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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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Martins NT, Macagnan LB, Cassano V, Gurgel CFD. Brazilian marine phylogeography: A literature synthesis and analysis of barriers. Mol Ecol 2022; 31:5423-5439. [PMID: 36073087 DOI: 10.1111/mec.16684] [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: 02/10/2021] [Revised: 08/15/2022] [Accepted: 08/30/2022] [Indexed: 12/24/2022]
Abstract
In the last 30 years a plethora of phylogeography studies have been published targeting Brazilian marine species. To date, several historical and extant physical and ecological processes have been identified as drivers of allopatric, sympatric and parapatric population genetic differentiation detected along the Brazilian coast. Examples of extant physical barriers include the split of the South Equatorial Current into the Brazil and North Brazil boundary currents, the mouth of major rivers (e.g., Amazon, São Francisco and Doce rivers) and coastal upwellings. Examples of historical barriers include the Vitória-Trindade seamount chain promoting genetic differentiation during periods of glacial maxima and lower sea levels. Examples of ecological speciation include adaptations to different substrata, resource use and reproductive biology. We used published data to build data sets and generalized additive models to identify patterns of spatial phylogeographical concordance across multiple taxa and markers. Our results identify Cape São Roque as the most dominant extant barrier to gene flow along the Brazilian coast, followed by the Vitória-Trindade seamount chain and Cape Santa Marta. Cape Santa Marta is the northern winter limit of the Rio da Plata plume and is intermittently influenced by the Malvinas Current. This study provides a novel explicit quantitative approach to comparative phylogeography that recognizes four Brazilian phylogeographical regions delimited by processes associated with barriers to gene flow.
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Affiliation(s)
- Nuno T Martins
- Departamento de Botânica, Universidade de São Paulo, Instituto de Biociências, São Paulo, São Paulo, Brazil
| | - Leonardo B Macagnan
- NUPEM - Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Valéria Cassano
- Departamento de Botânica, Universidade de São Paulo, Instituto de Biociências, São Paulo, São Paulo, Brazil
| | - Carlos Frederico D Gurgel
- NUPEM - Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
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Martins NT, Cassano V, Gurgel CFD. Phylogeography of Colpomenia sinuosa (Ectocarpales, Phaeophyceae) along the Brazilian coast. JOURNAL OF PHYCOLOGY 2022; 58:543-554. [PMID: 35545902 DOI: 10.1111/jpy.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/19/2022] [Indexed: 06/15/2023]
Abstract
Colpomenia sinuosa is a cosmopolitan brown macroalgal species complex and hence a great candidate for evolutionary studies in the marine environment. Since 2009, three major C. sinuosa phylogenetic lineages, subdivided into eight subgroups, have been identified based on cox3 DNA sequences from worldwide collections. However, worldwide sampling remains limited and spotty. To date molecular data from Brazilian C. sinuosa populations have been limited to 10 specimens collected in a single locality. Nonetheless, C. sinuosa populations occur along the entire ~8,000 km Brazilian coast. Consequently, knowledge on population genetic diversity and spatial genetic structuring along most of the Brazilian coastline is nonexistent. To fulfill this gap in knowledge, we performed a phylogeographic analysis of C. sinuosa populations in Brazil. The highly variable cox3 marker was sequenced for 148 individuals collected in 12 localities in Brazil. Results identified two genetically distinct population groups (north vs. south) separated at 20.5° S latitude. Genetic diversity in northern populations is 14.6 and 15.5 times greater than southern populations in terms of haplotype and nucleotide diversity, respectively. Among northern populations, the Bahia state holds the largest genetic diversity. The southern populations had lower genetic diversity and no internal genetic sub-structure suggesting past bottlenecks followed by recent colonization from northern haplotypes. Our results do not indicate recent introductions of foreign haplotypes in Brazil and reinforce the crucial importance of historical and extant allopatric, parapatric, and sympatric processes driving marine macroalgal evolution in the Southwestern Atlantic Ocean.
