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Pratt EAL, Beheregaray LB, Fruet P, Tezanos-Pinto G, Bilgmann K, Zanardo N, Diaz-Aguirre F, Secchi ER, Freitas TRO, Möller LM. Genomic Divergence and the Evolution of Ecotypes in Bottlenose Dolphins (Genus Tursiops). Genome Biol Evol 2023; 15:evad199. [PMID: 37935115 PMCID: PMC10655200 DOI: 10.1093/gbe/evad199] [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: 10/27/2023] [Revised: 10/03/2023] [Accepted: 10/14/2023] [Indexed: 11/09/2023] Open
Abstract
Climatic changes have caused major environmental restructuring throughout the world's oceans. Marine organisms have responded to novel conditions through various biological systems, including genomic adaptation. Growing accessibility of next-generation DNA sequencing methods to study nonmodel species has recently allowed genomic changes underlying environmental adaptations to be investigated. This study used double-digest restriction-site associated DNA (ddRAD) sequence data to investigate the genomic basis of ecotype formation across currently recognized species and subspecies of bottlenose dolphins (genus Tursiops) in the Southern Hemisphere. Subspecies-level genomic divergence was confirmed between the offshore common bottlenose dolphin (T. truncatus truncatus) and the inshore Lahille's bottlenose dolphin (T. t. gephyreus) from the southwestern Atlantic Ocean (SWAO). Similarly, subspecies-level divergence is suggested between inshore (eastern Australia) Indo-Pacific bottlenose dolphin (T. aduncus) and the proposed Burrunan dolphin (T. australis) from southern Australia. Inshore bottlenose dolphin lineages generally had lower genomic diversity than offshore lineages, a pattern particularly evident for T. t. gephyreus, which showed exceptionally low diversity. Genomic regions associated with cardiovascular, musculoskeletal, and energy production systems appear to have undergone repeated adaptive evolution in inshore lineages across the Southern Hemisphere. We hypothesize that comparable selective pressures in the inshore environment drove similar adaptive responses in each lineage, supporting parallel evolution of inshore bottlenose dolphins. With climate change altering marine ecosystems worldwide, it is crucial to gain an understanding of the adaptive capacity of local species and populations. Our study provides insights into key adaptive pathways that may be important for the long-term survival of cetaceans and other organisms in a changing marine environment.
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Affiliation(s)
- Eleanor A L Pratt
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Pedro Fruet
- Laboratório de Ecologia e Conservação da Megafauna Marinha (ECOMEGA), Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Museu Oceanográfico Prof. Eliézer de C. Rios, Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Kaosa, Rio Grande, Brazil
| | | | - Kerstin Bilgmann
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Department of Environment and Water, Adelaide, South Australia, Australia
| | - Fernando Diaz-Aguirre
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Eduardo R Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha (ECOMEGA), Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Museu Oceanográfico Prof. Eliézer de C. Rios, Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
| | - Thales R O Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
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do Amaral KB, Barragán-Barrera DC, Mesa-Gutiérrez RA, Farías-Curtidor N, Caballero Gaitán SJ, Méndez-Fernandez P, Santos MCO, Rinaldi C, Rinaldi R, Siciliano S, Martín V, Carrillo M, de Meirelles ACO, Franco-Trecu V, Fagundes NJR, Moreno IB, Lacey Knowles L, Amaral AR. Seascape Genetics of the Atlantic Spotted Dolphin (Stenella frontalis) Based on Mitochondrial DNA. J Hered 2021; 112:646-662. [PMID: 34453543 DOI: 10.1093/jhered/esab050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
The Atlantic spotted dolphin (Stenella frontalis) is endemic to tropical, subtropical, and warm temperate waters of the Atlantic Ocean. Throughout its distribution, both geographic distance and environmental variation may contribute to population structure of the species. In this study, we follow a seascape genetics approach to investigate population differentiation of Atlantic spotted dolphins based on a large worldwide dataset and the relationship with marine environmental variables. The results revealed that the Atlantic spotted dolphin exhibits population genetic structure across its distribution based on mitochondrial DNA control region (mtDNA-CR) data. Analyses based on the contemporary landscape suggested, at both the individual and population level, that the population genetic structure is consistent with the isolation-by-distance model. However, because geography and environmental matrices were correlated, and because in some, but not all analyses, we found a significant effect for the environment, we cannot rule out the addition contribution of environmental factors in structuring genetic variation. Future analyses based on nuclear data are needed to evaluate whether local processes, such as social structure and some level of philopatry within populations, may be contributing to the associations among genetic structure, geographic, and environmental distance.
