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Wijayaratna D, Sacchetta F, Pedraza-González L, Fanelli F, Sugihara T, Koyanagi M, Piyawardana S, Ghotra K, Thotamune W, Terakita A, Olivucci M, Karunarathne A. In-silico predicted mouse melanopsins with blue spectral shifts deliver efficient subcellular signaling. Cell Commun Signal 2024; 22:394. [PMID: 39118111 PMCID: PMC11312219 DOI: 10.1186/s12964-024-01753-0] [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: 03/12/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Melanopsin is a photopigment belonging to the G Protein-Coupled Receptor (GPCR) family expressed in a subset of intrinsically photosensitive retinal ganglion cells (ipRGCs) and responsible for a variety of processes. The bistability and, thus, the possibility to function under low retinal availability would make melanopsin a powerful optogenetic tool. Here, we aim to utilize mouse melanopsin to trigger macrophage migration by its subcellular optical activation with localized blue light, while simultaneously imaging the migration with red light. To reduce melanopsin's red light sensitivity, we employ a combination of in silico structure prediction and automated quantum mechanics/molecular mechanics modeling to predict minimally invasive mutations to shift its absorption spectrum towards the shorter wavelength region of the visible spectrum without compromising the signaling efficiency. The results demonstrate that it is possible to achieve melanopsin mutants that resist red light-induced activation but are activated by blue light and display properties indicating preserved bistability. Using the A333T mutant, we show that the blue light-induced subcellular melanopsin activation triggers localized PIP3 generation and macrophage migration, which we imaged using red light, demonstrating the optogenetic utility of minimally engineered melanopsins.
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Affiliation(s)
| | - Filippo Sacchetta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | | | - Francesca Fanelli
- Department of Life Sciences, Dulbecco Telethon Institute, University of Modena and Reggio Emilia, Modena, I-41125, Italy
| | - Tomohiro Sugihara
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
| | - Mitsumasa Koyanagi
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
- The OMU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Senuri Piyawardana
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Kiran Ghotra
- Department of Biology, Siena Heights University, Adrian, MI, 49221, USA
| | - Waruna Thotamune
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Akihisa Terakita
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
- The OMU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Ajith Karunarathne
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA.
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2
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Rossier V, Train C, Nevers Y, Robinson-Rechavi M, Dessimoz C. Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families. Genome Biol Evol 2024; 16:evae100. [PMID: 38742690 PMCID: PMC11149776 DOI: 10.1093/gbe/evae100] [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: 11/15/2023] [Revised: 04/17/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Studying gene family evolution strongly benefits from insightful visualizations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualizations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their children's information. Here, we introduce Matreex, a new dynamic tool to scale up the visualization of gene families. Matreex's key idea is to use "phylogenetic" profiles, which are dense representations of gene repertoires, to minimize the information loss when collapsing subtrees. We illustrate Matreex's usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multicopy gene families. Second, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5,500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence-absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoan Thelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreex's potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install Matreex) with the source code and documentation available at https://github.com/DessimozLab/matreex.
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Affiliation(s)
- Victor Rossier
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Comparative Genomics, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Clement Train
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Yannis Nevers
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Comparative Genomics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- SIB Swiss Institute of Bioinformatics, Comparative Genomics, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Comparative Genomics, Lausanne, Switzerland
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3
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Boyette JL, Bell RC, Fujita MK, Thomas KN, Streicher JW, Gower DJ, Schott RK. Diversity and Molecular Evolution of Nonvisual Opsin Genes across Environmental, Developmental, and Morphological Adaptations in Frogs. Mol Biol Evol 2024; 41:msae090. [PMID: 38736374 PMCID: PMC11181710 DOI: 10.1093/molbev/msae090] [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: 09/12/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024] Open
Abstract
Nonvisual opsins are transmembrane proteins expressed in the eyes and other tissues of many animals. When paired with a light-sensitive chromophore, nonvisual opsins form photopigments involved in various nonvisual, light-detection functions including circadian rhythm regulation, light-seeking behaviors, and seasonal responses. Here, we investigate the molecular evolution of nonvisual opsin genes in anuran amphibians (frogs and toads). We test several evolutionary hypotheses including the predicted loss of nonvisual opsins due to nocturnal ancestry and potential functional differences in nonvisual opsins resulting from environmental light variation across diverse anuran ecologies. Using whole-eye transcriptomes of 81 species, combined with genomes, multitissue transcriptomes, and independently annotated genes from an additional 21 species, we identify which nonvisual opsins are present in anuran genomes and those that are also expressed in the eyes, compare selective constraint among genes, and test for potential adaptive evolution by comparing selection between discrete ecological classes. At the genomic level, we recovered all 18 ancestral vertebrate nonvisual opsins, indicating that anurans demonstrate the lowest documented amount of opsin gene loss among ancestrally nocturnal tetrapods. We consistently found expression of 14 nonvisual opsins in anuran eyes and detected positive selection in a subset of these genes. We also found shifts in selective constraint acting on nonvisual opsins in frogs with differing activity periods, habitats, distributions, life histories, and pupil shapes, which may reflect functional adaptation. Although many nonvisual opsins remain poorly understood, these findings provide insight into the diversity and evolution of these genes across anurans, filling an important gap in our understanding of vertebrate opsins and setting the stage for future research on their functional evolution across taxa.