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Affiliation(s)
- Nuno Tavares Martins
- Departamento de Botânica, Universidade de São Paulo, Instituto de Biociências, São Paulo, São Paulo, 05508-090, Brazil
| | - Valéria Cassano
- Departamento de Botânica, Universidade de São Paulo, Instituto de Biociências, São Paulo, São Paulo, 05508-090, Brazil
| | - Carlos Frederico Deluqui Gurgel
- NUPEM - Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, 27965-045, Brazil
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New genetic evidences for distinct populations of the common minke whale (Balaenoptera acutorostrata) in the Southern Hemisphere. Polar Biol 2021. [DOI: 10.1007/s00300-021-02897-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Quintela FM, DA Rosa CA, FeijÓ A. Updated and annotated checklist of recent mammals from Brazil. AN ACAD BRAS CIENC 2020; 92 Suppl 2:e20191004. [PMID: 32813766 DOI: 10.1590/0001-3765202020191004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/02/2019] [Indexed: 11/21/2022] Open
Abstract
An updated and annotated checklist of mammals occurring in Brazil is presented. A total of 751 native species, distributed in 249 genera, 51 families and 11 orders were recorded to the country. The Brazilian mammalian fauna shows an elevated rate of endemism (30%; 223 species). Among the species evaluated by IUCN (668 species; 90%), a total of 80 (10.6% of total mammalian fauna) are Threatened, 28 (3.9%) are considered as Near Threatened, two species (0.3%) are presumable Extinct, 96 (12.8%) are considered with Deficient Data for conservation and 462 (61.6%) are considered as Least Concern. Fifteen new species were described since the last national compilation (published in 2017), which associated to new records to the country and synonimizations resulted in an increment of 30 species. Eight non-native species were introduced to the country, including the recently established Asiatic cervids Rusa unicolor (sambar) and Axis axis (chital). Seven native species (five primates and two hystricomorph rodents) have been translocated from their areas of natural occurrence to other areas inside the country.
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Affiliation(s)
- Fernando Marques Quintela
- Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Clarissa Alves DA Rosa
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Anderson FeijÓ
- Key Laboratory of Zoological Systematics and Evolution, Chinese Academy of Sciences, Beijing, China
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Moura AE, Shreves K, Pilot M, Andrews KR, Moore DM, Kishida T, Möller L, Natoli A, Gaspari S, McGowen M, Chen I, Gray H, Gore M, Culloch RM, Kiani MS, Willson MS, Bulushi A, Collins T, Baldwin R, Willson A, Minton G, Ponnampalam L, Hoelzel AR. Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers. Mol Phylogenet Evol 2020; 146:106756. [DOI: 10.1016/j.ympev.2020.106756] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/02/2020] [Accepted: 01/28/2020] [Indexed: 12/30/2022]
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Hohl LSL, Sicuro FL, Wickert JC, Moreno IB, Rocha-Barbosa O, Barreto AS. Skull morphology of bottlenose dolphins from different ocean populations with emphasis on South America. J Morphol 2020; 281:564-577. [PMID: 32249999 DOI: 10.1002/jmor.21121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 03/05/2020] [Accepted: 03/18/2020] [Indexed: 11/10/2022]
Abstract
The bottlenose dolphin, genus Tursiops, is cosmopolitan occurring in tropical and temperate regions, with morphological variation between and within different oceans. Since the genus' taxonomy has been under discussion for a long time, this work aimed at analyzing the cranial variability of T. truncatus from different regions of the world. Geometric Morphometrics analyses were performed in 201 skulls of adult specimens, on dorsal, ventral, and lateral views, from the Eastern North Pacific, Eastern North Atlantic, Eastern South Atlantic, and Western South Atlantic oceans. The results indicate differences between individuals that inhabit the Atlantic and Pacific oceans. Within the Atlantic Ocean, there is an evident longitudinal differentiation of specimens from the eastern and western regions. A latitudinal separation was also observed, considering specimens from the North and South Atlantic Ocean. In the Western South Atlantic statistical differences were found between two morphological groups, identified as T. gephyreus (sensu Lahille, 1908) and T. truncatus, and the cross-validation presented 98% as minimum confidence for correct classification of these two groups. The present study provides strong morphological support to consider these two lineages as separate species.
