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Torres-Dowdall J, Karagic N, Prabhukumar F, Meyer A. Differential Regulation of Opsin Gene Expression in Response to Internal and External Stimuli. Genome Biol Evol 2024; 16:evae125. [PMID: 38860496 DOI: 10.1093/gbe/evae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 05/24/2024] [Accepted: 06/01/2024] [Indexed: 06/12/2024] Open
Abstract
Determining how internal and external stimuli interact to determine developmental trajectories of traits is a challenge that requires the integration of different subfields of biology. Internal stimuli, such as hormones, control developmental patterns of phenotypic changes, which might be modified by external environmental cues (e.g. plasticity). Thyroid hormone (TH) modulates the timing of opsin gene expression in developing Midas cichlid fish (Amphilophus citrinellus). Moreover, fish reared in red light accelerate this developmental timing compared to fish reared in white light. Hence, we hypothesized that plasticity caused by variation in light conditions has coopted the TH signaling pathway to induce changes in opsin gene expression. We treated Midas cichlids with TH and crossed this treatment with two light conditions, white and red. We observed that not only opsin expression responded similarly to TH and red light but also that, at high TH levels, there is limited capacity for light-induced plasticity. Transcriptomic analysis of the eye showed that genes in the TH pathway were affected by TH, but not by light treatments. Coexpression network analyses further suggested that response to light was independent of the response to TH manipulations. Taken together, our results suggest independent mechanisms mediating development and plasticity during development of opsin gene expression, and that responses to environmental stimuli may vary depending on internal stimuli. This conditional developmental response to external factors depending on internal ones (e.g. hormones) might play a fundamental role in the patterns of phenotypic divergence observed in Midas cichlids and potentially other organisms.
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Affiliation(s)
- 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
| | - Nidal Karagic
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Femina Prabhukumar
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
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2
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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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De-Kayne R, Perry BW, McGowan KL, Landers J, Arias-Rodriguez L, Greenway R, Rodríguez Peña CM, Tobler M, Kelley JL. Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes. Genome Biol Evol 2024; 16:evae087. [PMID: 38788745 PMCID: PMC11126329 DOI: 10.1093/gbe/evae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2024] [Indexed: 05/26/2024] Open
Abstract
Adaptation to extreme environments often involves the evolution of dramatic physiological changes. To better understand how organisms evolve these complex phenotypic changes, the repeatability and predictability of evolution, and possible constraints on adapting to an extreme environment, it is important to understand how adaptive variation has evolved. Poeciliid fishes represent a particularly fruitful study system for investigations of adaptation to extreme environments due to their repeated colonization of toxic hydrogen sulfide-rich springs across multiple species within the clade. Previous investigations have highlighted changes in the physiology and gene expression in specific species that are thought to facilitate adaptation to hydrogen sulfide-rich springs. However, the presence of adaptive nucleotide variation in coding and regulatory regions and the degree to which convergent evolution has shaped the genomic regions underpinning sulfide tolerance across taxa are unknown. By sampling across seven independent lineages in which nonsulfidic lineages have colonized and adapted to sulfide springs, we reveal signatures of shared evolutionary rate shifts across the genome. We found evidence of genes, promoters, and putative enhancer regions associated with both increased and decreased convergent evolutionary rate shifts in hydrogen sulfide-adapted lineages. Our analysis highlights convergent evolutionary rate shifts in sulfidic lineages associated with the modulation of endogenous hydrogen sulfide production and hydrogen sulfide detoxification. We also found that regions with shifted evolutionary rates in sulfide spring fishes more often exhibited convergent shifts in either the coding region or the regulatory sequence of a given gene, rather than both.
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Affiliation(s)
- Rishi De-Kayne
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Kerry L McGowan
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Jake Landers
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, México
| | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Carlos M Rodríguez Peña
- Instituto de Investigaciones Botánicas y Zoológicas, Universidad Autónoma de Santo Domingo, Santo Domingo 10105, Dominican Republic
| | - Michael Tobler
- Department of Biology, University of Missouri–St. Louis, St. Louis, MO 63131, USA
- Whitney R. Harris World Ecology Center, University of Missouri–St. Louis, St. Louis, MO 63121, USA
- WildCare Institute, Saint Louis Zoo, St. Louis, MO 63110, USA
| | - Joanna L Kelley
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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4
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Bertinetti C, Härer A, Karagic N, Meyer A, Torres-Dowdall J. Repeated Divergence in Opsin Gene Expression Mirrors Photic Habitat Changes in Rapidly Evolving Crater Lake Cichlid Fishes. Am Nat 2024; 203:604-617. [PMID: 38635367 DOI: 10.1086/729420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
AbstractSelection pressures differ along environmental gradients, and traits tightly linked to fitness (e.g., the visual system) are expected to track such variation. Along gradients, adaptation to local conditions might be due to heritable and nonheritable environmentally induced variation. Disentangling these sources of phenotypic variation requires studying closely related populations in nature and in the laboratory. The Nicaraguan lakes represent an environmental gradient in photic conditions from clear crater lakes to very turbid great lakes. From two old, turbid great lakes, Midas cichlid fish (Amphilophus cf. citrinellus) independently colonized seven isolated crater lakes of varying light conditions, resulting in a small adaptive radiation. We estimated variation in visual sensitivities along this photic gradient by measuring cone opsin gene expression among lake populations. Visual sensitivities observed in all seven derived crater lake populations shifted predictably in direction and magnitude, repeatedly mirroring changes in photic conditions. Comparing wild-caught and laboratory-reared fish revealed that 48% of this phenotypic variation is genetically determined and evolved rapidly. Decreasing intrapopulation variation as environments become spectrally narrower suggests that different selective landscapes operate along the gradient. We conclude that the power to predict phenotypic evolution along gradients depends on both the magnitude of environmental change and the selective landscape shape.
