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Di Rosa V, Frigato E, Negrini P, Cristiano W, López-Olmeda JF, Rétaux S, Sánchez-Vázquez FJ, Foulkes NS, Bertolucci C. Sporadic feeding regulates robust food entrainable circadian clocks in blind cavefish. iScience 2024; 27:110171. [PMID: 38974965 PMCID: PMC11225386 DOI: 10.1016/j.isci.2024.110171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/14/2024] [Accepted: 05/31/2024] [Indexed: 07/09/2024] Open
Abstract
The circadian clock represents a key timing system entrained by various periodic signals that ensure synchronization with the environment. Many investigations have pointed to the existence of two distinct circadian oscillators: one regulated by the light-dark cycle and the other set by feeding time. Blind cavefish have evolved under extreme conditions where they completely lack light exposure and experience food deprivation. Here, we have investigated feeding regulated clocks in two cavefish species, the Somalian cavefish Phreatichthys andruzzii and the Mexican cavefish Astyanax mexicanus, in comparison with the surface-dwelling zebrafish Danio rerio. Our results reveal that feeding represents an extremely strong synchronizer for circadian locomotor rhythmicity in subterranean cavefish. Indeed, we showed that consuming just one meal every 4 days is sufficient to entrain circadian rhythmicity in both cavefish species, but not in zebrafish. These profound adaptations to an extreme environment provide insight into the connections between feeding and circadian clocks.
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Affiliation(s)
- Viviana Di Rosa
- Department of Physiology, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, 30100 Murcia, Spain
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Elena Frigato
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Pietro Negrini
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Walter Cristiano
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Ecosystems and Health Unit, Environment and Health Department, Italian National Institute of Health, 00161 Rome, Italy
| | - Jose Fernando López-Olmeda
- Department of Physiology, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, 30100 Murcia, Spain
| | - Sylvie Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Francisco Javier Sánchez-Vázquez
- Department of Physiology, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, 30100 Murcia, Spain
| | - Nicholas S. Foulkes
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Cristiano Bertolucci
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
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2
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Lloyd E, Rastogi A, Holtz N, Aaronson B, Craig Albertson R, Keene AC. Ontogeny and social context regulate the circadian activity patterns of Lake Malawi cichlids. J Comp Physiol B 2024; 194:299-313. [PMID: 37910192 PMCID: PMC11233325 DOI: 10.1007/s00360-023-01523-3] [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: 05/27/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023]
Abstract
Activity patterns tend to be highly stereotyped and critical for executing many different behaviors including foraging, social interactions, and predator avoidance. Differences in the circadian timing of locomotor activity and rest periods can facilitate habitat partitioning and the exploitation of novel niches. As a consequence, closely related species often display highly divergent activity patterns, suggesting that shifts from diurnal to nocturnal behavior, or vice versa, are critical for survival. In Africa's Lake Malawi alone, there are over 500 species of cichlids, which inhabit diverse environments and exhibit extensive phenotypic variation. We have previously identified a substantial range in activity patterns across adult Lake Malawi cichlid species, from strongly diurnal to strongly nocturnal. In many species, including fishes, ecological pressures differ dramatically across life-history stages, raising the possibility that activity patterns may change over ontogeny. To determine if rest-activity patterns change across life stages, we compared the locomotor patterns of six Lake Malawi cichlid species. While total rest and activity did not change between early juvenile and adult stages, rest-activity patterns did, with juveniles displaying distinct activity rhythms that are more robust than adults. One distinct difference between juveniles and adults is the emergence of complex social behavior. To determine whether social context is required for activity rhythms, we next measured locomotor behavior in group-housed adult fish. We found that when normal social interactions were allowed, locomotor activity patterns were restored, supporting the notion that social interactions promote circadian regulation of activity in adult fish. These findings reveal a previously unidentified link between developmental stage and social interactions in the circadian timing of cichlid activity.
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Affiliation(s)
- Evan Lloyd
- Department of Biology, Texas A&M University, College Station, TX, 77840, USA
| | - Aakriti Rastogi
- Department of Biology, Texas A&M University, College Station, TX, 77840, USA
| | - Niah Holtz
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ben Aaronson
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - R Craig Albertson
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX, 77840, USA.
