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Vu T, Ebeling H, Di Santo V, Kenaley CP. Sexually dimorphic eye size in dragonfishes, a response to a bioluminescent signalling gap. Biol Lett 2024; 20:20240165. [PMID: 39046285 PMCID: PMC11268158 DOI: 10.1098/rsbl.2024.0165] [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: 03/28/2024] [Revised: 05/21/2024] [Accepted: 06/05/2024] [Indexed: 07/25/2024] Open
Abstract
Deep-sea fishes must overcome extremely large nearest-neighbour distances and darkness to find mates. Sexual dimorphism in the size of luminescent structures in many deep-sea taxa, including dragonfishes (family Stomiidae), indicates reproductive behaviours may be mediated by visual signalling. This presents a paradox: if male photophores are larger, females may find males at shorter distances than males find females. Solutions to this gap may include females closing this gap or by males gathering more photons with a larger eye. We examine the eye size of two species of dragonfishes (Malacosteus niger and Phostomias guernei) for sexual dimorphism and employ a model of detection distance to evaluate the potential for such dimorphism to bridge the detection gap. This model incorporates the flux of sexually dimorphic postorbital photophores and eye lens size to predict detection distances. In both species, we found a significant visual detection gap in which females find males before males find females and that male lens size is larger, marking the second known case of size dimorphism in the actinopterygian visual system. Our results indicate the larger eye affords males a significant improvement in detection distance. We conclude that this dimorphic phenotype may have evolved to close the detection gap.
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Affiliation(s)
- Thao Vu
- Department of Biology, Boston College, Chestnut Hill, MA02465, USA
| | - Helena Ebeling
- Department of Biology, Boston College, Chestnut Hill, MA02465, USA
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Brownstein CD, Near TJ. Colonization of the ocean floor by jawless vertebrates across three mass extinctions. BMC Ecol Evol 2024; 24:79. [PMID: 38867201 PMCID: PMC11170801 DOI: 10.1186/s12862-024-02253-y] [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: 01/16/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The deep (> 200 m) ocean floor is often considered to be a refugium of biodiversity; many benthic marine animals appear to share ancient common ancestry with nearshore and terrestrial relatives. Whether this pattern holds for vertebrates is obscured by a poor understanding of the evolutionary history of the oldest marine vertebrate clades. Hagfishes are jawless vertebrates that are either the living sister to all vertebrates or form a clade with lampreys, the only other surviving jawless fishes. RESULTS We use the hagfish fossil record and molecular data for all recognized genera to construct a novel hypothesis for hagfish relationships and diversification. We find that crown hagfishes persisted through three mass extinctions after appearing in the Permian ~ 275 Ma, making them one of the oldest living vertebrate lineages. In contrast to most other deep marine vertebrates, we consistently infer a deep origin of continental slope occupation by hagfishes that dates to the Paleozoic. Yet, we show that hagfishes have experienced marked body size diversification over the last hundred million years, contrasting with a view of this clade as morphologically stagnant. CONCLUSION Our results establish hagfishes as ancient members of demersal continental slope faunas and suggest a prolonged accumulation of deep sea jawless vertebrate biodiversity.
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Affiliation(s)
- Chase Doran Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA.
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
- Yale Peabody Museum, Yale University, New Haven, CT, 06511, USA
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3
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Sharma N, Shekhar P, Kumar V, Kaur H, Jayasena V. Microbial pigments: Sources, current status, future challenges in cosmetics and therapeutic applications. J Basic Microbiol 2024; 64:4-21. [PMID: 37861279 DOI: 10.1002/jobm.202300214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/19/2023] [Accepted: 09/23/2023] [Indexed: 10/21/2023]
Abstract
Color serves as the initial attraction and offers a pleasing aspect. While synthetic colorants have been popular for many years, their adverse environmental and health effects cannot be overlooked. This necessitates the search for natural colorants, especially microbial colorants, which have proven and more effective. Pigment-producing microorganisms offer substantial benefits. Natural colors improve product marketability and bestow additional benefits, including antioxidant, antiaging, anticancer, antiviral, antimicrobial, and antitumor properties. This review covers the various types of microbial pigments, the methods to enhance their production, and their cosmetic and therapeutic applications. We also address the challenges faced during the commercial production of microbial pigments and propose potential solutions.
