can readily be incorporated into the management of S. mentella and serve as a template for other exploited marine species exhibiting similar complex life history traits.
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37
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Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic. Proc Natl Acad Sci U S A 2021; 118:2025453118. [PMID: 33827928 PMCID: PMC8054022 DOI: 10.1073/pnas.2025453118] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.
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38
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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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39
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Benestan LM, Rougemont Q, Senay C, Normandeau E, Parent E, Rideout R, Bernatchez L, Lambert Y, Audet C, Parent GJ. Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus). Evol Appl 2021; 14:588-606. [PMID: 33664797 PMCID: PMC7896722 DOI: 10.1111/eva.13143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.
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Affiliation(s)
- Laura M. Benestan
- CEFEUniv Montpellier, CNRS, EPHE‐PSL UniversityIRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Caroline Senay
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Eric Parent
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Rick Rideout
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreN.L.St. John’sCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Yvan Lambert
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Céline Audet
- Institut des sciences de la mer de RimouskiUniversité du Québec à RimouskiRimouskiQCCanada
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40
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Enbody ED, Pettersson ME, Sprehn CG, Palm S, Wickström H, Andersson L. Ecological adaptation in European eels is based on phenotypic plasticity. Proc Natl Acad Sci U S A 2021; 118:e2022620118. [PMID: 33479174 PMCID: PMC7848574 DOI: 10.1073/pnas.2022620118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The relative role of genetic adaptation and phenotypic plasticity is of fundamental importance in evolutionary ecology [M. J. West-Eberhard, Proc. Natl. Acad. Sci. U.S.A. 102 (suppl. 1), 6543-6549 (2005)]. European eels have a complex life cycle, including transitions between life stages across ecological conditions in the Sargasso Sea, where spawning occurs, and those in brackish and freshwater bodies from northern Europe to northern Africa. Whether continental eel populations consist of locally adapted and genetically distinct populations or comprise a single panmictic population has received conflicting support. Here we use whole-genome sequencing and show that European eels belong to one panmictic population. A complete lack of geographical genetic differentiation is demonstrated. We postulate that this is possible because the most critical life stages-spawning and embryonic development-take place under near-identical conditions in the Sargasso Sea. We further show that within-generation selection, which has recently been proposed as a mechanism for genetic adaptation in eels, can only marginally change allele frequencies between cohorts of eels from different geographic regions. Our results strongly indicate plasticity as the predominant mechanism for how eels respond to diverse environmental conditions during postlarval stages, ultimately solving a long-standing question for a classically enigmatic species.
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Affiliation(s)
- Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Stefan Palm
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 178 93 Drottningholm, Sweden
| | - Håkan Wickström
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 178 93 Drottningholm, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden;
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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41
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Johansen T, Besnier F, Quintela M, Jorde PE, Glover KA, Westgaard J, Dahle G, Lien S, Kent MP. Genomic analysis reveals neutral and adaptive patterns that challenge the current management regime for East Atlantic cod Gadus morhua L. Evol Appl 2020; 13:2673-2688. [PMID: 33294016 PMCID: PMC7691467 DOI: 10.1111/eva.13070] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 01/03/2023] Open
Abstract
Challenging long-held perceptions of fish management units can help to protect vulnerable stocks. When a fishery consisting of multiple genetic stocks is managed as a single unit, overexploitation and depletion of minor genetic units can occur. Atlantic cod (Gadus morhua) is an economically and ecologically important marine species across the North Atlantic. The application of new genomic resources, including SNP arrays, allows us to detect and explore novel structure within specific cod management units. In Norwegian waters, coastal cod (i.e. those not undertaking extensive migrations) are divided into two arbitrary management units defined by ICES: one between 62° and 70°N (Norwegian coastal cod; NCC) and one between 58° and 62°N (Norwegian coastal south; NCS). Together, these capture a fishery area of >25,000 km2 containing many spawning grounds. To assess whether these geographic units correctly represent genetic stocks, we analysed spawning cod of NCC and NCS for more than 8,000 SNPs along with samples of Russian White Sea cod, north-east Arctic cod (NEAC: the largest Atlantic stock), and outgroup samples representing the Irish and Faroe Sea's. Our analyses revealed large differences in spatial patterns of genetic differentiation across the genome and revealed a complex biological structure within NCC and NCS. Haplotype maps from four chromosome sets show regional specific SNP indicating a complex genetic structure. The current management plan dividing the coastal cod into only two management units does not accurately reflect the genetic units and needs to be revised. Coastal cod in Norway, while highly heterogenous, is also genetically distinct from neighbouring stocks in the north (NEAC), west (Faroe Island) and the south. The White Sea cod are highly divergent from other cod, possibly yielding support to the earlier notion of subspecies rank.