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3
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Manahan DN, Nachman MW. Alternative splicing and environmental adaptation in wild house mice. Heredity (Edinb) 2024; 132:133-141. [PMID: 38012302 PMCID: PMC10923775 DOI: 10.1038/s41437-023-00663-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
A major goal of evolutionary genetics is to understand the genetic and molecular mechanisms underlying adaptation. Previous work has established that changes in gene regulation may contribute to adaptive evolution, but most studies have focused on mRNA abundance and only a few studies have investigated the role of post-transcriptional processing. Here, we use a combination of exome sequences and short-read RNA-Seq data from wild house mice (Mus musculus domesticus) collected along a latitudinal transect in eastern North America to identify candidate genes for local adaptation through alternative splicing. First, we identified alternatively spliced transcripts that differ in frequency between mice from the northern-most and southern-most populations in this transect. We then identified the subset of these transcripts that exhibit clinal patterns of variation among all populations in the transect. Finally, we conducted association studies to identify cis-acting splicing quantitative trait loci (cis-sQTL), and we identified cis-sQTL that overlapped with previously ascertained targets of selection from genome scans. Together, these analyses identified a small set of alternatively spliced transcripts that may underlie environmental adaptation in house mice. Many of these genes have known phenotypes associated with body size, a trait that varies clinally in these populations. We observed no overlap between these genes and genes previously identified by changes in mRNA abundance, indicating that alternative splicing and changes in mRNA abundance may provide separate molecular mechanisms of adaptation.
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Affiliation(s)
- David N Manahan
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA.
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA
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4
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Perry A, McGaugh SE, Keene AC, Blackmon H. CaveCrawler: an interactive analysis suite for cavefish bioinformatics. G3 GENES|GENOMES|GENETICS 2022; 12:6609176. [PMID: 35708643 PMCID: PMC9339328 DOI: 10.1093/g3journal/jkac132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022]
Abstract
The growing use of genomics in diverse organisms provides the basis for identifying genomic and transcriptional differences across species and experimental conditions. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but most emerging models lack such databases. The Mexican tetra, Astyanax mexicanus exists as 2 morphs: surface-dwelling and cave-dwelling. There exist at least 30 cave populations, providing a system to study convergent evolution. We have generated a web-based analysis suite that integrates datasets from different studies to identify how gene transcription and genetic markers of selection differ between populations and across experimental contexts. Results of diverse studies can be analyzed in conjunction with other genetic data (e.g. Gene Ontology information), to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built for A. mexicanus can be adapted for other emerging model systems.
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Affiliation(s)
- Annabel Perry
- Department of Biology, Texas A&M University , College Station, TX 77843, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota , Saint Paul, MN 55108, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University , College Station, TX 77843, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University , College Station, TX 77843, USA
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5
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Wright CJ, Smith CWJ, Jiggins CD. Alternative splicing as a source of phenotypic diversity. Nat Rev Genet 2022; 23:697-710. [PMID: 35821097 DOI: 10.1038/s41576-022-00514-4] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/27/2022]
Abstract
A major goal of evolutionary genetics is to understand the genetic processes that give rise to phenotypic diversity in multicellular organisms. Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits. It is well established that alternative splicing contributes to key innovations over long evolutionary timescales, such as brain development in bilaterians. However, recent developments in long-read sequencing and the generation of high-quality genome assemblies for diverse organisms has facilitated comparisons of splicing profiles between closely related species, providing insights into how alternative splicing evolves over shorter timescales. Although most splicing variants are probably non-functional, alternative splicing is nonetheless emerging as a dynamic, evolutionarily labile process that can facilitate adaptation and contribute to species divergence.
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Affiliation(s)
- Charlotte J Wright
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK. .,Department of Zoology, University of Cambridge, Cambridge, UK.
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
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6
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Xiong S, Wang W, Kenzior A, Olsen L, Krishnan J, Persons J, Medley K, Peuß R, Wang Y, Chen S, Zhang N, Thomas N, Miles JM, Alvarado AS, Rohner N. Enhanced lipogenesis through Pparγ helps cavefish adapt to food scarcity. Curr Biol 2022; 32:2272-2280.e6. [PMID: 35390280 DOI: 10.1016/j.cub.2022.03.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 01/11/2022] [Accepted: 03/11/2022] [Indexed: 12/18/2022]
Abstract
Nutrient availability varies seasonally and spatially in the wild. While many animals, such as hibernating animals or migrating birds, evolved strategies to overcome periods of nutrient scarcity,1,2 the cellular mechanisms of these strategies are poorly understood. Cave environments represent an example of nutrient-deprived environments, since the lack of sunlight and therefore primary energy production drastically diminishes the nutrient availability.3 Here, we used Astyanax mexicanus, which includes river-dwelling surface fish and cave-adapted cavefish populations, to study the genetic adaptation to nutrient limitations.4-9 We show that cavefish populations store large amounts of fat in different body regions when fed ad libitum in the lab. We found higher expression of lipogenesis genes in cavefish livers when fed the same amount of food as surface fish, suggesting an improved ability of cavefish to use lipogenesis to convert available energy into triglycerides for storage into adipose tissue.10-12 Moreover, the lipid metabolism regulator, peroxisome proliferator-activated receptor γ (Pparγ), is upregulated at both transcript and protein levels in cavefish livers. Chromatin immunoprecipitation sequencing (ChIP-seq) showed that Pparγ binds cavefish promoter regions of genes to a higher extent than surface fish and inhibiting Pparγ in vivo decreases fat accumulation in A. mexicanus. Finally, we identified nonsense mutations in per2, a known repressor of Pparγ, providing a possible regulatory mechanism of Pparγ in cavefish. Taken together, our study reveals that upregulated Pparγ promotes higher levels of lipogenesis in the liver and contributes to higher body fat accumulation in cavefish populations, an important adaptation to nutrient-limited environments.
