1
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Lin JJ, Wang FY, Chung WY, Wang TY. The genomic evolution of visual opsin genes in amphibians. Vision Res 2024; 222:108447. [PMID: 38906036 DOI: 10.1016/j.visres.2024.108447] [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: 09/14/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/23/2024]
Abstract
Among tetrapod (terrestrial) vertebrates, amphibians remain more closely tied to an amphibious lifestyle than amniotes, and their visual opsin genes may be adapted to this lifestyle. Previous studies have discussed physiological, morphological, and molecular changes in the evolution of amphibian vision. We predicted the locations of the visual opsin genes, their neighboring genes, and the tuning sites of the visual opsins, in 39 amphibian genomes. We found that all of the examined genomes lacked the Rh2 gene. The caecilian genomes have further lost the SWS1 and SWS2 genes; only the Rh1 and LWS genes were retained. The loss of the SWS1 and SWS2 genes in caecilians may be correlated with their cryptic lifestyles. The opsin gene syntenies were predicted to be highly similar to those of other bony vertebrates. Moreover, dual syntenies were identified in allotetraploid Xenopus laevis and X. borealis. Tuning site analysis showed that only some Caudata species might have UV vision. In addition, the S164A that occurred several times in LWS evolution might either functionally compensate for the Rh2 gene loss or fine-tuning visual adaptation. Our study provides the first genomic evidence for a caecilian LWS gene and a genomic viewpoint of visual opsin genes by reviewing the gains and losses of visual opsin genes, the rearrangement of syntenies, and the alteration of spectral tuning in the course of amphibians' evolution.
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Affiliation(s)
- Jinn-Jy Lin
- National Center for High-performance Computing, National Applied Research Laboratories, Hsinchu, Taiwan
| | - Feng-Yu Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, Taiwan
| | - Wen-Yu Chung
- Department of Computer Science and Information Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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Gerwin J, Torres-Dowdall J, Brown TF, Meyer A. Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes. J Mol Evol 2024:10.1007/s00239-024-10181-0. [PMID: 38861038 DOI: 10.1007/s00239-024-10181-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/25/2024] [Indexed: 06/12/2024]
Abstract
Gene duplication is one of the most important sources of novel genotypic diversity and the subsequent evolution of phenotypic diversity. Determining the evolutionary history and functional changes of duplicated genes is crucial for a comprehensive understanding of adaptive evolution. The evolutionary history of visual opsin genes is very dynamic, with repeated duplication events followed by sub- or neofunctionalization. While duplication of the green-sensitive opsins rh2 is common in teleost fish, fewer cases of multiple duplication events of the red-sensitive opsin lws are known. In this study, we investigate the visual opsin gene repertoire of the anabantoid fishes, focusing on the five lws opsin genes found in the genus Betta. We determine the evolutionary history of the lws opsin gene by taking advantage of whole-genome sequences of nine anabantoid species, including the newly assembled genome of Betta imbellis. Our results show that at least two independent duplications of lws occurred in the Betta lineage. The analysis of amino acid sequences of the lws paralogs of Betta revealed high levels of diversification in four of the seven transmembrane regions of the lws protein. Amino acid substitutions at two key-tuning sites are predicted to lead to differentiation of absorption maxima (λmax) between the paralogs within Betta. Finally, eye transcriptomics of B. splendens at different developmental stages revealed expression shifts between paralogs for all cone opsin classes. The lws genes are expressed according to their relative position in the lws opsin cluster throughout ontogeny. We conclude that temporal collinearity of lws expression might have facilitated subfunctionalization of lws in Betta and teleost opsins in general.
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Affiliation(s)
- Jan Gerwin
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Julián Torres-Dowdall
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany.
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Thomas F Brown
- Max Planck Institute of Molecular Cellular Biology and Genetics, Dresden, Germany
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany.
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3
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Sakamoto S, Matsushita Y, Itoigawa A, Ezawa T, Fujitani T, Takakura K, Zhou Y, Zhang G, Grutzner F, Kawamura S, Hayakawa T. Color vision evolution in egg-laying mammals: insights from visual photoreceptors and daily activities of Australian echidnas. ZOOLOGICAL LETTERS 2024; 10:2. [PMID: 38167154 PMCID: PMC10759620 DOI: 10.1186/s40851-023-00224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Egg-laying mammals (monotremes) are considered "primitive" due to traits such as oviparity, cloaca, and incomplete homeothermy, all of which they share with reptiles. Two groups of monotremes, the terrestrial echidna (Tachyglossidae) and semiaquatic platypus (Ornithorhynchidae), have evolved highly divergent characters since their emergence in the Cenozoic era. These evolutionary differences, notably including distinct electrosensory and chemosensory systems, result from adaptations to species-specific habitat conditions. To date, very few studies have examined the visual adaptation of echidna and platypus. In the present study, we show that echidna and platypus have different light absorption spectra in their dichromatic visual sensory systems at the molecular level. We analyzed absorption spectra of monotreme color opsins, long-wavelength sensitive opsin (LWS) and short-wavelength sensitive opsin 2 (SWS2). The wavelength of maximum absorbance (λmax) in LWS was 570.2 in short-beaked echidna (Tachyglossus aculeatus) and 560.6 nm in platypus (Ornithorhynchus anatinus); in SWS2, λmax was 451.7 and 442.6 nm, respectively. Thus, the spectral range in echidna color vision is ~ 10 nm longer overall than in platypus. Natural selection analysis showed that the molecular evolution of monotreme color opsins is generally functionally conserved, suggesting that these taxa rely on species-specific color vision. In order to understand the usage of color vision in monotremes, we made 24-h behavioral observations of captive echidnas at warm temperatures and analyzed the resultant ethograms. Echidnas showed cathemeral activity and various behavioral repertoires such as feeding, traveling, digging, and self-grooming without light/dark environment selectivity. Halting (careful) behavior is more frequent in dark conditions, which suggests that echidnas may be more dependent on vision during the day and olfaction at night. Color vision functions have contributed to dynamic adaptations and dramatic ecological changes during the ~ 60 million years of divergent monotreme evolution. The ethogram of various day and night behaviors in captive echidnas also contributes information relevant to habitat conservation and animal welfare in this iconic species, which is locally endangered.
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Affiliation(s)
- Shiina Sakamoto
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yuka Matsushita
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Akihiro Itoigawa
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Takumi Ezawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | | | | | - Yang Zhou
- BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
| | - Guojie Zhang
- Center of Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Frank Grutzner
- The Environment Institute, University of Adelaide, Adelaide, SA, Australia
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan.
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Guo J, Chi H, Zhang L, Song S, Rossiter SJ, Liu Y. Convergent evolutionary shifts in rhodopsin retinal release explain shared opsin repertoires in monotremes and crocodilians. Proc Biol Sci 2023; 290:20230530. [PMID: 37040807 PMCID: PMC10089720 DOI: 10.1098/rspb.2023.0530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
The visual ecology of early mammals remains poorly resolved. Studies of ancestral photopigments suggest an ancient transition from nocturnal to more crepuscular conditions. By contrast, the phenotypic shifts following the split of monotremes and therians-which lost their SWS1 and SWS2 opsins, respectively-are less clear. To address this, we obtained new phenotypic data on the photopigments of extant and ancestral monotremes. We then generated functional data for another vertebrate group that shares the same photopigment repertoire as monotremes: the crocodilians. By characterizing resurrected ancient pigments, we show that the ancestral monotreme underwent a dramatic acceleration in its rhodopsin retinal release rate. Moreover, this change was likely mediated by three residue replacements, two of which also arose on the ancestral branch of crocodilians, which exhibit similarly accelerated retinal release. Despite this parallelism in retinal release, we detected minimal to moderate changes in the spectral tuning of cone visual pigments in these groups. Our results imply that ancestral forms of monotremes and crocodilians independently underwent niche expansion to encompass quickly changing light conditions. This scenario-which accords with reported crepuscular activity in extant monotremes-may help account for their loss of the ultraviolet-sensitive SWS1 pigment but retention of the blue-sensitive SWS2.
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Affiliation(s)
- Jinqu Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Hai Chi
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Linghan Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Shengjing Song
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
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Corredor VH, Hauzman E, Gonçalves ADS, Ventura DF. Genetic characterization of the visual pigments of the red-eared turtle (Trachemys scripta elegans) and computational predictions of the spectral sensitivity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2022. [DOI: 10.1016/j.jpap.2022.100141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Genomic insights into the secondary aquatic transition of penguins. Nat Commun 2022; 13:3912. [PMID: 35853876 PMCID: PMC9296559 DOI: 10.1038/s41467-022-31508-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth. This study examines the tempo and drivers of penguin diversification by combining genomes from all extant and recently extinct penguin lineages, stratigraphic data from fossil penguins and morphological and biogeographic data from all extant and extinct species. Together, these datasets provide new insights into the genetic basis and evolution of adaptations in penguins.
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White ND, Batz ZA, Braun EL, Braun MJ, Carleton KL, Kimball RT, Swaroop A. A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution. Mol Ecol Resour 2021; 22:587-601. [PMID: 34652059 DOI: 10.1111/1755-0998.13496] [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: 05/14/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022]
Abstract
The diversity of avian visual phenotypes provides a framework for studying mechanisms of trait diversification generally, and the evolution of vertebrate vision, specifically. Previous research has focused on opsins, but to fully understand visual adaptation, we must study the complete phototransduction cascade (PTC). Here, we developed a probe set that captures exonic regions of 46 genes representing the PTC and other light responses. For a subset of species, we directly compared gene capture between our probe set and low-coverage whole genome sequencing (WGS), and we discuss considerations for choosing between these methods. Finally, we developed a unique strategy to avoid chimeric assembly by using "decoy" reference sequences. We successfully captured an average of 64% of our targeted exome in 46 species across 14 orders using the probe set and had similar recovery using the WGS data. Compared to WGS or transcriptomes, our probe set: (1) reduces sequencing requirements by efficiently capturing vision genes, (2) employs a simpler bioinformatic pipeline by limiting required assembly and negating annotation, and (3) eliminates the need for fresh tissues, enabling researchers to leverage existing museum collections. We then utilized our vision exome data to identify positively selected genes in two evolutionary scenarios-evolution of night vision in nocturnal birds and evolution of high-speed vision specific to manakins (Pipridae). We found parallel positive selection of SLC24A1 in both scenarios, implicating the alteration of rod response kinetics, which could improve color discrimination in dim light conditions and/or facilitate higher temporal resolution.