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Affiliation(s)
| | | | | | | | - Kevin A. Glover
- Institute of Marine Research (IMR)BergenNorway
- Department of BiologyUniversity of BergenBergenNorway
| | | | - Geir Dahle
- Institute of Marine Research (IMR)BergenNorway
- Department of BiologyUniversity of BergenBergenNorway
| | - Sigbjørn Lien
- Department of Animal and Aquaculture SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Matthew P. Kent
- Department of Animal and Aquaculture SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
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Abstract
The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.
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Affiliation(s)
- Joana Damas
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Marco Corbo
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Harris A Lewin
- The Genome Center, University of California, Davis, California 95616, USA; , , .,Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616, USA
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43
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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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44
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Stange M, Barrett RDH, Hendry AP. The importance of genomic variation for biodiversity, ecosystems and people. Nat Rev Genet 2020; 22:89-105. [PMID: 33067582 DOI: 10.1038/s41576-020-00288-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 11/09/2022]
Abstract
The 2019 United Nations Global assessment report on biodiversity and ecosystem services estimated that approximately 1 million species are at risk of extinction. This primarily human-driven loss of biodiversity has unprecedented negative consequences for ecosystems and people. Classic and emerging approaches in genetics and genomics have the potential to dramatically improve these outcomes. In particular, the study of interactions among genetic loci within and between species will play a critical role in understanding the adaptive potential of species and communities, and hence their direct and indirect effects on biodiversity, ecosystems and people. We explore these population and community genomic contexts in the hope of finding solutions for maintaining and improving ecosystem services and nature's contributions to people.
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Affiliation(s)
- Madlen Stange
- Redpath Museum, McGill University, Montreal, QC, Canada
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45
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Otterå H, Johansen T, Folkvord A, Dahle G, Solvang Bingh MK, Westgaard JI, Glover KA. The pantophysin gene and its relationship with survival in early life stages of Atlantic cod. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191983. [PMID: 33204437 PMCID: PMC7657904 DOI: 10.1098/rsos.191983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Genetic markers are widely used in fisheries management around the world. While the genetic structure and markers selected are usually based on samples from the wild, very few controlled experiments have been carried out to investigate possible differences in influence on traits between markers. Here we examine the bi-allelic gene pantophysin (Pan I), widely used in the management of Atlantic cod, in a series of in vitro crosses under a range of temperatures. It has been proposed that this gene, or another tightly linked gene, may be under strong divergent selection. Resolving this issue is essential in order to interpret results when using this gene marker for stock management. We found no evidence of departure from the expected 1 : 2 : 1 Mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12°C temperature regimes in tank experiments favoured the survival of the Pan IAA genotype. No difference in genotype survival was, however, found in a more natural mesocosm environment. Collectively, these results suggest that for the early life stages of Atlantic cod, and under the current experimental conditions, there is no strong consistent influence of Pan I genotype on survival. The results also emphasize the importance of varied experimental studies to verify the importance of environmental factors influencing genotype selection.
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Affiliation(s)
- Håkon Otterå
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
| | - Torild Johansen
- Institute of Marine Research, Tromsø Division, Framsenteret 9296 Tromsø, Norway
| | - Arild Folkvord
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
- Department of Biological Sciences, University of Bergen, Thormøhlensgt. 53, 5020Bergen
| | - Geir Dahle
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
| | | | - Jon-Ivar Westgaard
- Institute of Marine Research, Tromsø Division, Framsenteret 9296 Tromsø, Norway
| | - Kevin A. Glover
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
- Department of Biological Sciences, University of Bergen, Thormøhlensgt. 53, 5020Bergen
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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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47
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Oomen RA, Kuparinen A, Hutchings JA. Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change. J Hered 2020; 111:319-332. [PMID: 32620014 PMCID: PMC7423069 DOI: 10.1093/jhered/esaa020] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/25/2020] [Indexed: 12/26/2022] Open
Abstract
Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modeling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multilocus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.