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Affiliation(s)
- Leandro S L Hohl
- Departamento de Zoologia, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Laboratório de Zoologia de Vertebrados-Tetrapoda (LAZOVERTE), Rio de Janeiro, RJ, Brazil.,Departamento de Ecologia, Instituto de Biologia Roberto Alcantara Gomes Universidade do Estado do Rio de Janeiro, Programa de Pós-Graduação em Ecologia e Evolução, Rio de Janeiro, RJ, Brazil
| | - Fernando L Sicuro
- Departamento de Ciências Fisiológicas, Universidade do Estado do Rio de Janeiro, Laboratório de Pesquisas Clínicas e Experimentais em Biologia Vascular (BIOVASC), Rio de Janeiro, RJ, Brazil
| | - Janaína C Wickert
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, Rua Bento Gonçalves, Torres, RS, Brazil.,Centro de Estudos Costeiros, Limnológicos e Marinhos (CECLIMAR), Universidade Federal do Rio Grande do Sul, (UFRGS Campus Litoral Norte), Rio Grande do Sul, RS, Brazil
| | - Ignacio B Moreno
- Centro de Estudos Costeiros, Limnológicos e Marinhos (CECLIMAR), Universidade Federal do Rio Grande do Sul, (UFRGS Campus Litoral Norte), Rio Grande do Sul, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal (PPGBan), Departamento de Zoologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Oscar Rocha-Barbosa
- Departamento de Zoologia, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Laboratório de Zoologia de Vertebrados-Tetrapoda (LAZOVERTE), Rio de Janeiro, RJ, Brazil.,Departamento de Ecologia, Instituto de Biologia Roberto Alcantara Gomes Universidade do Estado do Rio de Janeiro, Programa de Pós-Graduação em Ecologia e Evolução, Rio de Janeiro, RJ, Brazil
| | - André S Barreto
- Universidade do Vale do Itajaí, Laboratório de Informática da Biodiversidade e Geomática, Itajaí, SC, Brazil
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Costa APB, Fruet PF, Secchi ER, Daura-Jorge FG, Simões-Lopes PC, Di Tullio JC, Rosel PE. Ecological divergence and speciation in common bottlenose dolphins in the western South Atlantic. J Evol Biol 2019; 34:16-32. [PMID: 31808214 DOI: 10.1111/jeb.13575] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 11/01/2019] [Accepted: 11/28/2019] [Indexed: 01/02/2023]
Abstract
Coastal and offshore ecotypes of common bottlenose dolphins have been recognized in the western South Atlantic, and it is possible that trophic niche divergence associated with social interactions is leading them to genetic and phenotypic differentiation. The significant morphological differentiation observed between these ecotypes suggests they represent two different subspecies. However, there is still a need to investigate whether there is congruence between morphological and genetic data to rule out the possibility of ecophenotypic variation accompanied by gene flow. Mitochondrial DNA (mtDNA) control region sequence data and 10 microsatellite loci collected from stranded and biopsied dolphins sampled in coastal and offshore waters of Brazil as well as 106 skulls for morphological analyses were used to determine whether the morphological differentiation was supported by genetic differentiation. There was congruence among the data sets, reinforcing the presence of two distinct ecotypes. The divergence may be relatively recent, however, given the moderate values of mtDNA nucleotide divergence (dA = 0.008), presence of one shared mtDNA haplotype and possibly low levels of gene flow (around 1% of migrants per generation). Results suggest the ecotypes may be in the process of speciation and reinforce they are best described as two different subspecies until the degree of nuclear genetic divergence is thoroughly evaluated: Tursiops truncatus gephyreus (coastal ecotype) and T. t. truncatus (offshore ecotype). The endemic distribution of T. t. gephyreus in the western South Atlantic and number of anthropogenic threats in the area reinforces the importance of protecting this ecotype and its habitat.
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Affiliation(s)
- Ana P B Costa
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Pedro F Fruet
- Museu Oceanográfico 'Prof. Eliézer C. Rios', Universidade Federal do Rio Grande, Rio Grande, Brazil.,Laboratório de Ecologia e Conservação da Megafauna Marinha (EcoMega), Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil.,Kaosa, Rio Grande, Brazil.,Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos - ICMBio/CMA, Santos, Brazil
| | - Eduardo R Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha (EcoMega), Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Fábio G Daura-Jorge
- Laboratório de Mamíferos Aquáticos (LAMAQ), Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Paulo C Simões-Lopes
- Laboratório de Mamíferos Aquáticos (LAMAQ), Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Juliana C Di Tullio
- Museu Oceanográfico 'Prof. Eliézer C. Rios', Universidade Federal do Rio Grande, Rio Grande, Brazil.,Laboratório de Ecologia e Conservação da Megafauna Marinha (EcoMega), Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil.,Kaosa, Rio Grande, Brazil
| | - Patricia E Rosel
- National Marine Fisheries Service, Southeast Fisheries Science Center, Lafayette, LA, USA
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