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Affiliation(s)
- John L Boyette
- Department of Biological Sciences, The Pennsylvania State University, State College, PA, USA
- Department of Biology, Berry College, Rome, GA, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - Matthew K Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Kate N Thomas
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
- Natural History Museum, London, UK
| | | | | | - Ryan K Schott
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Department of Biology & Centre for Vision Research, York University, Toronto, ON, Canada
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4
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Policarpo M, Baldwin MW, Casane D, Salzburger W. Diversity and evolution of the vertebrate chemoreceptor gene repertoire. Nat Commun 2024; 15:1421. [PMID: 38360851 PMCID: PMC10869828 DOI: 10.1038/s41467-024-45500-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: 09/22/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
Chemoreception - the ability to smell and taste - is an essential sensory modality of most animals. The number and type of chemical stimuli that animals can perceive depends primarily on the diversity of chemoreceptors they possess and express. In vertebrates, six families of G protein-coupled receptors form the core of their chemosensory system, the olfactory/pheromone receptor gene families OR, TAAR, V1R and V2R, and the taste receptors T1R and T2R. Here, we study the vertebrate chemoreceptor gene repertoire and its evolutionary history. Through the examination of 1,527 vertebrate genomes, we uncover substantial differences in the number and composition of chemoreceptors across vertebrates. We show that the chemoreceptor gene families are co-evolving, highly dynamic, and characterized by lineage-specific expansions (for example, OR in tetrapods; TAAR, T1R in teleosts; V1R in mammals; V2R, T2R in amphibians) and losses. Overall, amphibians, followed by mammals, are the vertebrate clades with the largest chemoreceptor repertoires. While marine tetrapods feature a convergent reduction of chemoreceptor numbers, the number of OR genes correlates with habitat in mammals and birds and with migratory behavior in birds, and the taste receptor repertoire correlates with diet in mammals and with aquatic environment in fish.
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Affiliation(s)
- Maxime Policarpo
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Didier Casane
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
- Université Paris Cité, UFR Sciences du Vivant, Paris, France
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
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Sakamoto S, Matsushita Y, Itoigawa A, Ezawa T, Fujitani T, Takakura K, Zhou Y, Zhang G, Grutzner F, Kawamura S, Hayakawa T. Color vision evolution in egg-laying mammals: insights from visual photoreceptors and daily activities of Australian echidnas. ZOOLOGICAL LETTERS 2024; 10:2. [PMID: 38167154 PMCID: PMC10759620 DOI: 10.1186/s40851-023-00224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Egg-laying mammals (monotremes) are considered "primitive" due to traits such as oviparity, cloaca, and incomplete homeothermy, all of which they share with reptiles. Two groups of monotremes, the terrestrial echidna (Tachyglossidae) and semiaquatic platypus (Ornithorhynchidae), have evolved highly divergent characters since their emergence in the Cenozoic era. These evolutionary differences, notably including distinct electrosensory and chemosensory systems, result from adaptations to species-specific habitat conditions. To date, very few studies have examined the visual adaptation of echidna and platypus. In the present study, we show that echidna and platypus have different light absorption spectra in their dichromatic visual sensory systems at the molecular level. We analyzed absorption spectra of monotreme color opsins, long-wavelength sensitive opsin (LWS) and short-wavelength sensitive opsin 2 (SWS2). The wavelength of maximum absorbance (λmax) in LWS was 570.2 in short-beaked echidna (Tachyglossus aculeatus) and 560.6 nm in platypus (Ornithorhynchus anatinus); in SWS2, λmax was 451.7 and 442.6 nm, respectively. Thus, the spectral range in echidna color vision is ~ 10 nm longer overall than in platypus. Natural selection analysis showed that the molecular evolution of monotreme color opsins is generally functionally conserved, suggesting that these taxa rely on species-specific color vision. In order to understand the usage of color vision in monotremes, we made 24-h behavioral observations of captive echidnas at warm temperatures and analyzed the resultant ethograms. Echidnas showed cathemeral activity and various behavioral repertoires such as feeding, traveling, digging, and self-grooming without light/dark environment selectivity. Halting (careful) behavior is more frequent in dark conditions, which suggests that echidnas may be more dependent on vision during the day and olfaction at night. Color vision functions have contributed to dynamic adaptations and dramatic ecological changes during the ~ 60 million years of divergent monotreme evolution. The ethogram of various day and night behaviors in captive echidnas also contributes information relevant to habitat conservation and animal welfare in this iconic species, which is locally endangered.