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5
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D MO, C TZ, R SP. Human orphan cytochromes P450: An update. Curr Drug Metab 2022; 23:CDM-EPUB-128186. [PMID: 36503398 DOI: 10.2174/1389200224666221209153032] [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: 08/05/2022] [Revised: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022]
Abstract
Orphan cytochromes P450 (CYP) are enzymes whose biological functions and substrates are unknown. However, the use of new experimental strategies has allowed obtaining more information about their relevance in the metabolism of endogenous and exogenous compounds. Likewise, the modulation of their expression and activity has been associated with pathogenesis and prognosis in different diseases. In this work, we review the regulatory pathways and the possible role of orphan CYP to provide evidence that allow us to stop considering some of them as orphan enzymes and to propose them as possible therapeutic targets in the design of new strategies for the treatment of diseases associated with CYP-mediated metabolism.
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Affiliation(s)
- Molina-Ortiz D
- Laboratorio de Toxicología Genética, Instituto Nacional de Pediatría, Coyoacán, Mexico City, México, 04530
| | - Torres-Zárate C
- Laboratorio de Toxicología Genética, Instituto Nacional de Pediatría, Coyoacán, Mexico City, México, 04530
| | - Santes-Palacios R
- Laboratorio de Toxicología Genética, Instituto Nacional de Pediatría, Coyoacán, Mexico City, México, 04530
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6
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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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7
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Wilwert E, Etienne RS, van de Zande L, Maan ME. Contribution of opsins and chromophores to cone pigment variation across populations of Lake Victoria cichlids. JOURNAL OF FISH BIOLOGY 2022; 101:365-377. [PMID: 34860424 PMCID: PMC9543281 DOI: 10.1111/jfb.14969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/24/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Adaptation to heterogeneous sensory environments has been implicated as a key parameter in speciation. Cichlid fish are a textbook example of divergent visual adaptation, mediated by variation in the sequences and expression levels of cone opsin genes (encoding the protein component of visual pigments). In some vertebrates including fish, visual sensitivity is also tuned by the ratio of vitamin A1 /A2 -derived chromophores (i.e., the light-sensitive component of the visual pigment bound to the opsin protein), where higher proportions of A2 cause a more red-shifted wavelength absorbance. This study explores the variation in chromophore ratios across multiple cichlid populations in Lake Victoria, using as a proxy the expression of the gene Cyp27c1, which has been shown to regulate the conversion of vitamin A1 into vitamin A2 in several vertebrates. This study focuses on sympatric Pundamilia cichlids, where species with blue or red male coloration co-occur at multiple islands but occupy different depths and consequently different visual habitats. In the red species, we found higher cyp27c1 expression in populations from turbid waters than from clear waters, but there was no such pattern in the blue species. Across populations, differences between the sympatric species in cyp27c1 expression had a consistent relationship with species differences in opsin expression patterns, but the red/blue identity reversed between clear and turbid waters. To assess the contribution of heritable vs. environmental causes of variation, we tested whether light manipulations induce a change in cyp27c1 expression in the laboratory. We found that cyp27c1 expression was not influenced by experimental light conditions, suggesting that the observed variation in the wild is due to genetic differences. Nonetheless, compared to other cichlid species, cyp27c1 is expressed at very low levels in Pundamilia, suggesting that it may not be relevant for visual adaptation in this species. Conclusively, establishing the biological importance of this variation requires testing of actual A1 /A2 ratios in the eye, as well as its consequences for visual performance.