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Affiliation(s)
- Nitin Sharma
- Chandigarh Group of Colleges, Landran, Mohali, Punjab, India
| | | | - Vikas Kumar
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Harpreet Kaur
- Chandigarh Group of Colleges, Landran, Mohali, Punjab, India
| | - Vijay Jayasena
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
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Schnell NK, Kriwet J, López‐Romero FA, Lecointre G, Pfaff C. Musculotendinous system of mesopelagic fishes: Stomiiformes (Teleostei). J Anat 2022; 240:1095-1126. [PMID: 34927245 PMCID: PMC9119618 DOI: 10.1111/joa.13614] [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: 05/19/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022] Open
Abstract
Every night the greatest migration on Earth starts in the deep pelagic oceans where organisms move up to the meso- and epipelagic to find food and return to the deeper zones during the day. One of the dominant fish taxa undertaking vertical migrations are the dragonfishes (Stomiiformes). However, the functional aspects of locomotion and the architecture of the musculotendinous system (MTS) in these fishes have never been examined. In general, the MTS is organized in segmented blocks of specific three-dimensional 'W-shaped' foldings, the myomeres, separated by thin sheets of connective tissue, the myosepta. Within a myoseptum characteristic intermuscular bones or tendons may be developed. Together with the fins, the MTS forms the functional unit for locomotion in fishes. For this study, microdissections of cleared and double stained specimens of seven stomiiform species (Astronesthes sp., Chauliodus sloani, Malacosteus australis, Eustomias simplex, Polymetme sp., Sigmops elongatus, Argyropelecus affinis) were conducted to investigate their MTS. Soft tissue was investigated non-invasively in E. schmidti using a micro-CT scan of one specimen stained with iodine. Additionally, classical histological serial sections were consulted. The investigated stomiiforms are characterized by the absence of anterior cones in the anteriormost myosepta. These cones are developed in myosepta at the level of the dorsal fin and elongate gradually in more posterior myosepta. In all but one investigated stomiiform taxon the horizontal septum is reduced. The amount of connective tissue in the myosepta is very low anteriorly, but increases gradually with body length. Red musculature overlies laterally the white musculature and exhibits strong tendons in each myomere within the muscle bundles dorsal and ventral to the horizontal midline. The amount of red musculature increases immensely towards the caudal fin. The elongated lateral tendons of the posterior body segments attach in a highly complex pattern on the caudal-fin rays, which indicates that the posterior most myosepta are equipped for a multisegmental force transmission towards the caudal fin. This unique anatomical condition might be essential for steady swimming during diel vertical migrations, when prey is rarely available.
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Affiliation(s)
- Nalani K. Schnell
- Institut Systématique, Evolution, Biodiversité (ISYEB)Muséum National d'Histoire NaturelleCNRSSUEPHEUAConcarneauFrance
| | - Jürgen Kriwet
- Department of PalaeontologyUniversity of ViennaViennaAustria
| | | | - Guillaume Lecointre
- Institut Systématique, Evolution, Biodiversité (ISYEB)Muséum national d'Histoire naturelleCNRSSUEPHEUAParisFrance
| | - Cathrin Pfaff
- Department of PalaeontologyUniversity of ViennaViennaAustria
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Lupše N, Cortesi F, Freese M, Marohn L, Pohlman JD, Wysujack K, Hanel R, Musilova Z. Visual gene expression reveals a cone to rod developmental progression in deep-sea fishes. Mol Biol Evol 2021; 38:5664-5677. [PMID: 34562090 PMCID: PMC8662630 DOI: 10.1093/molbev/msab281] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Vertebrates use cone cells in the retina for colour vision and rod cells to see in dim light. Many deep-sea fishes have adapted to their environment to have only rod cells in the retina, while both rod and cone genes are still preserved in their genomes. As deep-sea fish larvae start their lives in the shallow, and only later submerge to the depth, they have to cope with diverse environmental conditions during ontogeny. Using a comparative transcriptomic approach in 20 deep-sea fish species from eight teleost orders, we report on a developmental cone-to-rod switch. While adults mostly rely on rod opsin (RH1) for vision in dim light, larvae almost exclusively express middle-wavelength-sensitive ("green") cone opsins (RH2) in their retinas. The phototransduction cascade genes follow a similar ontogenetic pattern of cone- followed by rod-specific gene expression in most species, except for the pearleye and sabretooth (Aulopiformes), in which the cone cascade remains dominant throughout development. By inspecting the whole genomes of five deep-sea species (four of them sequenced within this study: Idiacanthus fasciola, Chauliodus sloani; Stomiiformes; Coccorella atlantica, and Scopelarchus michaelsarsi; Aulopiformes), we found that deep-sea fish possess one or two copies of the rod RH1 opsin gene, and up to seven copies of the cone RH2 opsin genes in their genomes, while other cone opsin classes have been mostly lost. Our findings hence provide molecular evidence for a limited opsin gene repertoire and a conserved vertebrate pattern whereby cone photoreceptors develop first and rod photoreceptors are added only at later developmental stages.