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Affiliation(s)
- Shaolei Xiong
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Wei Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Howard Hughes Medical Institute, Kansas City, MO 64110, USA; National Institute of Biological Sciences, Beijing 102206, China
| | | | - Luke Olsen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular & Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jaya Krishnan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jenna Persons
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Kyle Medley
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Robert Peuß
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Institute for Evolution and Biodiversity, University of Münster, Münster 48149, Germany
| | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Shiyuan Chen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ning Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Nancy Thomas
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - John M Miles
- Department of Medicine, Division of Metabolism, Endocrinology & Genetics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Howard Hughes Medical Institute, Kansas City, MO 64110, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular & Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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7
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Moran RL, Jaggard JB, Roback EY, Kenzior A, Rohner N, Kowalko JE, Ornelas-García CP, McGaugh SE, Keene AC. Hybridization underlies localized trait evolution in cavefish. iScience 2022; 25:103778. [PMID: 35146393 PMCID: PMC8819016 DOI: 10.1016/j.isci.2022.103778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/13/2021] [Accepted: 01/12/2022] [Indexed: 11/04/2022] Open
Abstract
Introgressive hybridization may play an integral role in local adaptation and speciation (Taylor and Larson, 2019). In the Mexican tetra Astyanax mexicanus, cave populations have repeatedly evolved traits including eye loss, sleep loss, and albinism. Of the 30 caves inhabited by A. mexicanus, Chica cave is unique because it contains multiple pools inhabited by putative hybrids between surface and cave populations (Mitchell et al., 1977), providing an opportunity to investigate the impact of hybridization on complex trait evolution. We show that hybridization between cave and surface populations may contribute to localized variation in traits associated with cave evolution, including pigmentation, eye development, and sleep. We also uncover an example of convergent evolution in a circadian clock gene in multiple cavefish lineages and burrowing mammals, suggesting a shared genetic mechanism underlying circadian disruption in subterranean vertebrates. Our results provide insight into the role of hybridization in facilitating phenotypic evolution. Hybridization leads to a localized difference in sleep duration within a single cave Genomic analysis identifies coding differences in Cry1A across cave pools Changes in Cry1A appear to be conserved in cavefish and burrowing mammals
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Mack KL, Jaggard JB, Persons JL, Roback EY, Passow CN, Stanhope BA, Ferrufino E, Tsuchiya D, Smith SE, Slaughter BD, Kowalko J, Rohner N, Keene AC, McGaugh SE. Repeated evolution of circadian clock dysregulation in cavefish populations. PLoS Genet 2021; 17:e1009642. [PMID: 34252077 PMCID: PMC8297936 DOI: 10.1371/journal.pgen.1009642] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 07/22/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022] Open
Abstract
Circadian rhythms are nearly ubiquitous throughout nature, suggesting they are critical for survival in diverse environments. Organisms inhabiting largely arrhythmic environments, such as caves, offer a unique opportunity to study the evolution of circadian rhythms in response to changing ecological pressures. Populations of the Mexican tetra, Astyanax mexicanus, have repeatedly invaded caves from surface rivers, where individuals must contend with perpetual darkness, reduced food availability, and limited fluctuations in daily environmental cues. To investigate the molecular basis for evolved changes in circadian rhythms, we investigated rhythmic transcription across multiple independently-evolved cavefish populations. Our findings reveal that evolution in a cave environment has led to the repeated disruption of the endogenous biological clock, and its entrainment by light. The circadian transcriptome shows widespread reductions and losses of rhythmic transcription and changes to the timing of the activation/repression of core-transcriptional clock. In addition to dysregulation of the core clock, we find that rhythmic transcription of the melatonin regulator aanat2 and melatonin rhythms are disrupted in cavefish under darkness. Mutants of aanat2 and core clock gene rorca disrupt diurnal regulation of sleep in A. mexicanus, phenocopying circadian modulation of sleep and activity phenotypes of cave populations. Together, these findings reveal multiple independent mechanisms for loss of circadian rhythms in cavefish populations and provide a platform for studying how evolved changes in the biological clock can contribute to variation in sleep and circadian behavior.
