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Knutsen H, Catarino D, Rogers L, Sodeland M, Mattingsdal M, Jahnke M, Hutchings JA, Mellerud I, Espeland SH, Johanneson K, Roth O, Hansen MM, Jentoft S, André C, Jorde PE. Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species. Mol Ecol 2022; 31:2562-2577. [PMID: 35229385 PMCID: PMC9311693 DOI: 10.1111/mec.16415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022]
Abstract
Gene flow shapes spatial genetic structure and the potential for local adaptation. Among marine animals with nonmigratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats is expected to influence the distribution of biological populations and their connectivity patterns. We used whole genome sequencing to study demographic history and reduced representation (double‐digest restriction associated DNA) sequencing data to analyse spatial genetic structure in broadnosed pipefish (Syngnathus typhle). Its main habitat is eelgrass beds, which are patchily distributed along the study area in southern Norway. Demographic connectivity among populations was inferred from long‐term (~30‐year) population counts that uncovered a rapid decline in spatial correlations in abundance with distance as short as ~2 km. These findings were contrasted with data for two other fish species that have a pelagic larval stage (corkwing wrasse, Symphodus melops; black goby, Gobius niger). For these latter species, we found wider spatial scales of connectivity and weaker genetic isolation‐by‐distance patterns, except where both species experienced a strong barrier to gene flow, seemingly due to lack of suitable habitat. Our findings verify expectations that a fragmented habitat and absence of a pelagic larval stage promote genetic structure, while presence of a pelagic larvae stage increases demographic connectivity and gene flow, except perhaps over extensive habitat gaps.
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Affiliation(s)
- Halvor Knutsen
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Diana Catarino
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Lauren Rogers
- Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Marte Sodeland
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Morten Mattingsdal
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Marlene Jahnke
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Jeffrey A Hutchings
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway.,Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Ida Mellerud
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway
| | - Sigurd H Espeland
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Kerstin Johanneson
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Germany
| | - Michael M Hansen
- Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
| | - Sissel Jentoft
- University of Oslo, Department of Biology, 0316, Oslo, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Per Erik Jorde
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway
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Faust E, Jansson E, André C, Halvorsen KT, Dahle G, Knutsen H, Quintela M, Glover KA. Not that clean: Aquaculture-mediated translocation of cleaner fish has led to hybridization on the northern edge of the species' range. Evol Appl 2021; 14:1572-1587. [PMID: 34178105 PMCID: PMC8210792 DOI: 10.1111/eva.13220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Translocation and introduction of non-native organisms can have major impacts on local populations and ecosystems. Nevertheless, translocations are common practices in agri- and aquaculture. Each year, millions of wild-caught wrasses are transported large distances to be used as cleaner fish for parasite control in marine salmon farms. Recently, it was documented that translocated cleaner fish are able to escape and reproduce with local wild populations. This is especially a challenge in Norway, which is the world's largest salmon producer. Here, a panel of 84 informative SNPs was developed to identify the presence of nonlocal corkwing wrasse (Symphodus melops) escapees and admixed individuals in wild populations in western Norway. Applying this panel to ~2000 individuals, escapees and hybrids were found to constitute up to 20% of the local population at the northern edge of the species' distribution. The introduction of southern genetic material at the northern edge of the species distribution range has altered the local genetic composition and could obstruct local adaptation and further range expansion. Surprisingly, in other parts of the species distribution where salmon farming is also common, few escapees and hybrids were found. Why hybridization seems to be common only in the far north is discussed in the context of demographic and transport history. However, the current lack of reporting of escapes makes it difficult to evaluate possible causes for why some aquaculture-dense areas have more escapees and hybrids than others. The results obtained in this study, and the observed high genomic divergence between the main export and import regions, puts the sustainability of mass translocation of nonlocal wild wrasse into question and suggests that the current management regime needs re-evaluation.
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Affiliation(s)
- Ellika Faust
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | | | - Carl André
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | - Halvor Knutsen
- Institute of Marine ResearchHisNorway
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | | | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Institute of BiologyUniversity of BergenBergenNorway
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Jansson E, Besnier F, Malde K, André C, Dahle G, Glover KA. Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations. BMC Genet 2020; 21:118. [PMID: 33036553 PMCID: PMC7547435 DOI: 10.1186/s12863-020-00921-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
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Affiliation(s)
- Eeva Jansson
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Francois Besnier
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Ketil Malde
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Geir Dahle
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.,Institute of Biology, University of Bergen, P. O. Box 7803, 5020, Bergen, Norway
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