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Affiliation(s)
- Nik Lupše
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 12844 Prague, Czech Republic
| | - Fabio Cortesi
- Queensland Brain Institute, University of Queensland, Brisbane 4072 QLD, Australia
| | - Marko Freese
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Lasse Marohn
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Jan-Dag Pohlman
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Klaus Wysujack
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Reinhold Hanel
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 12844 Prague, Czech Republic
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Zheng S, Shao F, Tao W, Liu Z, Long J, Wang X, Zhang S, Zhao Q, Carleton KL, Kocher TD, Jin L, Wang Z, Peng Z, Wang D, Zhang Y. Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles. Mol Ecol Resour 2021; 21:1575-1592. [PMID: 33503304 DOI: 10.1111/1755-0998.13338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 01/07/2023]
Abstract
The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.
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Affiliation(s)
- Shuqing Zheng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zhilong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Juan Long
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Xiaoshuang Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Shuai Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Li Jin
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Yaoguang Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
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7
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Lemopoulos A, Montoya-Burgos JI. From scales to armor: Scale losses and trunk bony plate gains in ray-finned fishes. Evol Lett 2021; 5:240-250. [PMID: 34136272 PMCID: PMC8190451 DOI: 10.1002/evl3.219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/04/2021] [Indexed: 11/25/2022] Open
Abstract
Actinopterygians (ray‐finned fishes) are the most diversified group of vertebrates and are characterized by a variety of protective structures covering their integument, the evolution of which has intrigued biologists for decades. Paleontological records showed that the first mineralized vertebrate skeleton was composed of dermal bony plates covering the body, including odontogenic and skeletogenic components. Later in evolution, the exoskeleton of actinopterygian's trunk was composed of scale structures. Although scales are nowadays a widespread integument cover, some contemporary lineages do not have scales but bony plates covering their trunk, whereas other lineages are devoid of any such structures. To understand the evolution of the integument coverage and particularly the transition between different structures, we investigated the pattern of scale loss events along with actinopterygian evolution and addressed the functional relationship between the scaleless phenotype and the ecology of fishes. Furthermore, we examined whether the emergence of trunk bony plates was dependent over the presence or absence of scales. To this aim, we used two recently published actinopterygian phylogenies, one including >11,600 species, and by using stochastic mapping and Bayesian methods, we inferred scale loss events and trunk bony plate acquisitions. Our results reveal that a scaled integument is the most frequent state in actinopterygians, but multiple independent scale loss events occurred along their phylogeny with essentially no scale re‐acquisition. Based on linear mixed models, we found evidence supporting that after a scale loss event, fishes tend to change their ecology and adopt a benthic lifestyle. Furthermore, we show that trunk bony plates appeared independently multiple times along the phylogeny. By using fitted likelihood models for character evolution, we show that trunk bony plate acquisitions were dependent on a previous scale loss event. Overall, our findings support the hypothesis that integument cover is a key evolutionary trait underlying actinopterygian radiation.
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Affiliation(s)
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution University of Geneva Geneva Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva Geneva Switzerland
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Chatragadda R, Dufossé L. Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments. Microorganisms 2021; 9:637. [PMID: 33803896 PMCID: PMC8003166 DOI: 10.3390/microorganisms9030637] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/04/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022] Open
Abstract
Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.