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Affiliation(s)
- Shiina Sakamoto
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yuka Matsushita
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Akihiro Itoigawa
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Takumi Ezawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | | | | | - Yang Zhou
- BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
| | - Guojie Zhang
- Center of Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Frank Grutzner
- The Environment Institute, University of Adelaide, Adelaide, SA, Australia
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan.
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6
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Pan D, Wang Z, Chen Y, Cao J. Melanopsin-mediated optical entrainment regulates circadian rhythms in vertebrates. Commun Biol 2023; 6:1054. [PMID: 37853054 PMCID: PMC10584931 DOI: 10.1038/s42003-023-05432-7] [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: 07/08/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023] Open
Abstract
Melanopsin (OPN4) is a light-sensitive protein that plays a vital role in the regulation of circadian rhythms and other nonvisual functions. Current research on OPN4 has focused on mammals; more evidence is needed from non-mammalian vertebrates to fully assess the significance of the non-visual photosensitization of OPN4 for circadian rhythm regulation. There are species differences in the regulatory mechanisms of OPN4 for vertebrate circadian rhythms, which may be due to the differences in the cutting variants, tissue localization, and photosensitive activation pathway of OPN4. We here summarize the distribution of OPN4 in mammals, birds, and teleost fish, and the classical excitation mode for the non-visual photosensitive function of OPN4 in mammals is discussed. In addition, the role of OPN4-expressing cells in regulating circadian rhythm in different vertebrates is highlighted, and the potential rhythmic regulatory effects of various neuropeptides or neurotransmitters expressed in mammalian OPN4-expressing ganglion cells are summarized among them.
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Affiliation(s)
- Deng Pan
- Laboratory of Anatomy of Domestic Animals, National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Haidian, 100193, Beijing, China
| | - Zixu Wang
- Laboratory of Anatomy of Domestic Animals, National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Haidian, 100193, Beijing, China
| | - Yaoxing Chen
- Laboratory of Anatomy of Domestic Animals, National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Haidian, 100193, Beijing, China
| | - Jing Cao
- Laboratory of Anatomy of Domestic Animals, National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Haidian, 100193, Beijing, China.
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7
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Silva L, Mendes T, Ramos L, Zhang G, Antunes A. Parallel evolution of fish bi-modal breathing and expansion of olfactory receptor (OR) genes: toward a universal ORs nomenclature. J Genet Genomics 2023; 50:600-610. [PMID: 36935037 DOI: 10.1016/j.jgg.2023.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/27/2023] [Accepted: 03/04/2023] [Indexed: 03/19/2023]
Abstract
Olfactory receptors (ORs) play a key role in the prime sensorial perception, being highly relevant for intra/interspecific interactions. ORs are a subgroup of G-protein coupled receptors that exhibit highly complex subgenomes in vertebrates. However, OR repertoires remain poorly studied in fish lineages, precluding finely retracing their origin, evolution, and diversification, especially in the most basal groups. Here, we conduct an exhaustive gene screening upon 43 high-quality fish genomes exhibiting varied gene repertoires (2-583 genes). While the early vertebrates performed gas exchange through gills, we hypothesize that the emergence of new breathing structures (swim bladder and paired lungs) in early osteichthyans may be associated with expansions in the ORs gene families sensitive to airborne molecules. Additionally, we verify that the OR repertoire of moderns actinopterygians has not increased as expected following a whole genome duplication, likely due to regulatory mechanisms compensating the gene load excess. Finally, we identify 25 distinct OR families, allowing us to propose an updated universal nomenclature for the fish ORs.