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Affiliation(s)
- Elodie Wilwert
- Groningen Institute for Evolutionary Life Sciences (GELIFES)GroningenThe Netherlands
| | - Rampal S. Etienne
- Groningen Institute for Evolutionary Life Sciences (GELIFES)GroningenThe Netherlands
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences (GELIFES)GroningenThe Netherlands
| | - Martine E. Maan
- Groningen Institute for Evolutionary Life Sciences (GELIFES)GroningenThe Netherlands
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8
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Audino JA, Adams DC, Serb JM. Variation in eye abundance among scallops reveals ontogenetic and evolutionary convergence associated with life habits. Evolution 2022; 76:1607-1618. [PMID: 35709485 DOI: 10.1111/evo.14541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/09/2022] [Accepted: 05/23/2022] [Indexed: 01/22/2023]
Abstract
Eyes are remarkable systems to investigate the complex interaction between ecological drivers and phenotypic outcomes. Some animals, such as scallops, have many eyes for visual perception, but to date, the evolution of multiple-eye systems remains obscure. For instance, it is unclear whether eye number changes over a lifetime or varies among species. Scallops are a suitable model group to investigate these questions considering the interspecific variation of adult size and ecological diversity. We tested whether eye abundance scales with body size among individuals and species and whether it varies with life habits. We performed comparative analyses, including a phylogenetic ANCOVA and evolutionary model comparisons, based on eye count and shell height (as a proxy of body size) across 31 scallop species. Our analyses reveal that patterns of increasing relationship with body size are not concordant among taxa and suggest ontogenetic convergence caused by similar ecologies. Accordingly, selective optima in eye numbers are associated with shifts in life habits. For instance, species with increased mobility have significantly more eyes than less mobile species. The convergent evolution of greater eye abundance in more mobile scallops likely indicates a visual improvement based on increased levels of oversampling of the surrounding environment.
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Affiliation(s)
- Jorge A Audino
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011
| | - Dean C Adams
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011
| | - Jeanne M Serb
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011
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9
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Karagic N, Härer A, Meyer A, Torres-Dowdall J. Thyroid hormone tinkering elicits integrated phenotypic changes potentially explaining rapid adaptation of color vision in cichlid fish. Evolution 2022; 76:837-845. [PMID: 35247267 DOI: 10.1111/evo.14455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 01/05/2022] [Indexed: 01/21/2023]
Abstract
Vision is critical for most vertebrates, including fish. One challenge that aquatic habitats pose is the high variability in spectral properties depending on depth and the inherent optical properties of the water. By altering opsin gene expression and chromophore usage, cichlid fish modulate visual sensitivities to maximize sensory input from the available light in their respective habitat. Thyroid hormone (TH) has been proposed to play a role in governing adaptive diversification in visual sensitivity in Nicaraguan Midas cichlids, which evolved in less than 4000 generations. As suggested by indirect measurements of TH levels (i.e., expression of deiodinases), populations adapted to short wavelength light in clear lakes have lower TH levels than ones inhabiting turbid lakes enriched in long-wavelength light. We experimentally manipulated TH levels by exposing 2-week-old Midas cichlids to exogenous TH or a TH inhibitor and measured opsin gene expression and chromophore usage (via cyp27c1 expression). Although exogenous TH induces long-wavelength sensitivity by changing opsin gene expression and chromophore usage in a concerted manner, TH-inhibited fish exhibit a visual phenotype with sensitivities shifted to shorter wavelengths. Tinkering with TH levels in eyes results in concerted phenotypic changes that can provide a rapid mechanism of adaptation to novel light environments.
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Affiliation(s)
- Nidal Karagic
- Department of Biology, University of Konstanz, Konstanz, 78464, Germany
| | - Andreas Härer
- Department of Biology, University of Konstanz, Konstanz, 78464, Germany.,Division of Biological Sciences, Section of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, 92093
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, 78464, Germany
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10
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Musilova Z, Salzburger W, Cortesi F. The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function. Annu Rev Cell Dev Biol 2021; 37:441-468. [PMID: 34351785 DOI: 10.1146/annurev-cellbio-120219-024915] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Visual opsin genes expressed in the rod and cone photoreceptor cells of the retina are core components of the visual sensory system of vertebrates. Here, we provide an overview of the dynamic evolution of visual opsin genes in the most species-rich group of vertebrates, teleost fishes. The examination of the rich genomic resources now available for this group reveals that fish genomes contain more copies of visual opsin genes than are present in the genomes of amphibians, reptiles, birds, and mammals. The expansion of opsin genes in fishes is due primarily to a combination of ancestral and lineage-specific gene duplications. Following their duplication, the visual opsin genes of fishes repeatedly diversified at the same key spectral-tuning sites, generating arrays of visual pigments sensitive from the ultraviolet to the red spectrum of the light. Species-specific opsin gene repertoires correlate strongly with underwater light habitats, ecology, and color-based sexual selection. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Zuzana Musilova
- Department of Zoology, Charles University, Prague 128 44, Czech Republic;
| | | | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane 4072, Queensland, Australia;
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11
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Sanderson S, Derry AM, Hendry AP. Phenotypic stability in scalar calcium of freshwater fish across a wide range of aqueous calcium availability in nature. Ecol Evol 2021; 11:6053-6065. [PMID: 34141202 PMCID: PMC8207426 DOI: 10.1002/ece3.7386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/02/2022] Open
Abstract
Spatial environmental gradients can promote adaptive differences among conspecific populations as a result of local adaptation or phenotypic plasticity. Such divergence can be opposed by various constraints, including gene flow, limited genetic variation, temporal fluctuations, or developmental constraints. We focus on the constraint that can be imposed when some populations are found in locations characterized by low levels of an essential nutrient. We use scales of wild fish to investigate phenotypic effects of spatial variation in a potentially limiting nutrient-calcium. If scale calcium (we use "scalar" calcium for consistency with the physiology literature) simply reflects environmental calcium availability, we expect higher levels of scalar calcium in fish from calcium-rich water, compared to fish from calcium-poor water. To consider this "passive response" scenario, we analyzed scalar calcium concentrations from three native fish species (Lepomis gibbosus, Percina caprodes, and Perca flavescens) collected at multiple sites across a dissolved calcium gradient in the Upper St. Lawrence River. Contradicting the "passive response" scenario, we did not detect strong or consistent relationships between scalar calcium and water calcium. Instead, for a given proportional increase in water calcium across the wide environmental gradient, the corresponding proportional change in scalar calcium was much smaller. We thus favor the alternative "active homeostasis" scenario, wherein fish from calcium-poor water are better able to uptake, mobilize, and deposit calcium than are fish from calcium-rich water. We further highlight the importance of studying functional traits, such as scales, in their natural setting as opposed to only laboratory studies.