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Affiliation(s)
- Noor D White
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA
| | - Zachary A Batz
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Michael J Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA.,Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Karen L Carleton
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA.,Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Anand Swaroop
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
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Chang CH, Catchen J, Moran RL, Rivera-Colón AG, Wang YC, Fuller RC. Sequence Analysis and Ontogenetic Expression Patterns of Cone Opsin Genes in the Bluefin Killifish (Lucania goodei). J Hered 2021; 112:357-366. [PMID: 33837393 DOI: 10.1093/jhered/esab017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Sensory systems allow for the transfer of environmental stimuli into internal cues that can alter physiology and behavior. Many studies of visual systems focus on opsins to compare spectral sensitivity among individuals, populations, and species living in different lighting environments. This requires an understanding of the cone opsins, which can be numerous. The bluefin killifish is a good model for studying the interaction between environments and visual systems as they are found in both clear springs and tannin-stained swamps. We conducted a genome-wide screening and demonstrated that the bluefin killifish has 9 cone opsins: 1 SWS1 (354 nm), 2 SWS2 (SWS2B: 359 nm, SWS2A: 448 nm), 2 RH2 (RH2-2: 476 nm, RH2-1: 537 nm), and 4 LWS (LWS-1: 569 nm, LWS-2: 524 nm, LWS-3: 569 nm, LWS-R: 560 or 569 nm). These 9 cone opsins were located on 4 scaffolds. One scaffold contained the 2 SWS2 and 3 of the 4 LWS opsins in the same syntenic order as found in other cyprinodontoid fishes. We also compared opsin expression in larval and adult killifish under clear water conditions, which mimic springs. Two of the newly discovered opsins (LWS-2 and LWS-3) were expressed at low levels (<0.2%). Whether these opsins make meaningful contributions to visual perception in other contexts (i.e., swamp conditions) is unclear. In contrast, there was an ontogenetic change from using LWS-R to LWS-1 opsin. Bluefin killifish adults may be slightly more sensitive to longer wavelengths, which might be related to sexual selection and/or foraging preferences.
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Affiliation(s)
- Chia-Hao Chang
- TIGP, Biodiversity Program, Tunghai University, Taiwan Boulevard, Taichung City, Taiwan
| | - Julian Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, South Goodwin, Urbana, IL
| | - Rachel L Moran
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, South Goodwin, Urbana, IL
| | - Yu-Chun Wang
- Planning and Information Division, Fisheries Research Institute, Keelung City, Taiwan
| | - Rebecca C Fuller
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, 606 East Healey Street, Champaign, IL
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Matsumoto Y, Oda S, Mitani H, Kawamura S. Orthologous Divergence and Paralogous Anticonvergence in Molecular Evolution of Triplicated Green Opsin Genes in Medaka Fish, Genus Oryzias. Genome Biol Evol 2021; 12:911-923. [PMID: 32467976 PMCID: PMC7337190 DOI: 10.1093/gbe/evaa111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2020] [Indexed: 11/30/2022] Open
Abstract
Gene duplication of green (RH2) opsin genes and their spectral differentiation are well documented in many teleost fish. However, their evolutionary divergence or conservation patterns among phylogenetically close but ecologically diverse species is not well explored. Medaka fish (genus Oryzias) are broadly distributed in fresh and brackish waters of Asia, with many species being laboratory-housed and feasible for genetic studies. We previously showed that a Japan strain (HNI) of medaka (Oryzias latipes) possessed three RH2 opsin genes (RH2-A, RH2-B, and RH2-C) encoding spectrally divergent photopigments. Here, we examined the three RH2 opsin genes from six Oryzias species representing three species groups: the latipes, the celebensis, and the javanicus. Photopigment reconstitution revealed that the peak absorption spectra (λmax) of RH2-A were divergent among the species (447–469 nm), whereas those of RH2-B and RH2-C were conservative (516–519 and 486–493 nm, respectively). For the RH2-A opsins, the largest spectral shift was detected in the phylogenetic branch leading to the latipes group. A single amino acid replacement T94C explained most of the spectral shift. For RH2-B and -C opsins, we detected tracts of gene conversion between the two genes homogenizing them. Nevertheless, several amino acid differences were maintained. We showed that the spectral difference between the two opsins was attributed to largely the E/Q amino acid difference at the site 122 and to several sites with individually small spectral effects. These results depict dynamism of spectral divergence of orthologous and paralogous green opsin genes in phylogenetically close but ecologically diverse species exemplified by medaka.
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Affiliation(s)
- Yoshifumi Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.,Live Imaging Center, Central Institute for Experimental Animals (CIEA), Kawasaki, Kanagawa, Japan
| | - Shoji Oda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Mitani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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Veilleux CC, Kawamura S, Montague MJ, Hiwatashi T, Matsushita Y, Fernandez‐Duque E, Link A, Di Fiore A, Snodderly DM. Color vision and niche partitioning in a diverse neotropical primate community in lowland Amazonian Ecuador. Ecol Evol 2021; 11:5742-5758. [PMID: 34026044 PMCID: PMC8131790 DOI: 10.1002/ece3.7479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 01/05/2023] Open
Abstract
A recent focus in community ecology has been on how within-species variability shapes interspecific niche partitioning. Primate color vision offers a rich system in which to explore this issue. Most neotropical primates exhibit intraspecific variation in color vision due to allelic variation at the middle-to-long-wavelength opsin gene on the X chromosome. Studies of opsin polymorphisms have typically sampled primates from different sites, limiting the ability to relate this genetic diversity to niche partitioning. We surveyed genetic variation in color vision of five primate species, belonging to all three families of the primate infraorder Platyrrhini, found in the Yasuní Biosphere Reserve in Ecuador. The frugivorous spider monkeys and woolly monkeys (Ateles belzebuth and Lagothrix lagotricha poeppigii, family Atelidae) each had two opsin alleles, and more than 75% of individuals carried the longest-wavelength (553-556 nm) allele. Among the other species, Saimiri sciureus macrodon (family Cebidae) and Pithecia aequatorialis (family Pitheciidae) had three alleles, while Plecturocebus discolor (family Pitheciidae) had four alleles-the largest number yet identified in a wild population of titi monkeys. For all three non-atelid species, the middle-wavelength (545 nm) allele was the most common. Overall, we identified genetic evidence of fourteen different visual phenotypes-seven types of dichromats and seven trichromats-among the five sympatric taxa. The differences we found suggest that interspecific competition among primates may influence intraspecific frequencies of opsin alleles. The diversity we describe invites detailed study of foraging behavior of different vision phenotypes to learn how they may contribute to niche partitioning.
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Affiliation(s)
- Carrie C. Veilleux
- Department of Anthropology and Primate Molecular Ecology and Evolution LaboratoryUniversity of Texas at AustinAustinTXUSA
- Department of AnatomyMidwestern UniversityGlendaleAZUSA
| | - Shoji Kawamura
- Department of Integrated BiosciencesUniversity of TokyoKashiwaJapan
| | | | | | - Yuka Matsushita
- Department of Integrated BiosciencesUniversity of TokyoKashiwaJapan
| | - Eduardo Fernandez‐Duque
- Department of Anthropology and School of the EnvironmentYale UniversityNew HavenCTUSA
- College of Biological and Environmental SciencesUniversidad San Francisco de QuitoCumbayáEcuador
| | - Andres Link
- College of Biological and Environmental SciencesUniversidad San Francisco de QuitoCumbayáEcuador
- Department of Biological SciencesUniversidad de Los AndesBogotaColombia
| | - Anthony Di Fiore
- Department of Anthropology and Primate Molecular Ecology and Evolution LaboratoryUniversity of Texas at AustinAustinTXUSA
- College of Biological and Environmental SciencesUniversidad San Francisco de QuitoCumbayáEcuador
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Hensley NM, Ellis EA, Leung NY, Coupart J, Mikhailovsky A, Taketa DA, Tessler M, Gruber DF, De Tomaso AW, Mitani Y, Rivers TJ, Gerrish GA, Torres E, Oakley TH. Selection, drift, and constraint in cypridinid luciferases and the diversification of bioluminescent signals in sea fireflies. Mol Ecol 2021; 30:1864-1879. [PMID: 33031624 DOI: 10.1111/mec.15673] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023]
Abstract
Understanding the genetic causes of evolutionary diversification is challenging because differences across species are complex, often involving many genes. However, cases where single or few genetic loci affect a trait that varies dramatically across a radiation of species provide tractable opportunities to understand the genetics of diversification. Here, we begin to explore how diversification of bioluminescent signals across species of cypridinid ostracods ("sea fireflies") was influenced by evolution of a single gene, cypridinid-luciferase. In addition to emission spectra ("colour") of bioluminescence from 21 cypridinid species, we report 13 new c-luciferase genes from de novo transcriptomes, including in vitro assays to confirm function of four of those genes. Our comparative analyses suggest some amino acid sites in c-luciferase evolved under episodic diversifying selection and may be associated with changes in both enzyme kinetics and colour, two enzymatic functions that directly impact the phenotype of bioluminescent signals. The analyses also suggest multiple other amino acid positions in c-luciferase evolved neutrally or under purifying selection, and may have impacted the variation of colour of bioluminescent signals across genera. Previous mutagenesis studies at candidate sites show epistatic interactions, which could constrain the evolution of c-luciferase function. This work provides important steps toward understanding the genetic basis of diversification of behavioural signals across multiple species, suggesting different evolutionary processes act at different times during a radiation of species. These results set the stage for additional mutagenesis studies that could explicitly link selection, drift, and constraint to the evolution of phenotypic diversification.