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Affiliation(s)
- Liliana Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Tito Mendes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Luana Ramos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
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At the root of the mammalian mind: The sensory organs, brain and behavior of pre-mammalian synapsids. PROGRESS IN BRAIN RESEARCH 2023; 275:25-72. [PMID: 36841570 DOI: 10.1016/bs.pbr.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
All modern mammals are descendants of the paraphyletic non-mammaliaform Synapsida, colloquially referred to as the "mammal-like reptiles." It has long been assumed that these mammalian ancestors were essentially reptile-like in their morphology, biology, and behavior, i.e., they had a small brain, displayed simple behavior, and their sensory organs were unrefined compared to those of modern mammals. Recent works have, however, revealed that neurological, sensory, and behavioral traits previously considered typically mammalian, such as whiskers, enhanced olfaction, nocturnality, parental care, and complex social interactions evolved before the origin of Mammaliaformes, among the early-diverging "mammal-like reptiles." In contrast, an enlarged brain did not evolve immediately after the origin of mammaliaforms. As such, in terms of paleoneurology, the last "mammal-like reptiles" were not significantly different from the earliest mammaliaforms. The abundant data and literature published in the last 10 years no longer supports the "three pulses" scenario of synapsid brain evolution proposed by Rowe and colleagues in 2011, but supports the new "outside-in" model of Rodrigues and colleagues proposed in 2018, instead. As Mesozoic reptiles were becoming the dominant taxa within terrestrial ecosystems, synapsids gradually adapted to smaller body sizes and nocturnality. This resulted in a sensory revolution in synapsids as olfaction, audition, and somatosensation compensated for the loss of visual cues. This altered sensory input is aligned with changes in the brain, the most significant of which was an increase in relative brain size.
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Hadden PW, Zhang J. An Overview of the Penguin Visual System. Vision (Basel) 2023; 7:vision7010006. [PMID: 36810310 PMCID: PMC9944954 DOI: 10.3390/vision7010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/03/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Penguins require vision that is adequate for both subaerial and submarine environments under a wide range of illumination. Here we provide a structured overview of what is known about their visual system with an emphasis on how and how well they achieve these goals. Amphibious vision is facilitated by a relatively flat cornea, the power in air varying from 10.2 dioptres (D) to 41.3 D depending on the species, and there is good evidence for emmetropia both above and below water. All penguins are trichromats with loss of rhodopsin 2, a nocturnal feature, but only deeper diving penguins have been noted to have pale oil droplets and a preponderance of rods. Conversely, the diurnal, shallow-diving little penguin has a higher ganglion cell density (28,867 cells/mm2) and f-number (3.5) than those that operate in dimmer light. In most species studied, there is some binocular overlap, but this reduces upon submergence. However, gaps in our knowledge remain, particularly with regard to the mechanism of accommodation, spectral transmission, behavioural measurements of visual function in low light, and neural adaptations to low light. The rarer species also deserve more attention.
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Tian R, Guo H, Jin Z, Zhang F, Zhao J, Seim I. Molecular evolution of vision-related genes may contribute to marsupial photic niche adaptations. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.982073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Vision plays an essential role in the life of many animals. While most mammals are night-active (nocturnal), many have adapted to novel light environments. This includes diurnal (day-active) and crepuscular (twilight-active) species. Here, we used integrative approaches to investigate the molecular evolution of 112 vision-related genes across 19 genomes representing most marsupial orders. We found that four genes (GUCA1B, GUCY2F, RGR, and SWS2) involved in retinal phototransduction likely became functionally redundant in the ancestor of marsupials, a group of largely obligate nocturnal mammals. We also show evidence of rapid evolution and positive selection of bright-light vision genes in the common ancestor of Macropus (kangaroos, wallaroos, and wallabies). Macropus-specific amino acid substitutions in opsin genes (LWS and SWS1), in particular, may be an adaptation for crepuscular vision in this genus via opsin spectral sensitivity tuning. Our study set the stage for functional genetics studies and provides a stepping stone to future research efforts that fully capture the visual repertoire of marsupials.