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Affiliation(s)
- Karina Bohrer do Amaral
- Laboratório de Sistemática e Ecologia de Aves e Mamíferos Marinhos (LABSMAR), Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435, 91501-70 Porto Alegre, RS, Brazil
| | - Dalia C Barragán-Barrera
- Centro de Investigaciones Oceanográficas de Hidrográficas del Caribe CIOH-DIMAR, Barrio Bosque, Sector Manzanillo Escuela Naval de Cadetes "Almirante Padilla," Cartagena, Colombia.,Fundación Macuáticos Colombia, Colombia, Medellín, Colombia.,Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departmento de Ciencias Biológicas, Universidad de los Andes, Carrera 1E No 18A-12, Bogotá, Colombia
| | | | | | - Susana Josefina Caballero Gaitán
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departmento de Ciencias Biológicas, Universidad de los Andes, Carrera 1E No 18A-12, Bogotá, Colombia
| | - Paula Méndez-Fernandez
- Observatoire PELAGIS, UMS 3462 La Rochelle Université / CNRS, Pôle Analytique, 5 allées de l'Océan, 17000 La Rochelle, France
| | - Marcos C Oliveira Santos
- Laboratório de Biologia da Conservação de Mamíferos Aquáticos (LABCMA), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico, 191, Sala 145-A, 05508-120 São Paulo, SP, Brazil
| | - Caroline Rinaldi
- Association Evasion Tropicale (AET), 1 Rue des Palétuviers, Pigeon Bouillante, 97125 Guadeloupe, France
| | - Renato Rinaldi
- Association Evasion Tropicale (AET), 1 Rue des Palétuviers, Pigeon Bouillante, 97125 Guadeloupe, France
| | - Salvatore Siciliano
- Fundação Oswaldo Cruz (Fiocruz), Av. Brasil 4.365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Vidal Martín
- Sociedad para el Estudio de Cetáceos del Archipélago Canario (SECAC), Casa de los Arroyo, Avda. Coll n.6, 35500 Arrecife, Lanzarote, Spain
| | - Manuel Carrillo
- Tenerife Conservación, C/Maya No. 8, La Laguna, Tenerife, Canary Islands, Spain
| | - Ana Carolina O de Meirelles
- AQUASIS-Associação de Pesquisa e Preservação de Ecossistemas Aquáticos, Praia de Iparana, s/no, SESC Iparana, 61600-000 Caucaia, CE, Brazil
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, UdelaR, Iguá 4225, 11400, Montevideo, Uruguay
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435, 91501-70 Porto Alegre, RS, Brazil.,Laboratório de Genética Médica e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul. Avenida Bento Gonçalves 9500, Prédio 43312, sala 113, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco III, Prédio 43312, 91501-970 Porto Alegre, RS, Brazil
| | - Ignacio Benites Moreno
- Laboratório de Sistemática e Ecologia de Aves e Mamíferos Marinhos (LABSMAR), Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435, 91501-70 Porto Alegre, RS, Brazil.,Centro de Estudos Costeiros, Limnológicos e Marinhos (CECLIMAR), Campus Litoral Norte, Universidade Federal do Rio Grande do Sul, Avenida Tramandaí, 976, Imbé, Rio Grande do Sul, 95625-000, Brazil
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, MI
| | - Ana Rita Amaral
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY 10024
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