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Affiliation(s)
- Nicholai M Hensley
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Emily A Ellis
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Nicole Y Leung
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - John Coupart
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Alexander Mikhailovsky
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Daryl A Taketa
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Michael Tessler
- American Museum of Natural History and New York University, New York, NY, USA
- Department of Biology, St. Francis College, Brooklyn, NY, USA
| | - David F Gruber
- Department of Biology and Environmental Science, City University of New York Baruch College, New York, NY, USA
| | - Anthony W De Tomaso
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Trevor J Rivers
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Gretchen A Gerrish
- Department of Biology, University of Wisconsin - La Crosse, La Crosse, WI, USA
| | - Elizabeth Torres
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA, USA
| | - Todd H Oakley
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
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12
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Lankford CK, Laird JG, Inamdar SM, Baker SA. A Comparison of the Primary Sensory Neurons Used in Olfaction and Vision. Front Cell Neurosci 2020; 14:595523. [PMID: 33250719 PMCID: PMC7676898 DOI: 10.3389/fncel.2020.595523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022] Open
Abstract
Vision, hearing, smell, taste, and touch are the tools used to perceive and navigate the world. They enable us to obtain essential resources such as food and highly desired resources such as mates. Thanks to the investments in biomedical research the molecular unpinning’s of human sensation are rivaled only by our knowledge of sensation in the laboratory mouse. Humans rely heavily on vision whereas mice use smell as their dominant sense. Both modalities have many features in common, starting with signal detection by highly specialized primary sensory neurons—rod and cone photoreceptors (PR) for vision, and olfactory sensory neurons (OSN) for the smell. In this chapter, we provide an overview of how these two types of primary sensory neurons operate while highlighting the similarities and distinctions.
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Affiliation(s)
- Colten K Lankford
- Department of Biochemistry, University of Iowa, Iowa City, IA, United States
| | - Joseph G Laird
- Department of Biochemistry, University of Iowa, Iowa City, IA, United States
| | - Shivangi M Inamdar
- Department of Biochemistry, University of Iowa, Iowa City, IA, United States
| | - Sheila A Baker
- Department of Biochemistry, University of Iowa, Iowa City, IA, United States.,Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
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13
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Hart NS, Lamb TD, Patel HR, Chuah A, Natoli RC, Hudson NJ, Cutmore SC, Davies WIL, Collin SP, Hunt DM. Visual Opsin Diversity in Sharks and Rays. Mol Biol Evol 2020; 37:811-827. [PMID: 31770430 DOI: 10.1093/molbev/msz269] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The diversity of color vision systems found in extant vertebrates suggests that different evolutionary selection pressures have driven specializations in photoreceptor complement and visual pigment spectral tuning appropriate for an animal's behavior, habitat, and life history. Aquatic vertebrates in particular show high variability in chromatic vision and have become important models for understanding the role of color vision in prey detection, predator avoidance, and social interactions. In this study, we examined the capacity for chromatic vision in elasmobranch fishes, a group that have received relatively little attention to date. We used microspectrophotometry to measure the spectral absorbance of the visual pigments in the outer segments of individual photoreceptors from several ray and shark species, and we sequenced the opsin mRNAs obtained from the retinas of the same species, as well as from additional elasmobranch species. We reveal the phylogenetically widespread occurrence of dichromatic color vision in rays based on two cone opsins, RH2 and LWS. We also confirm that all shark species studied to date appear to be cone monochromats but report that in different species the single cone opsin may be of either the LWS or the RH2 class. From this, we infer that cone monochromacy in sharks has evolved independently on multiple occasions. Together with earlier discoveries in secondarily aquatic marine mammals, this suggests that cone-based color vision may be of little use for large marine predators, such as sharks, pinnipeds, and cetaceans.
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Affiliation(s)
- Nathan S Hart
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Hardip R Patel
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Aaron Chuah
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Riccardo C Natoli
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Nicholas J Hudson
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Scott C Cutmore
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Wayne I L Davies
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
| | - Shaun P Collin
- School of Life Sciences, La Trobe University, Bundoora, VIC, Australia
| | - David M Hunt
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, The University of Western Australia, Crawley, WA, Australia
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14
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Sousa BRS, Loureiro TMG, Goulart PRK, Cortes MIT, Costa MF, Bonci DMO, Baran LCP, Hauzman E, Ventura DF, Miquilini L, Souza GS. Specificity of the chromatic noise influence on the luminance contrast discrimination to the color vision phenotype. Sci Rep 2020; 10:17897. [PMID: 33087826 PMCID: PMC7578001 DOI: 10.1038/s41598-020-74875-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 10/08/2020] [Indexed: 11/09/2022] Open
Abstract
Many studies have examined how color and luminance information are processed in the visual system. It has been observed that chromatic noise masked luminance discrimination in trichromats and that luminance thresholds increased as a function of noise saturation. Here, we aimed to compare chromatic noise inhibition on the luminance thresholds of trichromats and subjects with severe deutan or protan losses. Twenty-two age-matched subjects were evaluated, 12 trichromats and 10 with congenital color vision impairment: 5 protanopes/protanomalous, and 5 deuteranopes/deuteranomalous. We used a mosaic of circles containing chromatic noise consisting of 8 chromaticities around protan, deutan, and tritan confusion lines. A subset of the circles differed in the remaining circles by the luminance arising from a C-shaped central target. All the participants were tested in 4 chromatic noise saturation conditions (0.04, 0.02, 0.01, 0.005 u'v' units) and 1 condition without chromatic noise. We observed that trichromats had an increasing luminance threshold as a function of chromatic noise saturation under all chromatic noise conditions. The subjects with color vision deficiencies displayed no changes in the luminance threshold across the different chromatic noise saturations when the noise was composed of chromaticities close to their color confusion lines (protan and deutan chromatic noise). However, for tritan chromatic noise, they were found to have similar results to the trichromats. The use of chromatic noise masking on luminance threshold estimates could help to simultaneously examine the processing of luminance and color information. A comparison between luminance contrast discrimination obtained from no chromatic and high-saturated chromatic noise conditions could be initially undertaken in this double-duty test.
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Affiliation(s)
- Bruna Rafaela Silva Sousa
- Núcleo de Medicina Tropical, Universidade Federal do Pará, Av. Generalíssimo Deodoro 92, Umarizal, Belém, Pará, 66055-240, Brazil
| | | | | | | | | | | | | | - Einat Hauzman
- Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil
| | - Dora Fix Ventura
- Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil
| | - Leticia Miquilini
- Núcleo de Teoria e Pesquisa do Comportamento, Universidade Federal do Pará, Belém, Brazil
| | - Givago Silva Souza
- Núcleo de Medicina Tropical, Universidade Federal do Pará, Av. Generalíssimo Deodoro 92, Umarizal, Belém, Pará, 66055-240, Brazil. .,Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.
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15
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Baldwin MW, Ko MC. Functional evolution of vertebrate sensory receptors. Horm Behav 2020; 124:104771. [PMID: 32437717 DOI: 10.1016/j.yhbeh.2020.104771] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022]
Abstract
Sensory receptors enable animals to perceive their external world, and functional properties of receptors evolve to detect the specific cues relevant for an organism's survival. Changes in sensory receptor function or tuning can directly impact an organism's behavior. Functional tests of receptors from multiple species and the generation of chimeric receptors between orthologs with different properties allow for the dissection of the molecular basis of receptor function and identification of the key residues that impart functional changes in different species. Knowledge of these functionally important sites facilitates investigation into questions regarding the role of epistasis and the extent of convergence, as well as the timing of sensory shifts relative to other phenotypic changes. However, as receptors can also play roles in non-sensory tissues, and receptor responses can be modulated by numerous other factors including varying expression levels, alternative splicing, and morphological features of the sensory cell, behavioral validation can be instrumental in confirming that responses observed in heterologous systems play a sensory role. Expression profiling of sensory cells and comparative genomics approaches can shed light on cell-type specific modifications and identify other proteins that may affect receptor function and can provide insight into the correlated evolution of complex suites of traits. Here we review the evolutionary history and diversity of functional responses of the major classes of sensory receptors in vertebrates, including opsins, chemosensory receptors, and ion channels involved in temperature-sensing, mechanosensation and electroreception.
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Affiliation(s)
| | - Meng-Ching Ko
- Max Planck Institute for Ornithology, Seewiesen, Germany
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16
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Těšický M, Velová H, Novotný M, Kreisinger J, Beneš V, Vinkler M. Positive selection and convergent evolution shape molecular phenotypic traits of innate immunity receptors in tits (Paridae). Mol Ecol 2020; 29:3056-3070. [PMID: 32652716 DOI: 10.1111/mec.15547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/09/2020] [Accepted: 06/26/2020] [Indexed: 01/04/2023]
Abstract
Despite widespread variability and redundancy abounding animal immunity, little is currently known about the rate of evolutionary convergence (functionally analogous traits not inherited from a common ancestor) in host molecular adaptations to parasite selective pressures. Toll-like receptors (TLRs) provide the molecular interface allowing hosts to recognize pathogenic structures and trigger early danger signals initiating an immune response. Using a novel combination of bioinformatic approaches, here we explore genetic variation in ligand-binding regions of bacteria-sensing TLR4 and TLR5 in 29 species belonging to the tit family of passerine birds (Aves: Paridae). Three out of the four consensual positively selected sites in TLR4 and six out of 14 positively selected positions in TLR5 were located on the receptor surface near the functionally important sites, and based on the phylogenetic pattern evolved in a convergent (parallel) manner. This type of evolution was also seen at one N-glycosylation site and two positively selected phosphorylation sites, providing the first evidence of convergence in post-translational modifications in evolutionary immunology. Finally, the overall mismatch between phylogeny and the clustering of surface charge distribution demonstrates that convergence is common in overall TLR4 and TLR5 molecular phenotypes involved in ligand binding. Our analysis did not reveal any broad ecological traits explaining the convergence observed in electrostatic potentials, suggesting that information on microbial symbionts may be needed to explain TLR evolution. Adopting state-of-the-art predictive structural bionformatics, we have outlined a new broadly applicable methodological approach to estimate the functional significance of positively selected variation and test for the adaptive molecular convergence in protein-coding polymorphisms.