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11
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Aït-Ali N, Léveillard T. The Emergence of Rod-Cone Cellular Interaction. Front Genet 2022; 13:900849. [PMID: 36017494 PMCID: PMC9396122 DOI: 10.3389/fgene.2022.900849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/17/2022] [Indexed: 11/25/2022] Open
Abstract
We studied the origin of rod-derived cone viability factor (RdCVF) during evolution. In mammals, the nucleoredoxin-like 1 gene (NXNL1) produces a truncated thioredoxin-like protein, RdCVF, by intron retention in rod photoreceptors of the retina. This protein prevents the secondary cone degeneration in animal models of rod-cone degeneration. Extracellular RdCVF binds to a complex at the surface of the cones, composed of the basigin-1, a photoreceptor specific alternative splicing product of the basigin gene, and GLUT1, the glucose transporter. RdCVF accelerates glucose uptake allosterically. Glucose is either metabolized by aerobic glycolysis to sustain cone outer segment renewal or by the pentose phosphate pathway to support redox power to the thioredoxin RdCVFL. RdCVF signaling predates the appearance of the eye and evolved through two alternative splicing events. RdCVF signaling is observed first in hydra where it regulates an unknown signaling. A scallop RdCVF protein is produced by ciliated photoreceptors of the retina and binds its receptor, BSG1, the first occurrence of RdCVF/BSG1 signaling. In the lamprey, RdCVF metabolic signaling between rod and cones is fully operational. In the mouse, the production of BSG1 is regulated through alternative splicing. This signaling was extended to other regions of the brain, via its paralogue NXNL2.
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12
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Rial RV, Canellas F, Akaârir M, Rubiño JA, Barceló P, Martín A, Gamundí A, Nicolau MC. The Birth of the Mammalian Sleep. BIOLOGY 2022; 11:biology11050734. [PMID: 35625462 PMCID: PMC9138988 DOI: 10.3390/biology11050734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Mammals evolved from reptiles as a consequence of an evolutionary bottleneck. Some diurnal reptiles extended their activity, first to twilight and then to the entire dark time. This forced the change of the visual system. Pursuing maximal sensitivity, they abandoned the filters protecting the eyes against the dangerous diurnal light, which, in turn, forced immobility in lightproof burrows during light time. This was the birth of the mammalian sleep. Then, the Cretacic-Paleogene extinction of dinosaurs leaved free the diurnal niche and allowed the expansion of a few early mammals to diurnal life and the high variability of sleep traits. On the other hand, we propose that the idling rest is a state showing homeostatic regulation. Therefore, the difference between behavioral rest and wakeful idling is rather low: both show quiescence, raised sensory thresholds, reversibility, specific sleeping-resting sites and body positions, it is a pleasing state, and both are dependent of circadian and homeostatic regulation. Indeed, the most important difference is the unconsciousness of sleep and the consciousness of wakeful idling. Thus, we propose that sleep is a mere upgrade of the wakeful rest, and both may have the same function: guaranteeing rest during a part of the daily cycle. Abstract Mammals evolved from small-sized reptiles that developed endothermic metabolism. This allowed filling the nocturnal niche. They traded-off visual acuity for sensitivity but became defenseless against the dangerous daylight. To avoid such danger, they rested with closed eyes in lightproof burrows during light-time. This was the birth of the mammalian sleep, the main finding of this report. Improved audition and olfaction counterweighed the visual impairments and facilitated the cortical development. This process is called “The Nocturnal Evolutionary Bottleneck”. Pre-mammals were nocturnal until the Cretacic-Paleogene extinction of dinosaurs. Some early mammals returned to diurnal activity, and this allowed the high variability in sleeping patterns observed today. The traits of Waking Idleness are almost identical to those of behavioral sleep, including homeostatic regulation. This is another important finding of this report. In summary, behavioral sleep seems to be an upgrade of Waking Idleness Indeed, the trait that never fails to show is quiescence. We conclude that the main function of sleep consists in guaranteeing it during a part of the daily cycle.