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Affiliation(s)
- Ramesh Chatragadda
- Biological Oceanography Division (BOD), Council of Scientific and Industrial Research-National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, Goa, India
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products (CHEMBIOPRO Lab), Ecole Supérieure d’Ingénieurs Réunion Océan Indien (ESIROI), Département Agroalimentaire, Université de La Réunion, F-97744 Saint-Denis, France
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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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10
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Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser JC, Wilson JY, Alm Rosenblad M, Burguera D, Gutnik S, Michiels N, Töpel M, Pankov K, Schloissnig S, Winkler S. The round goby genome provides insights into mechanisms that may facilitate biological invasions. BMC Biol 2020; 18:11. [PMID: 31992286 PMCID: PMC6988351 DOI: 10.1186/s12915-019-0731-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Background The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. Results We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby’s capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. Conclusions The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish. Electronic supplementary material The online version of this article (10.1186/s12915-019-0731-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland. .,University of Bern, Institute for Fish and Wildlife Health, Länggassstrasse 122, 3012, Bern, Austria.
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Tomas Larsson
- Department of Marine Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Zuzana Musilova
- Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Claire R Peart
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152 Planegg-, Martinsried, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Monica Hongroe Solbakken
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371, Oslo, Norway
| | - Jaanus Suurväli
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674, Köln, Germany
| | - Jean-Claude Walser
- Genetic Diversity Centre, ETH, Universitätsstrasse 16, 8092, Zurich, Switzerland
| | - Joanna Yvonne Wilson
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Magnus Alm Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden.,NBIS Bioinformatics Infrastructure for Life Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Demian Burguera
- Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Silvia Gutnik
- Biocenter, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Nico Michiels
- Institute of Evolution and Ecology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Mats Töpel
- University of Bern, Institute for Fish and Wildlife Health, Länggassstrasse 122, 3012, Bern, Austria
| | - Kirill Pankov
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Siegfried Schloissnig
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
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11
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Kenaley CP, Marecki MC, Lauder GV. The role of an overlooked adductor muscle in the feeding mechanism of ray-finned fishes: Predictions from simulations of a deep-sea viperfish. ZOOLOGY 2019; 135:125678. [PMID: 31383297 DOI: 10.1016/j.zool.2019.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/13/2019] [Accepted: 02/25/2019] [Indexed: 10/27/2022]
Abstract
In a majority of ray-finned fishes (Actinopterygii), effective acquisition of food resources is predicated on rapid jaw adduction. Although the musculoskeletal architecture of the feeding system has been the subject of comparative research for many decades, individual contributions of the major adductor divisions to closing dynamics have not been elucidated. While it is understood that the dorsal divisions that arise from the head and insert on the posterior of the lower jaw are major contributors to closing dynamics, the contribution of the ventral components of the adductor system has been largely overlooked. In many ray-finned fishes, the ventral component is comprised of a single division, the Aω, that originates on an intersegmental aponeurosis of the facialis divisions and inserts on the medial face of the dentary, anterior to the Meckelian tendon. This configuration resembles a sling applied at two offset points of attachment on a third-order lever. The goal of this study was to elucidate the contributions of the Aω to jaw adduction by modeling jaw closing in the deep-sea viperfish Chauliodus sloani. To do this, we simulated adduction with a revised computational model that incorporates the geometry of the Aω. By comparing results between simulations that included and excluded Aω input, we show that the Aω adds substantially to lower-jaw adduction dynamics in C. sloani by acting as a steering motor and displacing the line of action of the dorsal facialis adductor muscles and increasing the mechanical advantage and input moment arms of the jaw lever system. We also explored the effect of the Aω on muscle dynamics and found that overall facialis muscle shortening velocities are higher and normalized force production is lower in simulations including the Aω. The net effect of these changes in muscle dynamics results in similar magnitudes of peak power in the facialis divisions between simulations, however, peak power is achieved earlier in adduction Modifications of muscle mechanics and posture result in significant increases in closing performance, including static bite force, angular velocity, and adduction time. We compare this configuration to a similar design in crocodilians and suggest that the Aω configuration and similar sling configurations across the vertebrate tree of life indicate the importance of this musculoskeletal design in feeding.