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Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
| | - Anna Kuparinen
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Jeffrey A Hutchings
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
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48
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Junker J, Rick JA, McIntyre PB, Kimirei I, Sweke EA, Mosille JB, Wehrli B, Dinkel C, Mwaiko S, Seehausen O, Wagner CE. Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines. Mol Ecol 2020; 29:3277-3298. [PMID: 32687665 DOI: 10.1111/mec.15559] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 01/03/2023]
Abstract
Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced-representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika's two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex-specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large chromosomal rearrangement in L. miodon, creating two homokaryotypes and one heterokaryotype. We found all karyotypes throughout Lake Tanganyika, but the frequencies vary along a north-south gradient and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation by distance, even over the hundreds of kilometres covered by our sampling, but we do find shallow population structure.
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Affiliation(s)
- Julian Junker
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
| | - Jessica A Rick
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Peter B McIntyre
- Department of Natural Resources, Cornell University, Ithaca, NY, USA
| | - Ismael Kimirei
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Emmanuel A Sweke
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania.,Deep Sea Fishing Authority (DSFA), Zanzibar, Tanzania
| | - Julieth B Mosille
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Bernhard Wehrli
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zürich, Switzerland
| | - Christian Dinkel
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Salome Mwaiko
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
| | - Catherine E Wagner
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, WY, USA
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49
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Cayuela H, Rougemont Q, Laporte M, Mérot C, Normandeau E, Dorant Y, Tørresen OK, Hoff SNK, Jentoft S, Sirois P, Castonguay M, Jansen T, Praebel K, Clément M, Bernatchez L. Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish. Mol Ecol 2020; 29:2379-2398. [DOI: 10.1111/mec.15499] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Siv Nam Khang Hoff
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Pascal Sirois
- Département des sciences fondamentales Université du Québec à Chicoutimi Chicoutimi QC Canada
| | - Martin Castonguay
- Fisheries and Oceans Canada Institut Maurice‐Lamontagne Mont‐Joli QC Canada
| | - Teunis Jansen
- GINR‐Greenland Institute of Natural Resources Nuuk Greenland
- DTU Aqua‐National Institute of Aquatic Resources Technical University of Denmark Charlottenlund Castle, Charlottenlund Denmark
| | - Kim Praebel
- Norwegian College of Fishery Science Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Marie Clément
- Center for Fisheries Ecosystems Research Fisheries and Marine Institute of Memorial University of Newfoundland St. John's NL Canada
- Labrador Institute of Memorial University of Newfoundland Happy Valley‐Goose Bay NL Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
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50
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Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout. G3-GENES GENOMES GENETICS 2020; 10:1929-1947. [PMID: 32284313 PMCID: PMC7263693 DOI: 10.1534/g3.120.401184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal homologies between lake trout and other salmonids of varying divergence. The resulting linkage map contains 15,740 single nucleotide polymorphisms (SNPs) mapped to 42 linkage groups, likely representing the 42 lake trout chromosomes. Female and male linkage group lengths ranged from 43.07 to 134.64 centimorgans, and 1.97 to 92.87 centimorgans, respectively. We improved the map by determining coordinates for 41 of 42 centromeres, resulting in a map with 8 metacentric chromosomes and 34 acrocentric or telocentric chromosomes. We use the map to localize the sex determination locus and multiple quantitative trait loci (QTL) associated with intraspecific phenotypic divergence including traits related to growth and body condition, patterns of skin pigmentation, and two composite geomorphometric variables quantifying body shape. Two QTL for the presence of vermiculations and spots mapped with high certainty to an arm of linkage group Sna3, growth related traits mapped to two QTL on linkage groups Sna1 and Sna12, and putative body shape QTL were detected on six separate linkage groups. The sex determination locus was mapped to Sna4 with high confidence. Synteny analysis revealed that lake trout and congener Arctic char (Salvelinus alpinus) are likely differentiated by three or four chromosomal fissions, possibly one chromosomal fusion, and 6 or more large inversions. Combining centromere mapping information with putative inversion coordinates revealed that the majority of detected inversions differentiating lake trout from other salmonids are pericentric and located on acrocentric and telocentric linkage groups. Our results suggest that speciation and adaptive divergence within the genus Salvelinus may have been associated with multiple pericentric inversions occurring primarily on acrocentric and telocentric chromosomes. The linkage map presented here will be a critical resource for advancing conservation oriented genomic research on lake trout and exploring chromosomal evolution within and between salmonid species.
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