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Affiliation(s)
- Rubén V. Rial
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- Correspondence: ; Tel.: +34-971-173-147; Fax: +34-971-173-184
| | - Francesca Canellas
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - Mourad Akaârir
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - José A. Rubiño
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - Pere Barceló
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - Aida Martín
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - Antoni Gamundí
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - M. Cristina Nicolau
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
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Borges R, Machado JP, Gomes C, Rocha AP, Antunes A. Measuring phylogenetic signal between categorical traits and phylogenies. Bioinformatics 2020; 35:1862-1869. [PMID: 30358816 DOI: 10.1093/bioinformatics/bty800] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 08/18/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION Determining whether a trait and phylogeny share some degree of phylogenetic signal is a flagship goal in evolutionary biology. Signatures of phylogenetic signal can assist the resolution of a broad range of evolutionary questions regarding the tempo and mode of phenotypic evolution. However, despite the considerable number of strategies to measure it, few and limited approaches exist for categorical traits. Here, we used the concept of Shannon entropy and propose the δ statistic for evaluating the degree of phylogenetic signal between a phylogeny and categorical traits. RESULTS We validated δ as a measure of phylogenetic signal: the higher the δ-value the higher the degree of phylogenetic signal between a given tree and a trait. Based on simulated data we proposed a threshold-based classification test to pinpoint cases of phylogenetic signal. The assessment of the test's specificity and sensitivity suggested that the δ approach should only be applied to 20 or more species. We have further tested the performance of δ in scenarios of branch length and topology uncertainty, unbiased and biased trait evolution and trait saturation. Our results showed that δ may be applied in a wide range of phylogenetic contexts. Finally, we investigated our method in 14 360 mammalian gene trees and found that olfactory receptor genes are significantly associated with the mammalian activity patterns, a result that is congruent with expectations and experiments from the literature. Our application shows that δ can successfully detect molecular signatures of phenotypic evolution. We conclude that δ represents a useful measure of phylogenetic signal since many phenotypes can only be measured in categories. AVAILABILITY AND IMPLEMENTATION https://github.com/mrborges23/delta_statistic. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rui Borges
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal.,CMUP, Centre of Mathematics of the University of Porto, Porto, Portugal
| | - João Paulo Machado
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal
| | - Cidália Gomes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal
| | - Ana Paula Rocha
- Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal.,CMUP, Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal
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14
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Fear of the dark? A mesopredator mitigates large carnivore risk through nocturnality, but humans moderate the interaction. Behav Ecol Sociobiol 2020. [DOI: 10.1007/s00265-020-02831-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Abstract
While constrained by endogenous rhythms, morphology and ecology, animals may still exhibit flexible activity patterns in response to risk. Temporal avoidance of interspecific aggression can enable access to resources without spatial exclusion. Apex predators, including humans, can affect mesopredator activity patterns. Human context might also modify temporal interactions between predators. We explored activity patterns, nocturnality and the effects of human activity upon a guild of carnivores (grey wolf, Canis lupus; Eurasian lynx, Lynx lynx; red fox, Vulpes vulpes) using travel routes in Plitvice Lakes National Park, Croatia. Humans were diurnal, foxes nocturnal and large carnivores active during the night, immediately after sunrise and before sunset. Carnivore activity patterns overlapped greatly and to a similar extent for all pairings. Activity curves followed expectations based on interspecific killing, with activity peaks coinciding where body size differences were small (wolf and lynx) but not when they were intermediate (foxes to large carnivores). Carnivore activity, particularly fox, overlapped much less with that of diurnal humans. Foxes responded to higher large carnivore activity by being more nocturnal. Low light levels likely provide safer conditions by reducing the visual detectability of mesopredators. The nocturnal effect of large carnivores was however moderated and reduced by human activity. This could perhaps be due to temporal shielding or interference with risk cues. Subtle temporal avoidance and nocturnality may enable mesopredators to cope with interspecific aggression at shared spatial resources. Higher human activity moderated the effects of top-down temporal suppression which could consequently affect the trophic interactions of mesopredators.
Significance statement
Temporal partitioning can provide an important mechanism for spatial resource access and species coexistence. Our findings show that carnivores partition the use of shared travel routes in time, using the cover of darkness to travel safely where their suppressors (large carnivores) are more active. We however observed fox nocturnality to be flexible, with responses depending on the activity levels but also the composition of apex predators. High human activity modified the top-down temporal suppression of mesopredators by large carnivores. The use of time by predators can have demographic and trophic consequences. Prey accessibility and susceptibility can be temporally variable. As such, the ecosystem services and the ecological roles of predators may be affected by human time use as well as that of intraguild competitors. Temporal interactions should not be overlooked when evaluating human use and conservation priorities in protected areas.