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Affiliation(s)
- Sarah Sanderson
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQCCanada
| | - Alison M. Derry
- Département des Sciences BiologiquesUniversité du Québec à MontréalMontréalQCCanada
| | - Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQCCanada
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12
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Karagic N, Schneider RF, Meyer A, Hulsey CD. A Genomic Cluster Containing Novel and Conserved Genes is Associated with Cichlid Fish Dental Developmental Convergence. Mol Biol Evol 2021; 37:3165-3174. [PMID: 32579214 DOI: 10.1093/molbev/msaa153] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The two toothed jaws of cichlid fishes provide textbook examples of convergent evolution. Tooth phenotypes such as enlarged molar-like teeth used to process hard-shelled mollusks have evolved numerous times independently during cichlid diversification. Although the ecological benefit of molar-like teeth to crush prey is known, it is unclear whether the same molecular mechanisms underlie these convergent traits. To identify genes involved in the evolution and development of enlarged cichlid teeth, we performed RNA-seq on the serially homologous-toothed oral and pharyngeal jaws as well as the fourth toothless gill arch of Astatoreochromis alluaudi. We identified 27 genes that are highly upregulated on both tooth-bearing jaws compared with the toothless gill arch. Most of these genes have never been reported to play a role in tooth formation. Two of these genes (unk, rpfA) are not found in other vertebrate genomes but are present in all cichlid genomes. They also cluster genomically with two other highly expressed tooth genes (odam, scpp5) that exhibit conserved expression during vertebrate odontogenesis. Unk and rpfA were confirmed via in situ hybridization to be expressed in developing teeth of Astatotilapia burtoni. We then examined expression of the cluster's four genes in six evolutionarily independent and phylogenetically disparate cichlid species pairs each with a large- and a small-toothed species. Odam and unk commonly and scpp5 and rpfA always showed higher expression in larger toothed cichlid jaws. Convergent trophic adaptations across cichlid diversity are associated with the repeated developmental deployment of this genomic cluster containing conserved and novel cichlid-specific genes.
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Affiliation(s)
- Nidal Karagic
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
| | - Ralf F Schneider
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
| | - C Darrin Hulsey
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
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13
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Hauser FE, Ilves KL, Schott RK, Alvi E, López-Fernández H, Chang BSW. Evolution, inactivation and loss of short wavelength-sensitive opsin genes during the diversification of Neotropical cichlids. Mol Ecol 2021; 30:1688-1703. [PMID: 33569886 DOI: 10.1111/mec.15838] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/29/2021] [Accepted: 02/03/2021] [Indexed: 12/30/2022]
Abstract
Natural variation in the number, expression and function of sensory genes in an organism's genome is often tightly linked to different ecological and evolutionary forces. Opsin genes, which code for the first step in visual transduction, are ideal models for testing how ecological factors such as light environment may influence visual system adaptation. Neotropical cichlid fishes are a highly ecologically diverse group that evolved in a variety of aquatic habitats, including black (stained), white (opaque) and clear waters. We used cross-species exon capture to sequence Neotropical cichlid short wavelength-sensitive (SWS) opsins, which mediate ultraviolet (UV) to blue visual sensitivity. Neotropical cichlid SWS1 opsin (UV-sensitive) underwent a relaxation of selective constraint during the early phases of cichlid diversification in South America, leading to pseudogenization and loss. Conversely, SWS2a (blue-sensitive) experienced a burst of episodic positive selection at the base of the South American cichlid radiation. This burst coincides with SWS1 relaxation and loss, and is consistent with findings in ecomorphological studies characterizing a period of extensive ecological divergence in Neotropical cichlids. We use ancestral sequence reconstruction and protein modelling to investigate mutations along this ancestral branch that probably modified SWS2a function. Together, our results suggest that variable light environments played a prominent early role in shaping SWS opsin diversity during the Neotropical cichlid radiation. Our results also illustrate that long-term evolution under light-limited conditions in South America may have reduced visual system plasticity; specifically, early losses of UV sensitivity may have constrained the evolutionary trajectory of Neotropical cichlid vision.
