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Van Nynatten A, Castiglione GM, de A Gutierrez E, Lovejoy NR, Chang BSW. Recreated Ancestral Opsin Associated with Marine to Freshwater Croaker Invasion Reveals Kinetic and Spectral Adaptation. Mol Biol Evol 2021; 38:2076-2087. [PMID: 33481002 PMCID: PMC8097279 DOI: 10.1093/molbev/msab008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim-light environments. Aquatic environments are particularly challenging for vision due to the spectrally dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine environments, croakers are known as highly visual benthic predators. In this study, we isolate rhodopsins from a diversity of freshwater and marine croakers and find that strong positive selection in rhodopsin is associated with a marine to freshwater transition in South American croakers. In order to determine if this is accompanied by significant shifts in visual abilities, we resurrected ancestral rhodopsin sequences and tested the experimental properties of ancestral pigments bracketing this transition using in vitro spectroscopic assays. We found the ancestral freshwater croaker rhodopsin is redshifted relative to its marine ancestor, with mutations that recapitulate ancestral amino acid changes along this transitional branch resulting in faster kinetics that are likely to be associated with more rapid dark adaptation. This could be advantageous in freshwater due to the redshifted spectrum and relatively narrow interface and frequent transitions between bright and dim-light environments. This study is the first to experimentally demonstrate that positively selected substitutions in ancestral visual pigments alter protein function to freshwater visual environments following a transition from an ancestrally marine state and provides insight into the molecular mechanisms underlying some of the physiological changes associated with this major habitat transition.
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Affiliation(s)
- Alexander Van Nynatten
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON, Canada
| | - Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nathan R Lovejoy
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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Bogotá-Gregory JD, Lima FCT, Correa SB, Silva-Oliveira C, Jenkins DG, Ribeiro FR, Lovejoy NR, Reis RE, Crampton WGR. Biogeochemical water type influences community composition, species richness, and biomass in megadiverse Amazonian fish assemblages. Sci Rep 2020; 10:15349. [PMID: 32948815 PMCID: PMC7501869 DOI: 10.1038/s41598-020-72349-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/26/2020] [Indexed: 11/09/2022] Open
Abstract
Amazonian waters are classified into three biogeochemical categories by dissolved nutrient content, sediment type, transparency, and acidity-all important predictors of autochthonous and allochthonous primary production (PP): (1) nutrient-poor, low-sediment, high-transparency, humic-stained, acidic blackwaters; (2) nutrient-poor, low-sediment, high-transparency, neutral clearwaters; (3) nutrient-rich, low-transparency, alluvial sediment-laden, neutral whitewaters. The classification, first proposed by Alfred Russel Wallace in 1853, is well supported but its effects on fish are poorly understood. To investigate how Amazonian fish community composition and species richness are influenced by water type, we conducted quantitative year-round sampling of floodplain lake and river-margin habitats at a locality where all three water types co-occur. We sampled 22,398 fish from 310 species. Community composition was influenced more by water type than habitat. Whitewater communities were distinct from those of blackwaters and clearwaters, with community structure correlated strongly to conductivity and turbidity. Mean per-sampling event species richness and biomass were significantly higher in nutrient-rich whitewater floodplain lakes than in oligotrophic blackwater and clearwater river-floodplain systems and light-limited whitewater rivers. Our study provides novel insights into the influences of biogeochemical water type and ecosystem productivity on Earth's most diverse aquatic vertebrate fauna and highlights the importance of including multiple water types in conservation planning.
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Affiliation(s)
| | - Flávio C T Lima
- Museu de Zoologia da Universidade Estadual de Campinas, Cidade Universitária, Campinas, São Paulo, 13083-863, Brazil
| | - Sandra B Correa
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Box 9680, Starkville, MS, 39762, USA
| | - Cárlison Silva-Oliveira
- Instituto Nacional de Pesquisas da Amazonia, Coleção de Peixes, Av. André Araújo, 2936, Petrópolis, Manaus, Amazonas, 69.067-375, Brazil
| | - David G Jenkins
- Department of Biology, University of Central Florida, 4100 Libra Dr, Orlando, FL, 32816, USA
| | - Frank R Ribeiro
- Coleção Ictiológica da Universidade Federal do Oeste do Pará. Campus Amazônia, Avenida Mendonça Furtado, 2946, Fátima, Santarém, Pará, CEP 68040-470, Brazil
| | - Nathan R Lovejoy
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Roberto E Reis
- Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6681, Porto Alegre, Rio Grande do Sul, 90619-900, Brazil
| | - William G R Crampton
- Department of Biology, University of Central Florida, 4100 Libra Dr, Orlando, FL, 32816, USA.
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