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15
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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: 53] [Impact Index Per Article: 13.3] [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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16
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Borges R, Fonseca J, Gomes C, Johnson WE, O'Brien SJ, Zhang G, Gilbert MTP, Jarvis ED, Antunes A. Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype. Genome Biol Evol 2020; 11:2244-2255. [PMID: 31386143 PMCID: PMC6735850 DOI: 10.1093/gbe/evz111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2019] [Indexed: 01/04/2023] Open
Abstract
Typical avian eyes are phenotypically engineered for photopic vision (daylight). In contrast, the highly derived eyes of the barn owl (Tyto alba) are adapted for scotopic vision (dim light). The dramatic modifications distinguishing barn owl eyes from other birds include: 1) shifts in frontal orientation to improve binocularity, 2) rod-dominated retina, and 3) enlarged corneas and lenses. Some of these features parallel mammalian eye patterns, which are hypothesized to have initially evolved in nocturnal environments. Here, we used an integrative approach combining phylogenomics and functional phenotypes of 211 eye-development genes across 48 avian genomes representing most avian orders, including the stem lineage of the scotopic-adapted barn owl. Overall, we identified 25 eye-development genes that coevolved under intensified or relaxed selection in the retina, lens, cornea, and optic nerves of the barn owl. The agtpbp1 gene, which is associated with the survival of photoreceptor populations, was pseudogenized in the barn owl genome. Our results further revealed that barn owl retinal genes responsible for the maintenance, proliferation, and differentiation of photoreceptors experienced an evolutionary relaxation. Signatures of relaxed selection were also observed in the lens and cornea morphology-associated genes, suggesting that adaptive evolution in these structures was essentially structural. Four eye-development genes (ephb1, phactr4, prph2, and rs1) evolved in positive association with the orbit convergence in birds and under relaxed selection in the barn owl lineage, likely contributing to an increased reliance on binocular vision in the barn owl. Moreover, we found evidence of coevolutionary interactions among genes that are expressed in the retina, lens, and optic nerve, suggesting synergetic adaptive events. Our study disentangles the genomic changes governing the binocularity and low-light perception adaptations of barn owls to nocturnal environments while revealing the molecular mechanisms contributing to the shift from the typical avian photopic vision to the more-novel scotopic-adapted eye.
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Affiliation(s)
- Rui Borges
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - João Fonseca
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal
| | - Cidália Gomes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia.,Walter Reed Biosystematics Unit, Smithsonian Institution, Suitland, Maryland
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia.,Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark.,China National GeneBank, BGI-Shenzen, Shenzhen, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, Rockefeller University.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Portugal
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17
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Hunnicutt KE, Tiley GP, Williams RC, Larsen PA, Blanco MB, Rasoloarison RM, Campbell CR, Zhu K, Weisrock DW, Matsunami H, Yoder AD. Comparative Genomic Analysis of the Pheromone Receptor Class 1 Family (V1R) Reveals Extreme Complexity in Mouse Lemurs (Genus, Microcebus) and a Chromosomal Hotspot across Mammals. Genome Biol Evol 2020; 12:3562-3579. [PMID: 31555816 PMCID: PMC6944220 DOI: 10.1093/gbe/evz200] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2019] [Indexed: 12/14/2022] Open
Abstract
Sensory gene families are of special interest for both what they can tell us about molecular evolution and what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within primates, with a special focus on the small-bodied nocturnal mouse and dwarf lemurs of Madagascar (genera Microcebus and Cheirogaleus, respectively). By doubling the existing genomic resources for strepsirrhine primates (i.e. the lemurs and lorises), we find that the highly speciose and morphologically cryptic mouse lemurs have experienced an elaborate proliferation of V1Rs that we argue is functionally related to their capacity for rapid lineage diversification. Contrary to a previous study that found equivalent degrees of V1R diversity in diurnal and nocturnal lemurs, our study finds a strong correlation between nocturnality and V1R elaboration, with nocturnal lemurs showing elaborate V1R repertoires and diurnal lemurs showing less diverse repertoires. Recognized subfamilies among V1Rs show unique signatures of diversifying positive selection, as might be expected if they have each evolved to respond to specific stimuli. Furthermore, a detailed syntenic comparison of mouse lemurs with mouse (genus Mus) and other mammalian outgroups shows that orthologous mammalian subfamilies, predicted to be of ancient origin, tend to cluster in a densely populated region across syntenic chromosomes that we refer to as a V1R "hotspot."