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Affiliation(s)
- Frances E Hauser
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Katriina L Ilves
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Erin Alvi
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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14
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Torres-Dowdall J, Karagic N, Härer A, Meyer A. Diversity in visual sensitivity across Neotropical cichlid fishes via differential expression and intraretinal variation of opsin genes. Mol Ecol 2021; 30:1880-1891. [PMID: 33619757 DOI: 10.1111/mec.15855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023]
Abstract
The visual system of vertebrates has greatly contributed to our understanding of how different molecular mechanisms shape adaptive phenotypic diversity. Extensive work on African cichlid fishes has shown how variation in opsin gene expression mediates diversification as well as convergent evolution in colour vision. This trait has received less attention in Neotropical cichlids, the sister lineage to African cichlids, but the work done so far led to the conclusion that colour vision is much less variable in Neotropical species. However, as only few taxa have been investigated and as recent work found contradicting patterns, the diversity in meotropical cichlids might be greatly underestimated. Here, we survey patterns of opsin gene expression in 35 representative species of Neotropical cichlids, revealing much more variation than previously known. This diversity can be attributed to two main mechanisms: (i) differential expression of the blue-sensitive sws2a, the green-sensitive rh2a, and the red-sensitive lws opsin genes, and (ii) simultaneous expression of up to five opsin genes, instead of only three as commonly found, in a striking dorsoventral pattern across the retina. This intraretinal variation in opsin genes expression results in steep gradients in visual sensitivity that may represent a convergent adaptation to clear waters with broad light environments. These results highlight the role and flexibility of gene expression in generating adaptive phenotypic diversification.
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Affiliation(s)
- Julián Torres-Dowdall
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nidal Karagic
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas Härer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
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15
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Corbo JC. Vitamin A 1/A 2 chromophore exchange: Its role in spectral tuning and visual plasticity. Dev Biol 2021; 475:145-155. [PMID: 33684435 DOI: 10.1016/j.ydbio.2021.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/01/2021] [Indexed: 01/20/2023]
Abstract
Vertebrate rod and cone photoreceptors detect light via a specialized organelle called the outer segment. This structure is packed with light-sensitive molecules known as visual pigments that consist of a G-protein-coupled, seven-transmembrane protein known as opsin, and a chromophore prosthetic group, either 11-cis retinal ('A1') or 11-cis 3,4-didehydroretinal ('A2'). The enzyme cyp27c1 converts A1 into A2 in the retinal pigment epithelium. Replacing A1 with A2 in a visual pigment red-shifts its spectral sensitivity and broadens its bandwidth of absorption at the expense of decreased photosensitivity and increased thermal noise. The use of vitamin A2-based visual pigments is strongly associated with the occupation of aquatic habitats in which the ambient light is red-shifted. By modulating the A1/A2 ratio in the retina, an organism can dynamically tune the spectral sensitivity of the visual system to better match the predominant wavelengths of light in its environment. As many as a quarter of all vertebrate species utilize A2, at least during a part of their life cycle or under certain environmental conditions. A2 utilization therefore represents an important and widespread mechanism of sensory plasticity. This review provides an up-to-date account of the A1/A2 chromophore exchange system.
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Affiliation(s)
- Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, United States.
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16
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Kautt AF, Kratochwil CF, Nater A, Machado-Schiaffino G, Olave M, Henning F, Torres-Dowdall J, Härer A, Hulsey CD, Franchini P, Pippel M, Myers EW, Meyer A. Contrasting signatures of genomic divergence during sympatric speciation. Nature 2020; 588:106-111. [PMID: 33116308 PMCID: PMC7759464 DOI: 10.1038/s41586-020-2845-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/23/2020] [Indexed: 01/25/2023]
Abstract
The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin1,2. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process3. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs4, but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories5. Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.
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Affiliation(s)
- Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Alexander Nater
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gonzalo Machado-Schiaffino
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Functional Biology, Area of Genetics, University of Oviedo, Oviedo, Spain
| | - Melisa Olave
- Department of Biology, University of Konstanz, Konstanz, Germany
- Argentine Dryland Research Institute of the National Council for Scientific Research (IADIZA-CONICET), Mendoza, Argentina
| | - Frederico Henning
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Andreas Härer
- Department of Biology, University of Konstanz, Konstanz, Germany
- Division of Biological Sciences, Section of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, CA, USA
| | - C Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
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17
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Chen YC, Kuo HC, Lo WS, Hung CM. Avian phenotypic convergence is subject to low genetic constraints based on genomic evidence. BMC Evol Biol 2020; 20:147. [PMID: 33160317 PMCID: PMC7648321 DOI: 10.1186/s12862-020-01711-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022] Open
Abstract
Background Phenotypic convergence between distinct species provides an opportunity to examine the predictability of genetic evolution. Unrelated species sharing genetic underpinnings for phenotypic convergence suggests strong genetic constraints, and thus high predictability of evolution. However, there is no clear big picture of the genomic constraints on convergent evolution. Genome-based phylogenies have confirmed many cases of phenotypic convergence in birds, making them a good system for examining genetic constraints in phenotypic convergence. In this study, we used hierarchical genomic approaches to estimate genetic constraints in three convergent avian traits: nocturnality, raptorial behavior and foot-propelled diving. Results Phylogeny-based hypothesis tests and positive selection tests were applied to compare 16 avian genomes, representing 14 orders, and identify genes with strong convergence signals. We found 43 adaptively convergent genes (ACGs) associated with the three phenotypic convergence cases and assessed genetic constraints in all three cases, from (amino acid) site mutations to genetic pathways. We found that the avian orders shared few site mutations in the ACGs that contributed to the convergent phenotypes, and that these ACGs were not enriched in any genetic pathways. In addition, different pairs of orders with convergent foot-propelled diving or raptorial behaviors shared few ACGs. We also found that closely related orders that shared foot-propelled diving behavior did not share more ACGs than did distinct orders, suggesting that convergence among these orders could not be explained by their initial genomic backgrounds. Conclusions Our analyses of three avian convergence events suggest low constraints for phenotypic convergence across multiple genetic levels, implying that genetic evolution is unpredictable at the phylogenetic level of avian order. Ours is one of first studies to apply hierarchical genomic examination to multiple avian convergent cases to assess the genetic constraints in life history trait evolution.