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Affiliation(s)
- Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Hana Velová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marian Novotný
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vladimír Beneš
- European Molecular Laboratory Heidelberg, Heidelberg, Germany
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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17
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Thyroid hormone receptors mediate two distinct mechanisms of long-wavelength vision. Proc Natl Acad Sci U S A 2020; 117:15262-15269. [PMID: 32541022 DOI: 10.1073/pnas.1920086117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thyroid hormone (TH) signaling plays an important role in the regulation of long-wavelength vision in vertebrates. In the retina, thyroid hormone receptor β (thrb) is required for expression of long-wavelength-sensitive opsin (lws) in red cone photoreceptors, while in retinal pigment epithelium (RPE), TH regulates expression of a cytochrome P450 enzyme, cyp27c1, that converts vitamin A1 into vitamin A2 to produce a red-shifted chromophore. To better understand how TH controls these processes, we analyzed the phenotype of zebrafish with mutations in the three known TH nuclear receptor transcription factors (thraa, thrab, and thrb). We found that no single TH nuclear receptor is required for TH-mediated induction of cyp27c1 but that deletion of all three (thraa -/- ;thrab -/- ;thrb -/- ) completely abrogates its induction and the resulting conversion of A1- to A2-based retinoids. In the retina, loss of thrb resulted in an absence of red cones at both larval and adult stages without disruption of the underlying cone mosaic. RNA-sequencing analysis revealed significant down-regulation of only five genes in adult thrb -/- retina, of which three (lws1, lws2, and miR-726) occur in a single syntenic cluster. In the thrb -/- retina, retinal progenitors destined to become red cones were transfated into ultraviolet (UV) cones and horizontal cells. Taken together, our findings demonstrate cooperative regulation of cyp27c1 by TH receptors and a requirement for thrb in red cone fate determination. Thus, TH signaling coordinately regulates both spectral sensitivity and sensory plasticity.
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18
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Escobar-Camacho D, Carleton KL, Narain DW, Pierotti MER. Visual pigment evolution in Characiformes: The dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning. Mol Ecol 2020; 29:2234-2253. [PMID: 32421918 DOI: 10.1111/mec.15474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 01/06/2023]
Abstract
Vision represents an excellent model for studying adaptation, given the genotype-to-phenotype map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light, making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we showcase the visual system evolution of neotropical Characiformes and the spectral tuning mechanisms they exhibit to modulate their visual sensitivities. Such mechanisms include gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1 /A2 -chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform's entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogues has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. Furthermore, characiforms' colour vision is based on the expression of both LWS-paralogues and SWS2. Finally, we found interspecific and intraspecific variation in A1 /A2 -chromophores proportions, correlating with the light environment. These multiple mechanisms may be a result of the diverse visual environments where Characiformes have evolved.
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Affiliation(s)
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Devika W Narain
- Environmental Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - Michele E R Pierotti
- Naos Marine Laboratories, Smithsonian Tropical Research Institute, Panama, Republic of Panama
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19
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Montenegro J, Mochida K, Matsui K, Mokodongan DF, Sumarto BKA, Lawelle SA, Nofrianto AB, Hadiaty RK, Masengi KWA, Yong L, Inomata N, Irie T, Hashiguchi Y, Terai Y, Kitano J, Yamahira K. Convergent evolution of body color between sympatric freshwater fishes via different visual sensory evolution. Ecol Evol 2019; 9:6389-6398. [PMID: 31236229 PMCID: PMC6580282 DOI: 10.1002/ece3.5211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/05/2019] [Accepted: 04/11/2019] [Indexed: 12/18/2022] Open
Abstract
Although there are many examples of color evolution potentially driven by sensory drive, only few studies have examined whether distinct species inhabiting the same environments evolve similar body colors via shared sensory mechanisms. In this study, we tested whether two sympatric freshwater fish taxa, halfbeaks of the genus Nomorhamphus and ricefishes of the genus Oryzias in Sulawesi Island, converge in both body color and visual sensitivity. After reconstructing the phylogeny separately for Nomorhamphus and Oryzias using transcriptome-wide sequences, we demonstrated positive correlations of body redness between these two taxa across environments, even after phylogenetic corrections, which support convergent evolution. However, substantial differences were observed in the expression profiles of opsin genes in the eyes between Nomorhamphus and Oryzias. Particularly, the expression levels of the long wavelength-sensitive genes were negatively correlated between the taxa, indicating that they have different visual sensitivities despite living in similar light environments. Thus, the convergence of body colorations between these two freshwater fish taxa was not accompanied by convergence in opsin sensitivities. This system presents a case in which body color convergence can occur between sympatric species via different mechanisms.
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Affiliation(s)
- Javier Montenegro
- Tropical Biosphere Research CenterUniversity of the RyukyusOkinawaJapan
| | - Koji Mochida
- Department of BiologyKeio UniversityYokohamaJapan
| | - Kumi Matsui
- School of Veterinary MedicineAzabu UniversitySagamiharaJapan
| | - Daniel F. Mokodongan
- Tropical Biosphere Research CenterUniversity of the RyukyusOkinawaJapan
- Faculty of Fisheries and Marine ScienceHalu Oleo UniversityKendariIndonesia
| | | | - Sjamsu A. Lawelle
- Faculty of Fisheries and Marine ScienceHalu Oleo UniversityKendariIndonesia
| | - Andy B. Nofrianto
- Faculty of Fisheries and Marine ScienceHalu Oleo UniversityKendariIndonesia
| | | | | | - Lengxob Yong
- Ecological Genetics LaboratoryNational Institute of GeneticsMishimaJapan
- Center for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterCornwallUK
| | - Nobuyuki Inomata
- Department of Environmental ScienceFukuoka Women's UniversityFukuokaJapan
| | | | | | - Yohey Terai
- Department of Evolutionary Studies of BiosystemsThe Graduate University for Advanced StudiesHayamaJapan
| | - Jun Kitano
- Ecological Genetics LaboratoryNational Institute of GeneticsMishimaJapan
| | - Kazunori Yamahira
- Tropical Biosphere Research CenterUniversity of the RyukyusOkinawaJapan
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20
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Divergence, evolution and adaptation in ray-finned fish genomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1003-1018. [PMID: 31098893 DOI: 10.1007/s11427-018-9499-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/12/2019] [Indexed: 02/06/2023]
Abstract
With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.
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21
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Abstract
For nearly a century adaptive landscapes have provided overviews of the evolutionary process and yet they remain metaphors. We redefine adaptive landscapes in terms of biological processes rather than descriptive phenomenology. We focus on the underlying mechanisms that generate emergent properties such as epistasis, dominance, trade-offs and adaptive peaks. We illustrate the utility of landscapes in predicting the course of adaptation and the distribution of fitness effects. We abandon aged arguments concerning landscape ruggedness in favor of empirically determining landscape architecture. In so doing, we transform the landscape metaphor into a scientific framework within which causal hypotheses can be tested.
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Affiliation(s)
- Xiao Yi
- BioTechnology Institute, University of Minnesota, St. Paul, MN
| | - Antony M Dean
- BioTechnology Institute, University of Minnesota, St. Paul, MN
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
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22
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Duytschaever G, Janiak MC, Ong PS, Wells K, Dominy NJ, Melin AD. Opsin genes of select treeshrews resolve ancestral character states within Scandentia. ROYAL SOCIETY OPEN SCIENCE 2019; 6:182037. [PMID: 31183134 PMCID: PMC6502361 DOI: 10.1098/rsos.182037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/21/2019] [Indexed: 06/09/2023]
Abstract
Treeshrews are small, squirrel-like mammals in the order Scandentia, which is nested together with Primates and Dermoptera in the superordinal group Euarchonta. They are often described as living fossils, and researchers have long turned to treeshrews as a model or ecological analogue for ancestral primates. A comparative study of colour vision-encoding genes within Scandentia found a derived amino acid substitution in the long-wavelength sensitive opsin gene (OPN1LW) of the Bornean smooth-tailed treeshrew (Dendrogale melanura). The opsin, by inference, is red-shifted by ca 6 nm with an inferred peak sensitivity of 561 nm. It is tempting to view this trait as a novel visual adaptation; however, the genetic and functional diversity of visual pigments in treeshrews is unresolved outside of Borneo. Here, we report gene sequences from the northern smooth-tailed treeshrew (Dendrogale murina) and the Mindanao treeshrew (Tupaia everetti, the senior synonym of Urogale everetti). We found that the opsin genes are under purifying selection and that D. murina shares the same substitution as its congener, a result that distinguishes Dendrogale from other treeshrews, including T. everetti. We discuss the implications of opsin functional variation in light of limited knowledge about the visual ecology of smooth-tailed treeshrews.