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Affiliation(s)
- Kelsie E Hunnicutt
- Department of Biology, Duke University, Durham, North Carolina
- Department of Biological Sciences, University of Denver, Denver, Colorado
| | - George P Tiley
- Department of Biology, Duke University, Durham, North Carolina
| | - Rachel C Williams
- Department of Biology, Duke University, Durham, North Carolina
- Duke Lemur Center, Duke University, Durham, North Carolina
| | - Peter A Larsen
- Department of Biology, Duke University, Durham, North Carolina
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota
| | | | - Rodin M Rasoloarison
- Behavioral Ecology and Sociobiology Unit, German Primate Centre, Göttingen, Germany
- Département de Biologie Animale, Université d’Antananarivo, Madagascar, Antananarivo, Madagascar
| | - C Ryan Campbell
- Department of Biology, Duke University, Durham, North Carolina
| | - Kevin Zhu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, Kentucky
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University Medical Center, Durham, North Carolina
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, North Carolina
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18
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Lovegrove BG. Obligatory Nocturnalism in Triassic Archaic Mammals: Preservation of Sperm Quality? Physiol Biochem Zool 2019; 92:544-553. [DOI: 10.1086/705440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Liu Y, Chi H, Li L, Rossiter SJ, Zhang S. Molecular Data Support an Early Shift to an Intermediate-Light Niche in the Evolution of Mammals. Mol Biol Evol 2019; 35:1130-1134. [PMID: 29462332 DOI: 10.1093/molbev/msy019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The visual ability and associated photic niche of early mammals is debated. The theory that ancestral mammals were nocturnal is supported by diverse adaptations. However, others argue that photopigment repertoires of early mammals are more consistent with a crepuscular niche, and support for this also comes from inferred spectral tuning of middle/long wavelength-sensitive (M/LWS) opsin sequences. Functional studies have suggested that the M/LWS pigment in the ancestor of Mammalia was either red- or green-sensitive; however, these were based on outdated phylogenies with key lineages omitted. By performing the most detailed study to date of middle/long-wave mammalian color vision, we provide the first experimental evidence that the M/LWS pigment of amniotes underwent a 9-nm spectral shift towards shorter wavelengths in the Mammalia ancestor, exceeding predictions from known critical sites. Our results suggest early mammals were yellow-sensitive, possibly representing an adaptive trade-off for both crepuscular (twilight) and nocturnal (moonlight) niches.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hai Chi
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Longfei Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Shuyi Zhang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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20
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Katsuura T, Lee S. A review of the studies on nonvisual lighting effects in the field of physiological anthropology. J Physiol Anthropol 2019; 38:2. [PMID: 30670097 PMCID: PMC6343353 DOI: 10.1186/s40101-018-0190-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/04/2018] [Indexed: 12/16/2022] Open
Abstract
Here, we review the history and the trends in the research on the nonvisual effect of light in the field of physiological anthropology. Research on the nonvisual effect of light in the field of physiological anthropology was pioneered by Sato and colleagues in the early 1990s. These authors found that the color temperature of light affected physiological functions in humans. The groundbreaking event with regard to the study of nonvisual effects of light was the discovery of the intrinsically photosensitive retinal ganglion cells in the mammalian retina in the early 2000s. The interest of the physiological anthropology scientific community in the nonvisual effects of light has been increasing since then. A total of 61 papers on nonvisual effects of light were published in the Journal of Physiological Anthropology (including its predecessor journals) until October 2018, 14 papers (1.4/year) in the decade from 1992 to 2001, 45 papers (2.8/year) in the 16 years between 2002 and 2017, and two papers in 2018 (January-October). The number of papers on this topic has been increasing in recent years. We categorized all papers according to light conditions, such as color temperature of light, light intensity, and monochromatic light. Among the 61 papers, 11 papers were related to color temperature, 20 papers were related to light intensity, 18 papers were related to monochromatic light, and 12 papers were classified as others. We provide an overview of these papers and mention future research prospects.
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Affiliation(s)
- Tetsuo Katsuura
- Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
| | - Soomin Lee
- Center for Environment, Health and Sciences, Chiba University, 6-2-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
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