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Affiliation(s)
- Yu-Chi Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Sui Lo
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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18
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Härer A, Torres-Dowdall J, Rometsch SJ, Yohannes E, Machado-Schiaffino G, Meyer A. Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish. MICROBIOME 2020; 8:149. [PMID: 33121541 PMCID: PMC7597055 DOI: 10.1186/s40168-020-00897-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Recent increases in understanding the ecological and evolutionary roles of microbial communities have underscored the importance of their hosts' biology. Yet, little is known about gut microbiota dynamics during the early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of Nicaraguan Midas cichlid fish (Amphilophus cf. citrinellus). Specifically, we tested the hypothesis that parallel divergence in trophic ecology in extremely young adaptive radiations from two crater lakes is associated with parallel changes of their gut microbiota. RESULTS Bacterial communities of fish guts and lake water were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Among individuals of the same crater lake, differentiation in trophic ecology was weakly associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across the two crater lakes, we could not detect conclusive evidence for parallel changes of the gut microbiota associated with trophic ecology. CONCLUSIONS A lack of clearly differentiated niches during the early stages of ecological diversification might result in non-parallel changes of gut microbial communities, as observed in our study system as well as in other recently diverged fish species. Video Abstract.
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Affiliation(s)
- Andreas Härer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
- Current address: Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, California USA
| | - Julián Torres-Dowdall
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Sina J. Rometsch
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Elizabeth Yohannes
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Gonzalo Machado-Schiaffino
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
- Current address: Department of Functional Biology, University of Oviedo, Oviedo, Spain
| | - Axel Meyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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19
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Carleton KL, Yourick MR. Axes of visual adaptation in the ecologically diverse family Cichlidae. Semin Cell Dev Biol 2020; 106:43-52. [PMID: 32439270 DOI: 10.1016/j.semcdb.2020.04.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023]
Abstract
The family Cichlidae contains approximately 2000 species that live in diverse freshwater habitats including murky lakes, turbid rivers, and clear lakes from both the Old and New Worlds. Their visual systems are similarly diverse and have evolved specific sensitivities that differ along several axes of variation. Variation in cornea and lens transmission affect which wavelengths reach the retina. Variation in photoreceptor number and distribution affect brightness sensitivity, spectral sensitivity and resolution. Probably their most dynamic characteristic is the variation in visual pigment peak sensitivities. Visual pigments can be altered through changes in chromophore, opsin sequence and opsin expression. Opsin expression varies by altering which of the seven available cone opsins in their genomes are turned on. These opsins can even be coexpressed to produce seemingly infinitely tunable cone sensitivities. Both chromophore and opsin expression can vary on either rapid (hours or days), slower (seasonal or ontogenetic) or evolutionary timescales. Such visual system shifts have enabled cichlids to adapt to different habitats and foraging styles. Through both short term plasticity and longer evolutionary adaptations, cichlids have proven to be ecologically successful and an excellent model for studying organismal adaptation.
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Affiliation(s)
- Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, 20742, USA.
| | - Miranda R Yourick
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
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20
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Carleton KL, Escobar-Camacho D, Stieb SM, Cortesi F, Marshall NJ. Seeing the rainbow: mechanisms underlying spectral sensitivity in teleost fishes. J Exp Biol 2020; 223:jeb193334. [PMID: 32327561 PMCID: PMC7188444 DOI: 10.1242/jeb.193334] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Among vertebrates, teleost eye diversity exceeds that found in all other groups. Their spectral sensitivities range from ultraviolet to red, and the number of visual pigments varies from 1 to over 40. This variation is correlated with the different ecologies and life histories of fish species, including their variable aquatic habitats: murky lakes, clear oceans, deep seas and turbulent rivers. These ecotopes often change with the season, but fish may also migrate between ecotopes diurnally, seasonally or ontogenetically. To survive in these variable light habitats, fish visual systems have evolved a suite of mechanisms that modulate spectral sensitivities on a range of timescales. These mechanisms include: (1) optical media that filter light, (2) variations in photoreceptor type and size to vary absorbance and sensitivity, and (3) changes in photoreceptor visual pigments to optimize peak sensitivity. The visual pigment changes can result from changes in chromophore or changes to the opsin. Opsin variation results from changes in opsin sequence, opsin expression or co-expression, and opsin gene duplications and losses. Here, we review visual diversity in a number of teleost groups where the structural and molecular mechanisms underlying their spectral sensitivities have been relatively well determined. Although we document considerable variability, this alone does not imply functional difference per se. We therefore highlight the need for more studies that examine species with known sensitivity differences, emphasizing behavioral experiments to test whether such differences actually matter in the execution of visual tasks that are relevant to the fish.