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Affiliation(s)
- Christopher P Kenaley
- Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
| | - Mikhaila C Marecki
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - George V Lauder
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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12
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Visual modelling supports the potential for prey detection by means of diurnal active photolocation in a small cryptobenthic fish. Sci Rep 2019; 9:8089. [PMID: 31147614 PMCID: PMC6542814 DOI: 10.1038/s41598-019-44529-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 05/17/2019] [Indexed: 11/16/2022] Open
Abstract
Active sensing has been well documented in animals that use echolocation and electrolocation. Active photolocation, or active sensing using light, has received much less attention, and only in bioluminescent nocturnal species. However, evidence has suggested the diurnal triplefin Tripterygion delaisi uses controlled iris radiance, termed ocular sparks, for prey detection. While this form of diurnal active photolocation was behaviourally described, a study exploring the physical process would provide compelling support for this mechanism. In this paper, we investigate the conditions under which diurnal active photolocation could assist T. delaisi in detecting potential prey. In the field, we sampled gammarids (genus Cheirocratus) and characterized the spectral properties of their eyes, which possess strong directional reflectors. In the laboratory, we quantified ocular sparks size and their angle-dependent radiance. Combined with environmental light measurements and known properties of the visual system of T. delaisi, we modeled diurnal active photolocation under various scenarios. Our results corroborate that diurnal active photolocation should help T. delaisi detect gammarids at distances relevant to foraging, 4.5 cm under favourable conditions and up to 2.5 cm under average conditions. To determine the prevalence of diurnal active photolocation for micro-prey, we encourage further theoretical and empirical work.
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13
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Aguilar A, Truong BR, Gutierrez F. Complete mitochondrial DNA genomes for two northeast Pacific mesopelagic fishes, the Mexican lampfish ( Triphoturus mexicanus) and black-belly dragonfish ( Stomias atriventer). Mitochondrial DNA B Resour 2018; 3:21-23. [PMID: 30511017 PMCID: PMC6269098 DOI: 10.1080/23802359.2017.1413293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Mesopelagic fishes are an important component of marine ecosystems, providing an important link between lower and higher trophic levels. This group of fishes is also highly abundant and make up a large portion of the marine vertebrate biomass. Here we report on the full mitochondrial sequences for two common mesopelagic fishes from the southern California bight: the Mexican lampfish Triphoturus mexicanus (Actinopterygii: Myctophidae) and the black-belly dragonfish Stomias atriventer (Actinopterygii: Stomiidae). Triphoturus mexicanus showed previously reported gene rearrangements for the Myctophidae. Phylogenetic analysis grouped S. atriventer with other Stomiiformes and T. mexicanus within the Myctophiformes.
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Affiliation(s)
- Andres Aguilar
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032 USA
| | - Benson R Truong
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032 USA
| | - Frank Gutierrez
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032 USA
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14
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Ijichi M, Takano T, Hasegawa M, Yashiki H, Kogure K, Kojima S, Yoshizawa S. The complete mitochondrial genome of the longfin dragonfish Tactostoma macropus (Stomiiformes: Stomiidae). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:486-487. [PMID: 33490517 PMCID: PMC7800359 DOI: 10.1080/23802359.2018.1464411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The complete mitochondrial genome (mitogenome) was determined for the longfin dragonfish Tactostoma macropus, which is the first for the genus and the third within the family Stomiidae. The mitogenome sequence is 17,690 bp in length containing 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and a control region, as in most fishes. The gene order of T. macropus showed an unreported deviation from the typical vertebrate one. Phylogenetic reconstruction using the maximum likelihood method placed T. macropus in the monophyletic Stomiiformes. Three stomiid species were recovered as a moderately supported clade in the phylogenetic tree.