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Affiliation(s)
- Gwen Duytschaever
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Mareike C. Janiak
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Perry S. Ong
- Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines
| | - Konstans Wells
- Department of Biosciences, Swansea University, Wales, UK
| | - Nathaniel J. Dominy
- Department of Anthropology, Dartmouth College, Hanover, NH, USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Amanda D. Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
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23
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Liu Y, Chi H, Li L, Rossiter SJ, Zhang S. Molecular Data Support an Early Shift to an Intermediate-Light Niche in the Evolution of Mammals. Mol Biol Evol 2019; 35:1130-1134. [PMID: 29462332 DOI: 10.1093/molbev/msy019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The visual ability and associated photic niche of early mammals is debated. The theory that ancestral mammals were nocturnal is supported by diverse adaptations. However, others argue that photopigment repertoires of early mammals are more consistent with a crepuscular niche, and support for this also comes from inferred spectral tuning of middle/long wavelength-sensitive (M/LWS) opsin sequences. Functional studies have suggested that the M/LWS pigment in the ancestor of Mammalia was either red- or green-sensitive; however, these were based on outdated phylogenies with key lineages omitted. By performing the most detailed study to date of middle/long-wave mammalian color vision, we provide the first experimental evidence that the M/LWS pigment of amniotes underwent a 9-nm spectral shift towards shorter wavelengths in the Mammalia ancestor, exceeding predictions from known critical sites. Our results suggest early mammals were yellow-sensitive, possibly representing an adaptive trade-off for both crepuscular (twilight) and nocturnal (moonlight) niches.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hai Chi
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Longfei Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Shuyi Zhang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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24
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Evolutionary history of the medaka long-wavelength sensitive genes and effects of artificial regression by gene loss on behavioural photosensitivity. Sci Rep 2019; 9:2726. [PMID: 30804415 PMCID: PMC6389941 DOI: 10.1038/s41598-019-39978-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 11/28/2018] [Indexed: 01/28/2023] Open
Abstract
Tandem gene duplication has led to an expansion of cone-opsin repertoires in many fish, but the resulting functional advantages have only been conjectured without empirical demonstration. Medaka (Oryzias latipes and O. sakaizumii) have eight (two red, three green, two blue, and one violet) cone opsin genes. Absorbance maxima (λmax) of the proteins vary from 356 nm to 562 nm, but those of the red opsins (long-wavelength sensitive; LWS) are nearly identical, obscuring the necessity of their coexistence. Here, we compared the LWSa and LWSb loci of these sister species and found that the gene duplication occurred long before the latipes–sakaizumii speciation (4–18 million years ago), and the high sequence similarity between the paralogues is the result of at least two events of gene conversion. These repetitive gene conversions would indicate the importance for medaka of retaining two identical LWSs in the genome. However, a newly established medaka mutant with a single LWS showed no defect in LWS expression or behavioural red-light sensitivity, demonstrating functional redundancy of the paralogs. Thus, as with many other genes after whole-genome duplication, the redundant LWS might be on the way to being lost from the current cone opsin repertoire. Thus, non-allelic gene conversion may temporarily provide an easier and more frequent solution than gene loss for reducing genetic diversity, which should be considered when assessing history of gene evolution by phylogenetic analyses.
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25
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Simões BF, Foley NM, Hughes GM, Zhao H, Zhang S, Rossiter SJ, Teeling EC. As Blind as a Bat? Opsin Phylogenetics Illuminates the Evolution of Color Vision in Bats. Mol Biol Evol 2019; 36:54-68. [PMID: 30476197 PMCID: PMC6340466 DOI: 10.1093/molbev/msy192] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Through their unique use of sophisticated laryngeal echolocation bats are considered sensory specialists amongst mammals and represent an excellent model in which to explore sensory perception. Although several studies have shown that the evolution of vision is linked to ecological niche adaptation in other mammalian lineages, this has not yet been fully explored in bats. Recent molecular analysis of the opsin genes, which encode the photosensitive pigments underpinning color vision, have implicated high-duty cycle (HDC) echolocation and the adoption of cave roosting habits in the degeneration of color vision in bats. However, insufficient sampling of relevant taxa has hindered definitive testing of these hypotheses. To address this, novel sequence data was generated for the SWS1 and MWS/LWS opsin genes and combined with existing data to comprehensively sample species representing diverse echolocation types and niches (SWS1 n = 115; MWS/LWS n = 45). A combination of phylogenetic analysis, ancestral state reconstruction, and selective pressure analyses were used to reconstruct the evolution of these visual pigments in bats and revealed that although both genes are evolving under purifying selection in bats, MWS/LWS is highly conserved but SWS1 is highly variable. Spectral tuning analyses revealed that MWS/LWS opsin is tuned to a long wavelength, 555-560 nm in the bat ancestor and the majority of extant taxa. The presence of UV vision in bats is supported by our spectral tuning analysis, but phylogenetic analyses demonstrated that the SWS1 opsin gene has undergone pseudogenization in several lineages. We do not find support for a link between the evolution of HDC echolocation and the pseudogenization of the SWS1 gene in bats, instead we show the SWS1 opsin is functional in the HDC echolocator, Pteronotus parnellii. Pseudogenization of the SWS1 is correlated with cave roosting habits in the majority of pteropodid species. Together these results demonstrate that the loss of UV vision in bats is more widespread than was previously considered and further elucidate the role of ecological niche specialization in the evolution of vision in bats.
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Affiliation(s)
- Bruno F Simões
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
- School of Earth Science, University of Bristol, Bristol, United Kingdom
- School of Biological Science, The University of Adelaide, South Australia, Australia
| | - Nicole M Foley
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Graham M Hughes
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Huabin Zhao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Emma C Teeling
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
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Abstract
Although much is known about the visual system of vertebrates in general, studies regarding vision in reptiles, and snakes in particular, are scarce. Reptiles display diverse ocular structures, including different types of retinae such as pure cone, mostly rod, or duplex retinas (containing both rods and cones); however, the same five opsin-based photopigments are found in many of these animals. It is thought that ancestral snakes were nocturnal and/or fossorial, and, as such, they have lost two pigments, but retained three visual opsin classes. These are the RH1 gene (rod opsin or rhodopsin-like-1) expressed in rods and two cone opsins, namely LWS (long-wavelength-sensitive) and SWS1 (short-wavelength-sensitive-1) genes. Until recently, the study of snake photopigments has been largely ignored. However, its importance has become clear within the past few years as studies reconsider Walls’ transmutation theory, which was first proposed in the 1930s. In this study, the visual pigments of Bothrops atrox (the common lancehead), a South American pit viper, were examined. Specifically, full-length RH1 and LWS opsin gene sequences were cloned, as well as most of the SWS1 opsin gene. These sequences were subsequently used for phylogenetic analysis and to predict the wavelength of maximum absorbance (λmax) for each photopigment. This is the first report to support the potential for rudimentary color vision in a South American viper, specifically a species that is regarded as being nocturnal.
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27
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Sandkam BA, Joy JB, Watson CT, Breden F. Genomic Environment Impacts Color Vision Evolution in a Family with Visually Based Sexual Selection. Genome Biol Evol 2018; 9:3100-3107. [PMID: 29121209 PMCID: PMC5714168 DOI: 10.1093/gbe/evx228] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2017] [Indexed: 12/14/2022] Open
Abstract
Many models of evolution by sexual selection predict a coevolution of sensory systems and mate preferences, but the genomic architecture (number and arrangement of contributing loci) underlying these characters could constrain this coevolution. Here, we examine how the genomic organization and evolution of the opsin genes (responsible for tuning color vision) can influence the evolutionary trajectory of sexually selected traits across 15 species in the family Poeciliidae, which includes classic systems for studies of color-mediated sexual selection such as guppies, swordtails, and mollies. Although male coloration patterns and the importance of this coloration in female mate choice vary widely within and among genera, sequencing revealed low variability at amino acid sites that tune Long Wavelength-Sensitive (LWS) opsins in this speciose family. Although most opsin genes in these species appear to have evolved along traditional mutation-selection dynamics, we identified high rates of gene conversion between two of the LWS loci (LWS-1 and LWS-3), likely due to the inverted tandem repeat nature of these genes. Yet members of the subgenus Lebistes appear to resist LWS gene conversion. The LWS opsins are responsible for detecting and discriminating red and orange coloration-a key sexually selected trait in members of the subgenus Lebistes. Taken together these results suggest selection is acting against the homogenizing effects of gene conversion to maintain LWS-1/LWS-3 differences within this subgenus.
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Affiliation(s)
- Benjamin A Sandkam
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Biology, University of Maryland, Maryland, USA
| | - Jeffrey B Joy
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Corey T Watson
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Kentucky, USA
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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28
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Lower SE, Stanger-Hall KF, Hall DW. Molecular variation across populations of a widespread North American firefly, Photinus pyralis, reveals that coding changes do not underlie flash color variation or associated visual sensitivity. BMC Evol Biol 2018; 18:129. [PMID: 30170542 PMCID: PMC6119266 DOI: 10.1186/s12862-018-1251-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/20/2018] [Indexed: 01/22/2023] Open
Abstract
Background Genes underlying signal production and reception are expected to evolve to maximize signal detection in specific environments. Fireflies vary in their light signal color both within and between species, and thus provide an excellent system in which to study signal production and reception in the context of signaling environments. Differences in signal color have been hypothesized to be due to variation in the sequence of luciferase, the enzyme that catalyzes the light reaction. Similarly, differences in visual sensitivity, which are expected to match signal color, have been hypothesized to be due to variation in the sequence of opsins, the protein component of visual pigments. Here we investigated (1) whether sequence variation in luciferase correlates with variation in signal color and (2) whether sequence variation in opsins correlates with inferred matching visual sensitivity across populations of a widespread North American firefly species, Photinus pyralis. We further tested (3) whether selection has acted on these loci by examining their population-level differentiation relative to the distribution of differentiation derived from a genome-wide sample of loci generated by double-digest RADseq. Results We found virtually no coding variation in luciferase or opsins. However, there was extreme divergence in non-coding variation in luciferase across populations relative to a panel of random genomic loci. Conclusions The absence of protein variation at both loci challenges the paradigm that variation in signal color and visual sensitivity in fireflies is exclusively due to coding variation in luciferase and opsin genes. Instead, flash color variation within species must involve other mechanisms, such as abdominal pigmentation or regulation of light organ physiology. Evidence for selection at non-coding variation in luciferase suggests that selection is targeting luciferase regulation and may favor differ expression levels across populations. Electronic supplementary material The online version of this article (10.1186/s12862-018-1251-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah E Lower
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA. .,Present address: Department of Biology, Bucknell University, Lewisburg, PA, 17837, USA.