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Affiliation(s)
- Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | | | - Sara M Stieb
- Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Queensland Brain Institute, University of Queensland, Brisbane 4072 QLD, Australia
| | - Fabio Cortesi
- Queensland Brain Institute, University of Queensland, Brisbane 4072 QLD, Australia
| | - N Justin Marshall
- Queensland Brain Institute, University of Queensland, Brisbane 4072 QLD, Australia
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21
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From molecules to macroevolution: Venom as a model system for evolutionary biology across levels of life. Toxicon X 2020; 6:100034. [PMID: 32550589 PMCID: PMC7285901 DOI: 10.1016/j.toxcx.2020.100034] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 11/21/2022] Open
Abstract
Biological systems are inherently hierarchical. Consequently, any field which aims to understand an aspect of biology holistically requires investigations at each level of the hierarchy of life, and venom research is no exception. This article aims to illustrate the structure of the field in light of a ‘levels of life’ perspective. In doing so, I highlight how traditional fields and approaches fit into this structure as focussing on describing levels or investigating links between levels, and emphasise where implicit assumptions are made due to lack of direct information. Taking a ‘levels of life’ perspective to venom research enables us to understand the complementarity of different research programmes and identify avenues for future research. Moreover, it provides a broader view that, in itself, shows how new questions can be addressed. For instance, understanding how adaptations develop and function from molecular to organismal scales, and what the consequences are of those adaptations at scales from molecular to macroevolutionary, is a general question relevant to a great deal of biology. As a trait which is molecular in nature and has clearer and more direct links between genotype and phenotype than many other traits, venom provides a relatively simple system to address such questions. Furthermore, because venom is also diverse at each level of life, the complexity within the hierarchical structure provides variation that enables powerful analytical approaches to answering questions. As a result, venom provides an excellent model system for understanding big questions in evolutionary biology. Venom is a molecular trait used directly in fitness-relevant ecological interaction. Venom is consequently an ideal model system for evolutionary biology. A ‘levels of life’ perspective is well suited to research in venom biology. This structure of the field provides many advantages to guide future studies. Clinical implications can arise from studies of venom at all levels of life.
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22
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Schneider RF, Rometsch SJ, Torres-Dowdall J, Meyer A. Habitat light sets the boundaries for the rapid evolution of cichlid fish vision, while sexual selection can tune it within those limits. Mol Ecol 2020; 29:1476-1493. [PMID: 32215986 DOI: 10.1111/mec.15416] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/07/2020] [Accepted: 03/16/2020] [Indexed: 12/30/2022]
Abstract
Cichlid fishes' famous diversity in body coloration is accompanied by a highly diverse and complex visual system. Although cichlids possess an unusually high number of seven cone opsin genes, they express only a subset of these during their ontogeny, accounting for their astonishing interspecific variation in visual sensitivities. Much of this diversity is thought to have been shaped by natural selection as cichlids inhabit a variety of habitats with distinct light environments. Also, sexual selection might have contributed to the observed visual diversity, and sexual dimorphism in coloration potentially co-evolved with sexual dimorphism in opsin expression. We investigated sex-specific opsin expression of several cichlids from Africa and the Neotropics and collected and integrated data sets on sex-specific body coloration, species-specific visual sensitivities, lens transmission and habitat light properties for some of them. We comparatively analysed this wide range of molecular and ecological data, illustrating how integrative approaches can address specific questions on the factors and mechanisms driving diversification, and the evolution of cichlid vision in particular. We found that both sexes expressed opsins at the same levels-even in sexually dimorphic cichlid species-which argues against coevolution of sexual dichromatism and differences in sex-specific visual sensitivity. Rather, a combination of environmental light properties and body coloration shaped the diversity in spectral sensitivities among cichlids. We conclude that although cichlids are particularly colourful and diverse and often sexually dimorphic, it would appear that natural rather than sexual selection is a more powerful force driving visual diversity in this hyperdiverse lineage.