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Affiliation(s)
- Minoru Ijichi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Tsuyoshi Takano
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Masumi Hasegawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Haruka Yashiki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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15
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Michiels NK, Seeburger VC, Kalb N, Meadows MG, Anthes N, Mailli AA, Jack CB. Controlled iris radiance in a diurnal fish looking at prey. ROYAL SOCIETY OPEN SCIENCE 2018; 5:170838. [PMID: 29515824 PMCID: PMC5830713 DOI: 10.1098/rsos.170838] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/17/2018] [Indexed: 06/12/2023]
Abstract
Active sensing using light, or active photolocation, is only known from deep sea and nocturnal fish with chemiluminescent 'search' lights. Bright irides in diurnal fish species have recently been proposed as a potential analogue. Here, we contribute to this discussion by testing whether iris radiance is actively modulated. The focus is on behaviourally controlled iris reflections, called 'ocular sparks'. The triplefin Tripterygion delaisi can alternate between red and blue ocular sparks, allowing us to test the prediction that spark frequency and hue depend on background hue and prey presence. In a first experiment, we found that blue ocular sparks were significantly more often 'on' against red backgrounds, and red ocular sparks against blue backgrounds, particularly when copepods were present. A second experiment tested whether hungry fish showed more ocular sparks, which was not the case. However, background hue once more resulted in a significant differential use of ocular sparks. We conclude that iris radiance through ocular sparks in T. delaisi is not a side effect of eye movement, but adaptively modulated in response to the context under which prey are detected. We discuss the possible alternative functions of ocular sparks, including an as yet speculative role in active photolocation.
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Affiliation(s)
- Nico K. Michiels
- Animal Evolutionary Ecology, Institute for Evolution and Ecology, Department of Biology, Faculty of Science, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Victoria C. Seeburger
- Animal Evolutionary Ecology, Institute for Evolution and Ecology, Department of Biology, Faculty of Science, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Universität Hohenheim, Landesanstalt für Bienenkunde (730), August-von-Hartmann-Straße 13, 70599 Hohenheim, Germany
| | - Nadine Kalb
- Animal Evolutionary Ecology, Institute for Evolution and Ecology, Department of Biology, Faculty of Science, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Didaktik der Biologie, Faculty of Science, University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany
| | - Melissa G. Meadows
- Animal Evolutionary Ecology, Institute for Evolution and Ecology, Department of Biology, Faculty of Science, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Science Center 109, Biology Department, St Francis University, 117 Evergreen Drive, Loretto, PA 15940, USA
| | - Nils Anthes
- Animal Evolutionary Ecology, Institute for Evolution and Ecology, Department of Biology, Faculty of Science, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Amalia A. Mailli
- Animal Evolutionary Ecology, Institute for Evolution and Ecology, Department of Biology, Faculty of Science, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Marine Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Universitetsaléen 11, 8049 Bodø, Norway
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16
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Marranzino AN, Webb JF. Flow sensing in the deep sea: the lateral line system of stomiiform fishes. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Ashley N Marranzino
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Jacqueline F Webb
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
- Associate of Ichthyology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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17
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Woods KN, Pfeffer J, Klein-Seetharaman J. Chlorophyll-Derivative Modulation of Rhodopsin Signaling Properties through Evolutionarily Conserved Interaction Pathways. Front Mol Biosci 2017; 4:85. [PMID: 29312953 PMCID: PMC5733091 DOI: 10.3389/fmolb.2017.00085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 11/28/2017] [Indexed: 01/04/2023] Open
Abstract
Retinal is the light-absorbing chromophore that is responsible for the activation of visual pigments and light-driven ion pumps. Evolutionary changes in the intermolecular interactions of the retinal with specific amino acids allow for adaptation of the spectral characteristics, referred to as spectral tuning. However, it has been proposed that a specific species of dragon fish has bypassed the adaptive evolutionary process of spectral tuning and replaced it with a single evolutionary event: photosensitization of rhodopsin by chlorophyll derivatives. Here, by using a combination of experimental measurements and computational modeling to probe retinal-receptor interactions in rhodopsin, we show how the binding of the chlorophyll derivative, chlorin-e6 (Ce6) in the intracellular domain (ICD) of the receptor allosterically excites G-protein coupled receptor class A (GPCR-A) conserved long-range correlated fluctuations that connect distant parts of the receptor. These long-range correlated motions are associated with regulating the dynamics and intermolecular interactions of specific amino acids in the retinal ligand-binding pocket that have been associated with shifts in the absorbance peak maximum (λmax) and hence, spectral sensitivity of the visual system. Moreover, the binding of Ce6 affects the overall global properties of the receptor. Specifically, we find that Ce6-induced dynamics alter the thermal stability of rhodopsin by adjusting hydrogen-bonding interactions near the receptor active-site that consequently also influences the intrinsic conformational equilibrium of the receptor. Due to the conservation of the ICD residues amongst different receptors in this class and the fact that all GPCR-A receptors share a common mechanism of activation, it is possible that the allosteric associations excited in rhodopsin with Ce6 binding are a common feature in all class A GPCRs.