| | | | - David W Hall
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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29
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Mark MD, Donner M, Eickelbeck D, Stepien J, Nowrousian M, Kück U, Paris F, Hellinger J, Herlitze S. Visual tuning in the flashlight fish Anomalops katoptron to detect blue, bioluminescent light. PLoS One 2018; 13:e0198765. [PMID: 29995896 PMCID: PMC6040694 DOI: 10.1371/journal.pone.0198765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/24/2018] [Indexed: 01/23/2023] Open
Abstract
Bioluminescence is a fascinating phenomenon and can be found in many different organisms including fish. It has been suggested that bioluminescence is used for example for defense, prey attraction, and for intraspecific communication to attract for example sexual partners. The flashlight fish, Anomalops katoptron (A. katoptron), is a nocturnal fish that produces bioluminescence and lives in shallow waters, which makes it ideal for laboratory studies. In order to understand A. katoptron's ability to detect bioluminescent light (480 to 490 nm) at night, we characterized the visual system adaptation of A. katoptron using phylogenetic, electrophysiological and behavioral studies. We found that the retinae of A. katoptron contain rods and sparse cones. A. katoptron retinae express two main visual pigments, rhodopsin (RH1), and to a lesser extent, rhodopsin-like opsin (RH2). Interestingly, recombinant RH1 and RH2 are maximally sensitive to a wavelength of approximately 490 nm light (λmax), which correspond to the spectral peak of in vivo electroretinogram (ERG) measurements. In addition, behavioral assays revealed that A. katoptron is attracted by low intensity blue but not red light. Collectively, our results suggest that the A. katoptron visual system is optimized to detect blue light in the frequency range of its own bioluminescence and residual starlight.
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Affiliation(s)
- Melanie D. Mark
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
- * E-mail:
| | - Marcel Donner
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
| | - Dennis Eickelbeck
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
| | - Jennifer Stepien
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
| | - Minou Nowrousian
- Department of General and Molecular Botany, Ruhr-University Bochum, Bochum, Germany
| | - Ulrich Kück
- Department of General and Molecular Botany, Ruhr-University Bochum, Bochum, Germany
| | - Frank Paris
- Department of Animal Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Jens Hellinger
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
| | - Stefan Herlitze
- Department of General Zoology and Neurobiology, Ruhr-University Bochum, Bochum, Germany
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30
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Lind O, Henze MJ, Kelber A, Osorio D. Coevolution of coloration and colour vision? Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0338. [PMID: 28533455 DOI: 10.1098/rstb.2016.0338] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2017] [Indexed: 11/12/2022] Open
Abstract
The evolutionary relationship between signals and animal senses has broad significance, with potential consequences for speciation, and for the efficacy and honesty of biological communication. Here we outline current understanding of the diversity of colour vision in two contrasting groups: the phylogenetically conservative birds, and the more variable butterflies. Evidence for coevolution of colour signals and vision exists in both groups, but is limited to observations of phenotypic differences between visual systems, which might be correlated with coloration. Here, to illustrate how one might interpret the evolutionary significance of such differences, we used colour vision modelling based on an avian eye to evaluate the effects of variation in three key characters: photoreceptor spectral sensitivity, oil droplet pigmentation and the proportions of different photoreceptor types. The models predict that physiologically realistic changes in any one character will have little effect, but complementary shifts in all three can substantially affect discriminability of three types of natural spectra. These observations about the adaptive landscape of colour vision may help to explain the general conservatism of photoreceptor spectral sensitivities in birds. This approach can be extended to other types of eye and spectra to inform future work on coevolution of coloration and colour vision.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.
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Affiliation(s)
- Olle Lind
- Department of Philosophy, Cognitive Science, Helgonavägen 3, 22362 Lund, Sweden
| | - Miriam J Henze
- Queensland Brain Institute, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Almut Kelber
- Department of Biology, Lund Vision Group, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | - Daniel Osorio
- School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, BN1 9QG, UK
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31
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Dungan SZ, Chang BSW. Epistatic interactions influence terrestrial-marine functional shifts in cetacean rhodopsin. Proc Biol Sci 2018; 284:rspb.2016.2743. [PMID: 28250185 DOI: 10.1098/rspb.2016.2743] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/03/2017] [Indexed: 12/12/2022] Open
Abstract
Like many aquatic vertebrates, whales have blue-shifting spectral tuning substitutions in the dim-light visual pigment, rhodopsin, that are thought to increase photosensitivity in underwater environments. We have discovered that known spectral tuning substitutions also have surprising epistatic effects on another function of rhodopsin, the kinetic rates associated with light-activated intermediates. By using absorbance spectroscopy and fluorescence-based retinal release assays on heterologously expressed rhodopsin, we assessed both spectral and kinetic differences between cetaceans (killer whale) and terrestrial outgroups (hippo, bovine). Mutation experiments revealed that killer whale rhodopsin is unusually resilient to pleiotropic effects on retinal release from key blue-shifting substitutions (D83N and A292S), largely due to a surprisingly specific epistatic interaction between D83N and the background residue, S299. Ancestral sequence reconstruction indicated that S299 is an ancestral residue that predates the evolution of blue-shifting substitutions at the origins of Cetacea. Based on these results, we hypothesize that intramolecular epistasis helped to conserve rhodopsin's kinetic properties while enabling blue-shifting spectral tuning substitutions as cetaceans adapted to aquatic environments. Trade-offs between different aspects of molecular function are rarely considered in protein evolution, but in cetacean and other vertebrate rhodopsins, may underlie multiple evolutionary scenarios for the selection of specific amino acid substitutions.
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Affiliation(s)
- Sarah Z Dungan
- Department Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Belinda S W Chang
- Department Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2 .,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada M5S 3B2.,Department Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5
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32
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Lin JJ, Wang FY, Li WH, Wang TY. The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation. Sci Rep 2017; 7:15568. [PMID: 29138475 PMCID: PMC5686071 DOI: 10.1038/s41598-017-15868-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/03/2017] [Indexed: 01/25/2023] Open
Abstract
We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.
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Affiliation(s)
- Jinn-Jy Lin
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Feng-Yu Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, 852, Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan. .,Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan. .,Department of Ecology and Evolution, University of Chicago, Chicago, 60637, USA.
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
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33
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Jan AH, Dubreucq E, Drone J, Subileau M. A glimpse into the specialization history of the lipases/acyltransferases family of CpLIP2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [DOI: 10.1016/j.bbapap.2017.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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Goulart VDLR, Boubli JP, Young RJ. Medium/Long wavelength sensitive opsin diversity in Pitheciidae. Sci Rep 2017; 7:7737. [PMID: 28798406 PMCID: PMC5552705 DOI: 10.1038/s41598-017-08143-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/05/2017] [Indexed: 11/09/2022] Open
Abstract
New World primates feature a complex colour vision system. Most species have polymorphic colour vision where males have a dichromatic colour perception and females can be either dichromatic or trichromatic. The adaptive value of high allelic diversity of opsins, a light sensitive protein, found in primates' eyes remains unknown. Studies revealing the allelic diversity are important as they shed light on our understanding of the adaptive value of differences in the colouration of species and their ecologies. Here we investigate the allelic types found in Pitheciidae, an understudied New World primate family, revealing the diversity of medium/long wavelength sensitive opsins both in cryptic and conspicuous species of this primate family. We found five alleles in Cacajao, six in Callicebinae (i.e. Plecturocebus, Cheracebus, and Callicebus), four in Chiropotes, and three in Pithecia, some of them reported for the first time. Both cryptic and conspicuous species in this group presented high allelic diversity.
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Affiliation(s)
- Vinicius D L R Goulart
- CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, 70040-020, Brazil.
- School of Environment and Life Sciences, Peel Building, University of Salford Manchester, Salford, M5 4WT, UK.
| | - Jean P Boubli
- School of Environment and Life Sciences, Peel Building, University of Salford Manchester, Salford, M5 4WT, UK
| | - Robert J Young
- School of Environment and Life Sciences, Peel Building, University of Salford Manchester, Salford, M5 4WT, UK
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35
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Melin AD, Khetpal V, Matsushita Y, Zhou K, Campos FA, Welker B, Kawamura S. Howler monkey foraging ecology suggests convergent evolution of routine trichromacy as an adaptation for folivory. Ecol Evol 2017; 7:1421-1434. [PMID: 28261454 PMCID: PMC5330884 DOI: 10.1002/ece3.2716] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/28/2016] [Accepted: 12/18/2016] [Indexed: 02/03/2023] Open
Abstract
Primates possess remarkably variable color vision, and the ecological and social factors shaping this variation remain heavily debated. Here, we test whether central tenants of the folivory hypothesis of routine trichromacy hold for the foraging ecology of howler monkeys. Howler monkeys (genus Alouatta) and paleotropical primates (Parvorder: Catarrhini) have independently acquired routine trichromacy through fixation of distinct mid- to long-wavelength-sensitive (M/LWS) opsin genes on the X-chromosome. The presence of routine trichromacy in howlers, while other diurnal neotropical monkeys (Platyrrhini) possess polymorphic trichromacy, is poorly understood. A selective force proposed to explain the evolution of routine trichromacy in catarrhines-reliance on young, red leaves-has received scant attention in howlers, a gap we fill in this study. We recorded diet, sequenced M/LWS opsin genes in four social groups of Alouatta palliata, and conducted colorimetric analysis of leaves consumed in Sector Santa Rosa, Costa Rica. For a majority of food species, including Ficus trees, an important resource year-round, young leaves were more chromatically conspicuous from mature leaves to trichromatic than to hypothetical dichromatic phenotypes. We found that 18% of opsin genes were MWS/LWS hybrids; when combined with previous research, the incidence of hybrid M/LWS opsins in this species is 13%. In visual models of food discrimination ability, the hybrid trichromatic phenotype performed slightly poorer than normal trichromacy, but substantially better than dichromacy. Our results provide support for the folivory hypothesis of routine trichromacy. Similar ecological pressures, that is, the search for young, reddish leaves, may have driven the independent evolution of routine trichromacy in primates on separate continents. We discuss our results in the context of balancing selection acting on New World monkey opsin genes and hypothesize that howlers experience stronger selection against dichromatic phenotypes than other sympatric species, which rely more heavily on cryptic foods.