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Affiliation(s)
- Ralph F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Marine Ecology, GEOMAR, Kiel, Germany
| | - Sina J Rometsch
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Julián Torres-Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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23
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Losilla M, Luecke DM, Gallant JR. The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish. BMC Evol Biol 2020; 20:6. [PMID: 31918666 PMCID: PMC6953315 DOI: 10.1186/s12862-019-1572-3] [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: 05/07/2019] [Accepted: 12/24/2019] [Indexed: 01/10/2023] Open
Abstract
Background Understanding the genomic basis of phenotypic diversity can be greatly facilitated by examining adaptive radiations with hypervariable traits. In this study, we focus on a rapidly diverged species group of mormyrid electric fish in the genus Paramormyrops, which are characterized by extensive phenotypic variation in electric organ discharges (EODs). The main components of EOD diversity are waveform duration, complexity and polarity. Using an RNA-sequencing based approach, we sought to identify gene expression correlates for each of these EOD waveform features by comparing 11 specimens of Paramormyrops that exhibit variation in these features. Results Patterns of gene expression among Paramormyrops are highly correlated, and 3274 genes (16%) were differentially expressed. Using our most restrictive criteria, we detected 145–183 differentially expressed genes correlated with each EOD feature, with little overlap between them. The predicted functions of several of these genes are related to extracellular matrix, cation homeostasis, lipid metabolism, and cytoskeletal and sarcomeric proteins. These genes are of significant interest given the known morphological differences between electric organs that underlie differences in the EOD waveform features studied. Conclusions In this study, we identified plausible candidate genes that may contribute to phenotypic differences in EOD waveforms among a rapidly diverged group of mormyrid electric fish. These genes may be important targets of selection in the evolution of species-specific differences in mate-recognition signals.
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Affiliation(s)
- Mauricio Losilla
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.,Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - David Michael Luecke
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.,Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Jason R Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA. .,Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA.
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24
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Härer A, Karagic N, Meyer A, Torres-Dowdall J. Reverting ontogeny: rapid phenotypic plasticity of colour vision in cichlid fish. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190841. [PMID: 31417763 PMCID: PMC6689635 DOI: 10.1098/rsos.190841] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Phenotypic plasticity, particularly during development, allows organisms to rapidly adjust to different environmental conditions. Yet, it is often unclear whether the extent and direction of plastic changes are restricted by an individual's ontogeny. Many species of cichlid fishes go through ontogenetic changes in visual sensitivity, from short to long wavelengths, by switching expression of cone opsin genes crucial for colour vision. During this progression, individuals often exhibit phenotypic plasticity to the ambient light conditions. However, it is commonly assumed that once an adult visual phenotype is reached, reverting to an earlier ontogenetic state with higher sensitivity at shorter wavelengths is not common. In this study, we experimentally demonstrate that four-month-old Midas cichlid fish (Amphilophus astorquii) show plasticity in single cone opsin expression after experiencing drastic changes in light conditions. Resulting shifts of visual sensitivity occurred presumably in an adaptive direction-towards shorter or longer wavelengths when exposed to short- or long-wavelength light, respectively. Single cone opsin expression changed within only a few days and went through a transitional phase of co-expression. When the environment was experimentally enriched in long-wavelength light, the corresponding change occurred gradually along a dorsoventral gradient within the retina. This plasticity allowed individuals to revert earlier ontogenetic changes and return to a more juvenile visual phenotype demonstrating previously unrecognized insights into temporal and spatial dynamics of phenotypic plasticity of the visual system in response to ambient light.
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Affiliation(s)
- Andreas Härer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nidal Karagic
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Julián Torres-Dowdall
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
- Zukunftskolleg, University of Konstanz, Konstanz, Germany
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25
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Li G, Ni A, Yu M. Pretumor microenvironment of hepatocellular carcinoma: Cancerization or anticancerization? Gene 2019; 701:46-54. [PMID: 30902783 DOI: 10.1016/j.gene.2019.03.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/11/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Tumor microenvironment (TM) has been deeply concerned. However, the pretumor microenvironment (PTM) was poorly understood. The purpose in this study was to explore the possible pathophysiological features of PTM before hepatocellular carcinoma (HCC) appearance. METHODS Mouse livers with no swelling but with tumors present elsewhere in the body after subcutaneous injection of H22 in the fore underarm were considered a PTM, HCC tumors presenting far away from the PTM were regarded as a TM, and the healthy livers of mice without injection of H22 were regarded as a physiological microenvironment (PM). The transcriptomes of samples were generated using RNA-seq and validated using RT-qPCR. RESULTS Overall, 4483 differentially expressed genes (DEGs) were found in the TM compared with the PTM (TM/PTM), but only 194 were altered in the PTM compared with the PM (PTM/PM). Among those 194 DEGs, 104 displayed upregulation and 90 downregulation. Some of these DEGs could promote the ability to resist cancerization or facilitate cancer metastasis, while others indicated liver impairment. The DEGs were involved in 16 relevant pathways. Additionally, the frequency of alternative splicing (AS) in the DEGs in various samples was positively related to the expression of those DEGs. CONCLUSIONS The PTM initiatively armed itself to combat cancerization when its indications appeared although the PTM did not manifest any tissue swelling. However, the cancer cells were negatively influencing immunity to prevent clearance and positively promoting transformation to construct a suitable environment. During transformation by cancer cells, some genes with acquired AS participated in the construction of the PTM. This alteration created an invadable space and an appropriate environment for cancer cells.
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Affiliation(s)
- Genliang Li
- Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China.
| | - Anni Ni
- Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Mengyao Yu
- Donghai county hospital, Lianyungang 222000, Jiangsu, China
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