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Affiliation(s)
- Kristina N. Woods
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität, München, Germany
- *Correspondence: Kristina N. Woods
| | - Jürgen Pfeffer
- Bavarian School of Public Policy, Technical University of Munich, München, Germany
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18
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Zhang Y, Sun J, Chen C, Watanabe HK, Feng D, Zhang Y, Chiu JM, Qian PY, Qiu JW. Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species. Sci Rep 2017; 7:46205. [PMID: 28397791 PMCID: PMC5387418 DOI: 10.1038/srep46205] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 03/10/2017] [Indexed: 12/31/2022] Open
Abstract
Polynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids (Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid (Harmothoe imbricata). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes. Transcriptome assembly produced 98,806 to 225,709 contigs in the three species. There were more positively charged amino acids (i.e., histidine and arginine) and less negatively charged amino acids (i.e., aspartic acid and glutamic acid) in the deep-sea species. There were 120 genes showing clear evidence of positive selection. Among the 10% most highly expressed genes, there were more hemoglobin genes with high expression levels in both deep-sea species. The duplicated genes related to DNA recombination and metabolism, and gene expression were only enriched in deep-sea species. Deep-sea scale worms adopted two strategies of adaptation to hypoxia in the chemosynthesis-based habitats (i.e., rapid evolution of tetra-domain hemoglobin in Branchipolynoe or high expression of single-domain hemoglobin in Lepidonotopodium sp.).
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Affiliation(s)
- Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Jin Sun
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, P. R. China
| | - Chong Chen
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Hiromi K. Watanabe
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Dong Feng
- CAS Key Laboratory of Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, P. R. China
| | - Yu Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
| | - Jill M.Y. Chiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Pei-Yuan Qian
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, P. R. China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
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19
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Evolution of a Functional Head Joint in Deep-Sea Fishes (Stomiidae). PLoS One 2017; 12:e0170224. [PMID: 28146571 PMCID: PMC5287460 DOI: 10.1371/journal.pone.0170224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 01/01/2017] [Indexed: 11/19/2022] Open
Abstract
The head and anterior trunk region of most actinopterygian fishes is stiffened as, uniquely within vertebrates, the pectoral girdles have a direct and often strong connection through the posttemporal to the posterior region of the skull. Members of the mesopelagic fish family Stomiidae have their pectoral girdle separated from the skull. This connection is lost in several teleost groups, but the stomiids have an additional evolutionary novelty—a flexible connection between the occiput and the first vertebra, where only the notochord persists. Several studies suggested that stomiids engulf significantly large prey items and conjectured about the functional role of the anterior part of the vertebral column; however, there has been no precise anatomical description of this complex. Here we describe a unique configuration comprising the occiput and the notochordal sheath in Aristostomias, Eustomias, Malacosteus, Pachystomias, and Photostomias that represents a true functional head joint in teleosts and discuss its potential phylogenetic implications. In these genera, the chordal sheath is folded inward ventrally beneath its connection to the basioccipital and embraces the occipital condyle when in a resting position. In the resting position (wherein the head is not manipulatively elevated), this condyle is completely embraced by the ventral fold of the notochord. A manual manipulative elevation of the head in cleared and stained specimens unfolds the ventral sheath of the notochord. As a consequence, the cranium can be pulled up and back significantly farther than in all other teleost taxa that lack such a functional head joint and thereby can reach mouth gapes up to 120°.