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Affiliation(s)
- Amanda D. Melin
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABCanada
- Department of Medical Genetics and Alberta Children’s Hospital Research InstituteUniversity of CalgaryCalgaryABCanada
| | - Vishal Khetpal
- Department of AnthropologyWashington University in St. LouisSt. LouisMOUSA
| | - Yuka Matsushita
- Department of Integrated BiosciencesGraduate School of Frontier SciencesThe University of TokyoTokyoJapan
| | - Kaile Zhou
- Department of Integrated BiosciencesGraduate School of Frontier SciencesThe University of TokyoTokyoJapan
- Department of Plant ProtectionCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouZhejiangChina
| | - Fernando A. Campos
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABCanada
- Department of AnthropologyTulane UniversityNew OrleansLAUSA
| | - Barbara Welker
- Department of AnthropologyState University of New York at GeneseoGeneseoNYUSA
| | - Shoji Kawamura
- Department of Integrated BiosciencesGraduate School of Frontier SciencesThe University of TokyoTokyoJapan
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36
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Holinski A, Heyn K, Merkl R, Sterner R. Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex. Proteins 2017; 85:312-321. [PMID: 27936490 DOI: 10.1002/prot.25225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 01/20/2023]
Abstract
It is important to identify hotspot residues that determine protein-protein interactions in interfaces of macromolecular complexes. We have applied a combination of ancestral sequence reconstruction and protein design to identify hotspots within imidazole glycerol phosphate synthase (ImGPS). ImGPS is a key metabolic enzyme complex, which links histidine and de novo purine biosynthesis and consists of the cyclase subunit HisF and the glutaminase subunit HisH. Initial fluorescence titration experiments showed that HisH from Zymomonas mobilis (zmHisH) binds with high affinity to the reconstructed HisF from the last universal common ancestor (LUCA-HisF) but not to HisF from Pyrobaculum arsenaticum (paHisF), which differ by 103 residues. Subsequent titration experiments with a reconstructed evolutionary intermediate linking LUCA-HisF and paHisF and inspection of the subunit interface of a contemporary ImGPS allowed us to narrow down the differences crucial for zmHisH binding to nine amino acids of HisF. Homology modeling and in silico mutagenesis studies suggested that at most two of these nine HisF residues are crucial for zmHisH binding. These computational results were verified by experimental site-directed mutagenesis, which finally enabled us to pinpoint a single amino acid residue in HisF that is decisive for high-affinity binding of zmHisH. Our work shows that the identification of protein interface hotspots can be very efficient when reconstructed proteins with different binding properties are included in the analysis. Proteins 2017; 85:312-321. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alexandra Holinski
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Kristina Heyn
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
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37
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Kawamura S, Melin AD. Evolution of Genes for Color Vision and the Chemical Senses in Primates. EVOLUTION OF THE HUMAN GENOME I 2017. [DOI: 10.1007/978-4-431-56603-8_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Abstract
The convergence of several disparate research programmes raises the possibility that the long-term evolutionary processes of innovation and radiation may become amenable to laboratory experimentation. Ancestors might be resurrected directly from naturally stored propagules or tissues, or indirectly from the expression of ancestral genes in contemporary genomes. New kinds of organisms might be evolved through artificial selection of major developmental genes. Adaptive radiation can be studied by mimicking major ecological transitions in the laboratory. All of these possibilities are subject to severe quantitative and qualitative limitations. In some cases, however, laboratory experiments may be capable of illuminating the processes responsible for the evolution of new kinds of organisms.
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Affiliation(s)
- Graham Bell
- Biology Department, McGill University, 1205 avenue docteur Penfield, Montreal, Quebec, Canada H3A 1B1
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39
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Kawamura S, Kasagi S, Kasai D, Tezuka A, Shoji A, Takahashi A, Imai H, Kawata M. Spectral sensitivity of guppy visual pigments reconstituted in vitro to resolve association of opsins with cone cell types. Vision Res 2016; 127:67-73. [DOI: 10.1016/j.visres.2016.06.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/21/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
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40
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Kawamura S. Color vision diversity and significance in primates inferred from genetic and field studies. Genes Genomics 2016; 38:779-791. [PMID: 27594978 PMCID: PMC4987397 DOI: 10.1007/s13258-016-0448-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 11/26/2022]
Abstract
Color provides a reliable cue for object detection and identification during various behaviors such as foraging, mate choice, predator avoidance and navigation. The total number of colors that a visual system can discriminate is largely dependent on the number of different spectral types of cone opsins present in the retina and the spectral separations among them. Thus, opsins provide an excellent model system to study evolutionary interconnections at the genetic, phenotypic and behavioral levels. Primates have evolved a unique ability for three-dimensional color vision (trichromacy) from the two-dimensional color vision (dichromacy) present in the majority of other mammals. This was accomplished via allelic differentiation (e.g. most New World monkeys) or gene duplication (e.g. Old World primates) of the middle to long-wavelength sensitive (M/LWS, or red-green) opsin gene. However, questions remain regarding the behavioral adaptations of primate trichromacy. Allelic differentiation of the M/LWS opsins results in extensive color vision variability in New World monkeys, where trichromats and dichromats are found in the same breeding population, enabling us to directly compare visual performances among different color vision phenotypes. Thus, New World monkeys can serve as an excellent model to understand and evaluate the adaptive significance of primate trichromacy in a behavioral context. I shall summarize recent findings on color vision evolution in primates and introduce our genetic and behavioral study of vision-behavior interrelationships in free-ranging sympatric capuchin and spider monkey populations in Costa Rica.
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Affiliation(s)
- Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
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Abstract
To what extent is the convergent evolution of protein function attributable to convergent or parallel changes at the amino acid level? The mutations that contribute to adaptive protein evolution may represent a biased subset of all possible beneficial mutations owing to mutation bias and/or variation in the magnitude of deleterious pleiotropy. A key finding is that the fitness effects of amino acid mutations are often conditional on genetic background. This context dependence (epistasis) can reduce the probability of convergence and parallelism because it reduces the number of possible mutations that are unconditionally acceptable in divergent genetic backgrounds. Here, I review factors that influence the probability of replicated evolution at the molecular level.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
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Melin AD, Wells K, Moritz GL, Kistler L, Orkin JD, Timm RM, Bernard H, Lakim MB, Perry GH, Kawamura S, Dominy NJ. Euarchontan Opsin Variation Brings New Focus to Primate Origins. Mol Biol Evol 2016; 33:1029-41. [PMID: 26739880 PMCID: PMC4776711 DOI: 10.1093/molbev/msv346] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecological pressures. A problem with this approach is that opsin gene variation is incompletely known in the grandorder Euarchonta, that is, the orders Scandentia (treeshrews), Dermoptera (colugos), and Primates. The ancestral state of primate color vision is therefore uncertain. Here, we report on the genes (OPN1SW and OPN1LW) that encode SWS1 and M/LWS opsins in seven species of treeshrew, including the sole nocturnal scandentian Ptilocercus lowii. In addition, we examined the opsin genes of the Central American woolly opossum (Caluromys derbianus), an enduring ecological analogue in the debate on primate origins. Our results indicate: 1) retention of ultraviolet (UV) visual sensitivity in C. derbianus and a shift from UV to blue spectral sensitivities at the base of Euarchonta; 2) ancient pseudogenization of OPN1SW in the ancestors of P. lowii, but a signature of purifying selection in those of C. derbianus; and, 3) the absence of OPN1LW polymorphism among diurnal treeshrews. These findings suggest functional variation in the color vision of nocturnal mammals and a distinctive visual ecology of early primates, perhaps one that demanded greater spatial resolution under light levels that could support cone-mediated color discrimination.
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Affiliation(s)
- Amanda D Melin
- Department of Anthropology, Dartmouth College, Hanover, NH Department of Anthropology and Archaeology, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB
| | - Konstans Wells
- Environmental Futures Research Institute, Griffith University, Brisbane, QLD, Australia
| | - Gillian L Moritz
- Department of Biological Sciences, Class of 1978 Life Sciences Center, Dartmouth College, Hanover, NH Department of Evolutionary Anthropology, Duke University
| | - Logan Kistler
- Departments of Anthropology and Biology, Pennsylvania State University School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Joseph D Orkin
- Department of Anthropology and Archaeology, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB Department of Anthropology, Washington University in St. Louis
| | - Robert M Timm
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence
| | - Henry Bernard
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Maklarin B Lakim
- Sabah Parks, Lot 45 & 46 KK Times Square Coastal Highway, Kota Kinabalu, Sabah, Malaysia
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Nathaniel J Dominy
- Department of Anthropology, Dartmouth College, Hanover, NH Department of Biological Sciences, Class of 1978 Life Sciences Center, Dartmouth College, Hanover, NH
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Sotolongo-Lopez M, Alvarez-Delfin K, Saade CJ, Vera DL, Fadool JM. Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish. PLoS Genet 2016; 12:e1005968. [PMID: 27058886 PMCID: PMC4825938 DOI: 10.1371/journal.pgen.1005968] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/09/2016] [Indexed: 11/30/2022] Open
Abstract
The visual system of a particular species is highly adapted to convey detailed ecological and behavioral information essential for survival. The consequences of structural mutations of opsins upon spectral sensitivity and environmental adaptation have been studied in great detail, but lacking is knowledge of the potential influence of alterations in gene regulatory networks upon the diversity of cone subtypes and the variation in the ratio of rods and cones observed in numerous diurnal and nocturnal species. Exploiting photoreceptor patterning in cone-dominated zebrafish, we uncovered two independent mechanisms by which the sine oculis homeobox homolog 7 (six7) regulates photoreceptor development. In a genetic screen, we isolated the lots-of-rods-junior (ljrp23ahub) mutation that resulted in an increased number and uniform distribution of rods in otherwise normal appearing larvae. Sequence analysis, genome editing using TALENs and knockdown strategies confirm ljrp23ahub as a hypomorphic allele of six7, a teleost orthologue of six3, with known roles in forebrain patterning and expression of opsins. Based on the lack of predicted protein-coding changes and a deletion of a conserved element upstream of the transcription start site, a cis-regulatory mutation is proposed as the basis of the reduced expression of six7 in ljrp23ahub. Comparison of the phenotypes of the hypomorphic and knock-out alleles provides evidence of two independent roles in photoreceptor development. EdU and PH3 labeling show that the increase in rod number is associated with extended mitosis of photoreceptor progenitors, and TUNEL suggests that the lack of green-sensitive cones is the result of cell death of the cone precursor. These data add six7 to the small but growing list of essential genes for specification and patterning of photoreceptors in non-mammalian vertebrates, and highlight alterations in transcriptional regulation as a potential source of photoreceptor variation across species.
