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Bringloe TT, Bourret A, Cote D, Marie-Julie R, Herbig J, Robert D, Geoffroy M, Parent GJ. Genomic architecture and population structure of Boreogadus saida from Canadian waters. Sci Rep 2024; 14:19331. [PMID: 39164428 PMCID: PMC11336163 DOI: 10.1038/s41598-024-69782-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/08/2024] [Indexed: 08/22/2024] Open
Abstract
The polar cod, Boreogadus saida, is an abundant and ubiquitous forage fish and a crucial link in Arctic marine trophic dynamics. Our objective was to unravel layers of genomic structure in B. saida from Canadian waters, specifically screening for potential hybridization with the Arctic cod, Arctogadus glacialis, large chromosomal inversions, and sex-linked regions, prior to interpreting population structure. Our analysis of 53,384 SNPs in 522 individuals revealed hybridization and introgression between A. glacialis and B. saida. Subsequent population level analyses of B. saida using 12,305 SNPs in 511 individuals revealed three large (ca. 7.4-16.1 Mbp) chromosomal inversions, and a 2 Mbp region featuring sex-linked loci. We showcase population structuring across the Western and Eastern North American Arctic, and subarctic regions ranging from the Hudson Bay to the Canadian Atlantic maritime provinces. Genomic signal for the inferred population structure was highly aggregated into a handful of SNPs (13.8%), pointing to potentially important adaptive evolution across the Canadian range. Our study provides a high-resolution perspective on the genomic structure of B. saida, providing a foundation for work that could be expanded to the entire circumpolar range for the species.
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Affiliation(s)
- Trevor T Bringloe
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, QC, G5H 3Z4, Canada.
| | - Audrey Bourret
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, QC, G5H 3Z4, Canada
| | - David Cote
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, A0G 2M0, Canada
| | - Roux Marie-Julie
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, QC, G5H 3Z4, Canada
| | - Jennifer Herbig
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial, University of Newfoundland, St. John's, A1C 5R3, Canada
| | - Dominique Robert
- Institut Des Sciences de La Mer, Université du Québec à Rimouski, Rimouski, QC, G5L 3A1, Canada
| | - Maxime Geoffroy
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial, University of Newfoundland, St. John's, A1C 5R3, Canada
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9036, Tromsø, Norway
| | - Geneviève J Parent
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, QC, G5H 3Z4, Canada.
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Alvarez A, Anaya J, Arellano B, Bartlebaugh A, Capurro MC, Carrillo A, Chacon IR, Cordova L, Corral B, DaSilva M, Del Valle G, Diaz A, Diaz I, Donate C, Fusco I, Garcia B, Garcia J, Godoy C, Gonzalez V, Hertzog M, Horton N, Hughey JR, Kallison ER, Lopez R, Martinez J, Martinez R, Mendez K, Pacheco M, Ramirez M, Ramirez DM, Rios JM, Rossi F, Rua J, Sanchez A, Sanchez D, Sanchez M, Santos K, Sierra R, Soto D, Steinhardt A, Tavarez J, Tupas M, Valdez RT, Vargas C, Vargas R, Wong FL, Zamora A. Analysis of the complete organellar genomes of the rockweed Fucus spiralis (Fucaceae, Phaeophyceae) supports its infraspecific recognition as Fucus vesiculosus var. spiralis. Mitochondrial DNA B Resour 2018; 3:482-483. [PMID: 33490516 PMCID: PMC7801007 DOI: 10.1080/23802359.2018.1463829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Alejandra Alvarez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Juan Anaya
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Bibiana Arellano
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Austin Bartlebaugh
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Michael C. Capurro
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Adriana Carrillo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Isaiah R. Chacon
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Lizbeth Cordova
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Bethany Corral
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Melina DaSilva
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Giselle Del Valle
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Alexis Diaz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Isaac Diaz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Carlos Donate
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Isabella Fusco
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Brian Garcia
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Janette Garcia
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Christian Godoy
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Victor Gonzalez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Megan Hertzog
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Nicholas Horton
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Jeffery R. Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Eli R. Kallison
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Rafael Lopez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Jennifer Martinez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Rene Martinez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Kianna Mendez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Marie Pacheco
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Maria Ramirez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - David M. Ramirez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Jennifer M. Rios
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Franca Rossi
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Jorge Rua
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Alyssa Sanchez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Daniela Sanchez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Maria Sanchez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Karla Santos
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Rosaura Sierra
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Daniel Soto
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Alicia Steinhardt
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Jesus Tavarez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Mark Tupas
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Rolando T. Valdez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Christian Vargas
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Rudy Vargas
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Frances L. Wong
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Adrian Zamora
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
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Rothman MD, Mattio L, Anderson RJ, Bolton JJ. A phylogeographic investigation of the kelp genus Laminaria (Laminariales, Phaeophyceae), with emphasis on the South Atlantic Ocean. JOURNAL OF PHYCOLOGY 2017; 53:778-789. [PMID: 28434206 DOI: 10.1111/jpy.12544] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 03/06/2017] [Indexed: 06/07/2023]
Abstract
The genus Laminaria has a wide distribution range compared with other kelp genera because it is found in both the North and the South Atlantic, on both sides of the North Pacific, as well as in the Mediterranean. Hypotheses behind this biogeographical pattern have been discussed by several authors but have not yet been fully evaluated with time-calibrated phylogenies. Based on the analysis of four molecular markers (ITS2, rbcL, atp8 and trnWI), our goal was to reassess the Laminaria species diversity in South Africa, assess its relationship with the other species distributed in the South Atlantic and reconstruct the historical biogeography of the genus. Our results confirm the occurrence of a single species, L. pallida, in southern Africa, and its sister relationship with the North Atlantic L. ochroleuca. Both species belonged to a clade containing the other South Atlantic species: L. abyssalis from Brazil, and the Mediterranean L. rodriguezii. Our time-calibrated phylogenies suggest that Laminaria originated in the northern Pacific around 25 mya, followed by at least two migration events through the Bering Strait after its opening (~5.32 mya). Today, the first is represented by L. solidungula in the Arctic, while the second gave rise to the rest of the Atlantic species. The colonization of the North Atlantic was followed by a gradual colonization southward along the west coast of Europe, into the Mediterranean (~2.07 mya) and two recent, but disconnected, migrations (~1.34 and 0.87 mya) across the equator, giving rise to L. abyssalis in Brazil and L. pallida in southern Africa, respectively.
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Affiliation(s)
- Mark D Rothman
- Department of Agriculture, Forestry and Fisheries, Private bag X2, Rogge Bay, 8012, South Africa
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Cape Town, 7701, South Africa
| | - Lydiane Mattio
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Cape Town, 7701, South Africa
- School of Plant Biology and Oceans Institute, The University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Robert J Anderson
- Department of Agriculture, Forestry and Fisheries, Private bag X2, Rogge Bay, 8012, South Africa
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Cape Town, 7701, South Africa
| | - John J Bolton
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Cape Town, 7701, South Africa
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