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20
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Localisation and origin of the bacteriochlorophyll-derived photosensitizer in the retina of the deep-sea dragon fish Malacosteus niger. Sci Rep 2016; 6:39395. [PMID: 27996027 PMCID: PMC5171636 DOI: 10.1038/srep39395] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/22/2016] [Indexed: 11/08/2022] Open
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21
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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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22
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Guinot G, Cavin L. 'Fish' (Actinopterygii and Elasmobranchii) diversification patterns through deep time. Biol Rev Camb Philos Soc 2015; 91:950-981. [PMID: 26105527 DOI: 10.1111/brv.12203] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 05/20/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
Abstract
Actinopterygii (ray-finned fishes) and Elasmobranchii (sharks, skates and rays) represent more than half of today's vertebrate taxic diversity (approximately 33000 species) and form the largest component of vertebrate diversity in extant aquatic ecosystems. Yet, patterns of 'fish' evolutionary history remain insufficiently understood and previous studies generally treated each group independently mainly because of their contrasting fossil record composition and corresponding sampling strategies. Because direct reading of palaeodiversity curves is affected by several biases affecting the fossil record, analytical approaches are needed to correct for these biases. In this review, we propose a comprehensive analysis based on comparison of large data sets related to competing phylogenies (including all Recent and fossil taxa) and the fossil record for both groups during the Mesozoic-Cainozoic interval. This approach provides information on the 'fish' fossil record quality and on the corrected 'fish' deep-time phylogenetic palaeodiversity signals, with special emphasis on diversification events. Because taxonomic information is preserved after analytical treatment, identified palaeodiversity events are considered both quantitatively and qualitatively and put within corresponding palaeoenvironmental and biological settings. Results indicate a better fossil record quality for elasmobranchs due to their microfossil-like fossil distribution and their very low diversity in freshwater systems, whereas freshwater actinopterygians are diverse in this realm with lower preservation potential. Several important diversification events are identified at familial and generic levels for elasmobranchs, and marine and freshwater actinopterygians, namely in the Early-Middle Jurassic (elasmobranchs), Late Jurassic (actinopterygians), Early Cretaceous (elasmobranchs, freshwater actinopterygians), Cenomanian (all groups) and the Paleocene-Eocene interval (all groups), the latter two representing the two most exceptional radiations among vertebrates. For each of these events along with the Cretaceous-Paleogene extinction, we provide an in-depth review of the taxa involved and factors that may have influenced the diversity patterns observed. Among these, palaeotemperatures, sea-levels, ocean circulation and productivity as well as continent fragmentation and environment heterogeneity (reef environments) are parameters that largely impacted on 'fish' evolutionary history, along with other biotic constraints.
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Affiliation(s)
- Guillaume Guinot
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland.
| | - Lionel Cavin
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland
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23
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de Busserolles F, Hart NS, Hunt DM, Davies WI, Marshall NJ, Clarke MW, Hahne D, Collin SP. Spectral Tuning in the Eyes of Deep-Sea Lanternfishes (Myctophidae): A Novel Sexually Dimorphic Intra-Ocular Filter. BRAIN, BEHAVIOR AND EVOLUTION 2015; 85:77-93. [DOI: 10.1159/000371652] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/15/2014] [Indexed: 11/19/2022]
Abstract
Deep-sea fishes possess several adaptations to facilitate vision where light detection is pushed to its limit. Lanternfishes (Myctophidae), one of the world's most abundant groups of mesopelagic fishes, possess a novel and unique visual specialisation, a sexually dimorphic photostable yellow pigmentation, constituting the first record of a visual sexual dimorphism in any non-primate vertebrate. The topographic distribution of the yellow pigmentation across the retina is species specific, varying in location, shape and size. Spectrophotometric analyses reveal that this new retinal specialisation differs between species in terms of composition and acts as a filter, absorbing maximally between 356 and 443 nm. Microspectrophotometry and molecular analyses indicate that the species containing this pigmentation also possess at least 2 spectrally distinct rod visual pigments as a result of a duplication of the Rh1 opsin gene. After modelling the effect of the yellow pigmentation on photoreceptor spectral sensitivity, we suggest that this unique specialisation acts as a filter to enhance contrast, thereby improving the detection of bioluminescent emissions and possibly fluorescence in the extreme environment of the deep sea. The fact that this yellow pigmentation is species specific, sexually dimorphic and isolated within specific parts of the retina indicates an evolutionary pressure to visualise prey/predators/mates in a particular part of each species' visual field.
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