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Affiliation(s)
- Mailin Sotolongo-Lopez
- Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
| | - Karen Alvarez-Delfin
- Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
| | - Carole J. Saade
- Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
- Program in Neuroscience, The Florida State University, Tallahassee, Florida, United States of America
| | - Daniel L. Vera
- Center for Genomics and Personalized Medicine, The Florida State University, Tallahassee, Florida, United States of America
| | - James M. Fadool
- Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
- Program in Neuroscience, The Florida State University, Tallahassee, Florida, United States of America
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Yokoyama S, Tada T, Liu Y, Faggionato D, Altun A. A simple method for studying the molecular mechanisms of ultraviolet and violet reception in vertebrates. BMC Evol Biol 2016; 16:64. [PMID: 27001075 PMCID: PMC4802639 DOI: 10.1186/s12862-016-0637-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/16/2016] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Many vertebrate species use ultraviolet (UV) reception for such basic behaviors as foraging and mating, but many others switched to violet reception and improved their visual resolution. The respective phenotypes are regulated by the short wavelength-sensitive (SWS1) pigments that absorb light maximally (λmax) at ~360 and 395-440 nm. Because of strong epistatic interactions, the biological significance of the extensive mutagenesis results on the molecular basis of spectral tuning in SWS1 pigments and the mechanisms of their phenotypic adaptations remains uncertain. RESULTS The magnitudes of the λmax-shifts caused by mutations in a present-day SWS1 pigment and by the corresponding forward mutations in its ancestral pigment are often dramatically different. To resolve these mutagenesis results, the A/B ratio, in which A and B are the areas formed by amino acids at sites 90, 113 and 118 and by those at sites 86, 90 and 118 and 295, respectively, becomes indispensable. Then, all critical mutations that generated the λmax of a SWS1 pigment can be identified by establishing that 1) the difference between the λmax of the ancestral pigment with these mutations and that of the present-day pigment is small (3 ~ 5 nm, depending on the entire λmax-shift) and 2) the difference between the corresponding A/B ratios is < 0.002. CONCLUSION Molecular adaptation has been studied mostly by using comparative sequence analyses. These statistical results provide biological hypotheses and need to be tested using experimental means. This is an opportune time to explore the currently available and new genetic systems and test these statistical hypotheses. Evaluating the λmaxs and A/B ratios of mutagenized present-day and their ancestral pigments, we now have a method to identify all critical mutations that are responsible for phenotypic adaptation of SWS1 pigments. The result also explains spectral tuning of the same pigments, a central unanswered question in phototransduction.
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Affiliation(s)
- Shozo Yokoyama
- Department of Biology, Emory University, Atlanta, GA, 30322, USA.
| | - Takashi Tada
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Yang Liu
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | | | - Ahmet Altun
- Department of Physics, Fatih University, Istanbul, 34500, Turkey.,Department of Genetics and Bioengineering, Fatih University, Istanbul, 34500, Turkey
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45
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The genome of the miiuy croaker reveals well-developed innate immune and sensory systems. Sci Rep 2016; 6:21902. [PMID: 26902509 PMCID: PMC4763219 DOI: 10.1038/srep21902] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/27/2016] [Indexed: 01/08/2023] Open
Abstract
The miiuy croaker, Miichthys miiuy, is a representative Sciaenidae known for its exceptionally large otoliths. This species mainly inhabits turbid aquatic environments with mud to sandy mud bottoms. However, the characteristics of the immune system of this organism and its specific aquatic environment adaptations are poorly understood. Thus, we present a high-quality draft genome of miiuy croaker. The expansions of several gene families which are critical for the fish innate immune system were identified. Compared with the genomes of other fishes, some changes have occurred in the miiuy croaker sensory system including modification of vision and expansion of taste and olfaction receptors. These changes allow miiuy croaker to adapt to the environment during the long-term natural selection. The genome of miiuy croaker may elucidate its relatively well-developed immune defense and provide an adaptation model of the species thriving in turbid deep aquatic environments.
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Natarajan C, Projecto-Garcia J, Moriyama H, Weber RE, Muñoz-Fuentes V, Green AJ, Kopuchian C, Tubaro PL, Alza L, Bulgarella M, Smith MM, Wilson RE, Fago A, McCracken KG, Storz JF. Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level. PLoS Genet 2015; 11:e1005681. [PMID: 26637114 PMCID: PMC4670201 DOI: 10.1371/journal.pgen.1005681] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/27/2015] [Indexed: 11/18/2022] Open
Abstract
A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages), and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization). In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level. The convergent evolution of similar traits in different species could be due to repeated changes at the genetic level or different changes that produce the same phenotypic effect. To investigate the extent to which convergence in phenotype is caused by repeated mutations, we investigated the molecular basis of convergent changes in the oxygenation properties of hemoglobin (Hb) in eight pairs of high- and low-altitude waterfowl taxa from the Andes. The results revealed that convergent increases in Hb-O2 affinity in highland taxa involved a combination of unique and repeated amino acid replacements. However, convergent changes in Hb function generally did not involve parallel substitutions, indicating that repeatability in the evolution of protein function does not require repeatability at the sequence level.
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Affiliation(s)
- Chandrasekhar Natarajan
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Joana Projecto-Garcia
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Roy E. Weber
- Department of Bioscience, Zoophysiology, Aarhus University, Aarhus, Denmark
| | - Violeta Muñoz-Fuentes
- Estación Biológica de Doñana-CSIC, Sevilla, Spain
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | | | - Cecilia Kopuchian
- Centro de Ecología Aplicada del Litoral (CECOAL), Consejo Nacional de Investigaciones Cientificas y Técnicas (CONICET), Corrientes, Argentina
| | - Pablo L. Tubaro
- División Ornitología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
| | - Luis Alza
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Mariana Bulgarella
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Matthew M. Smith
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Robert E. Wilson
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Angela Fago
- Department of Bioscience, Zoophysiology, Aarhus University, Aarhus, Denmark
| | - Kevin G. McCracken
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
- Department of Biology and Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Coral Gables, Florida, United States of America
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
- * E-mail:
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47
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Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties. J Mol Evol 2015; 81:110-20. [PMID: 26349578 DOI: 10.1007/s00239-015-9697-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/03/2015] [Indexed: 12/22/2022]
Abstract
Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported--high thermostability and high catalytic activity--compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered "superior" to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network.
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48
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Bleiweiss R. Extrinsic Versus Intrinsic Control of Avian Communication Based on Colorful Plumage Porphyrins. Evol Biol 2015. [DOI: 10.1007/s11692-015-9343-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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49
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Fisher KJ, Recupero DL, Schrey AW, Draud MJ. Molecular Evidence of Long Wavelength Spectral Sensitivity in the Reverse Sexually Dichromatic Convict Cichlid (Amatitlania nigrofasciata). COPEIA 2015. [DOI: 10.1643/ci-14-088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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50
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Sander SE, Hall DW. Variation in opsin genes correlates with signalling ecology in North American fireflies. Mol Ecol 2015; 24:4679-96. [PMID: 26289828 PMCID: PMC4599352 DOI: 10.1111/mec.13346] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/30/2015] [Accepted: 08/16/2015] [Indexed: 12/27/2022]
Abstract
Genes underlying signal reception should evolve to maximize signal detection in a particular environment. In animals, opsins, the protein component of visual pigments, are predicted to evolve according to this expectation. Fireflies are known for their bioluminescent mating signals. The eyes of nocturnal species are expected to maximize the detection of conspecific signal colours emitted in the typical low-light environment. This is not expected for species that have transitioned to diurnal activity in bright daytime environments. Here, we test the hypothesis that opsin gene sequence plays a role in modifying firefly eye spectral sensitivity. We use genome and transcriptome sequencing in four firefly species, transcriptome sequencing in six additional species and targeted gene sequencing in 28 other species to identify all opsin genes present in North American fireflies and to elucidate amino acid sites under positive selection. We also determine whether amino acid substitutions in opsins are linked to evolutionary changes in signal mode, signal colour and light environment. We find only two opsins, one long wavelength and one ultraviolet, in all firefly species and identify 25 candidate sites that may be involved in determining spectral sensitivity. In addition, we find elevated rates of evolution at transitions to diurnal activity, and changes in selective constraint on long wavelength opsin associated with changes in light environment. Our results suggest that changes in eye spectral sensitivity are at least partially due to opsin sequence. Fireflies continue to be a promising system in which to investigate the evolution of signals, receptors and signalling environments.
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Affiliation(s)
- S E Sander
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - D W Hall
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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