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Affiliation(s)
- Katya L. Mack
- Biology, Stanford University, Stanford, California, United States of America
| | - James B. Jaggard
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
- Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, United States of America
| | - Jenna L. Persons
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Emma Y. Roback
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Courtney N. Passow
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Bethany A. Stanhope
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
| | - Estephany Ferrufino
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
- Wilkes Honors College, Florida Atlantic University, Jupiter, Florida, United States of America
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Sarah E. Smith
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Brian D. Slaughter
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Johanna Kowalko
- Wilkes Honors College, Florida Atlantic University, Jupiter, Florida, United States of America
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Alex C. Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, United States of America
| | - Suzanne E. McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
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9
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Policarpo M, Fumey J, Lafargeas P, Naquin D, Thermes C, Naville M, Dechaud C, Volff JN, Cabau C, Klopp C, Møller PR, Bernatchez L, García-Machado E, Rétaux S, Casane D. Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals. Mol Biol Evol 2021; 38:589-605. [PMID: 32986833 PMCID: PMC7826195 DOI: 10.1093/molbev/msaa249] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and nonvisual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time, and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems.
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Affiliation(s)
- Maxime Policarpo
- CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Julien Fumey
- CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Lafargeas
- CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Cedric Cabau
- SIGENAE, GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Christophe Klopp
- INRAE, SIGENAE, Genotoul Bioinfo, MIAT UR875, Castanet Tolosan, France
| | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen Ø, Denmark
| | - Louis Bernatchez
- Department of Biology, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Erik García-Machado
- Department of Biology, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada.,Centro de Investigaciones Marinas, Universidad de La Habana, La Habana, Cuba
| | - Sylvie Rétaux
- CNRS, Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Didier Casane
- CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, Gif-sur-Yvette, France.,UFR Sciences du Vivant, Université de Paris, Paris, France
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10
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Schalm G, Bruns K, Drachenberg N, Geyer N, Foulkes NS, Bertolucci C, Gerlach G. Finding Nemo's clock reveals switch from nocturnal to diurnal activity. Sci Rep 2021; 11:6801. [PMID: 33762724 PMCID: PMC7990958 DOI: 10.1038/s41598-021-86244-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/12/2021] [Indexed: 11/08/2022] Open
Abstract
Timing mechanisms play a key role in the biology of coral reef fish. Typically, fish larvae leave their reef after hatching, stay for a period in the open ocean before returning to the reef for settlement. During this dispersal, larvae use a time-compensated sun compass for orientation. However, the timing of settlement and how coral reef fish keep track of time via endogenous timing mechanisms is poorly understood. Here, we have studied the behavioural and genetic basis of diel rhythms in the clown anemonefish Amphiprion ocellaris. We document a behavioural shift from nocturnal larvae to diurnal adults, while juveniles show an intermediate pattern of activity which potentially indicates flexibility in the timing of settlement on a host anemone. qRTPCR analysis of six core circadian clock genes (bmal1, clocka, cry1b, per1b, per2, per3) reveals rhythmic gene expression patterns that are comparable in larvae and juveniles, and so do not reflect the corresponding activity changes. By establishing an embryonic cell line, we demonstrate that clown anemonefish possess an endogenous clock with similar properties to that of the zebrafish circadian clock. Furthermore, our study provides a first basis to study the multi-layered interaction of clocks from fish, anemones and their zooxanthellae endosymbionts.
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Affiliation(s)
- Gregor Schalm
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Ammerländer Heerstr. 114-118, 26129, Oldenburg, Germany.
| | - Kristina Bruns
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Ammerländer Heerstr. 114-118, 26129, Oldenburg, Germany
| | - Nina Drachenberg
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Ammerländer Heerstr. 114-118, 26129, Oldenburg, Germany
| | - Nathalie Geyer
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicholas S Foulkes
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Cristiano Bertolucci
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121, Ferrara, Italy
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, 80121, Naples, Italy
| | - Gabriele Gerlach
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Ammerländer Heerstr. 114-118, 26129, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Ammerländer Heerstr. 231, 26129, Oldenburg, Germany
- Centre of Excellence for Coral Reef Studies and School of Marine and Tropical Biology, James Cook University, Townsville, QLD, 4811, Australia
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Moreno JM, Jesus TF, Coelho MM, Sousa VC. Adaptation and convergence in circadian-related genes in Iberian freshwater fish. BMC Ecol Evol 2021; 21:38. [PMID: 33685402 PMCID: PMC7941933 DOI: 10.1186/s12862-021-01767-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock - positive loop) and repress expression (cryptochrome (cry) and period (per) - negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g., light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type. RESULTS We identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in 12 of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop, with 55 putatively adaptive substitutions, 16 located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence. We found evidence for increased nonsynonymous substitution rate in convergent lineages, likely due to positive selection at 27 sites, mostly in cry genes. CONCLUSIONS Our results support that temperature may be a selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.
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Affiliation(s)
- João M Moreno
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Tiago F Jesus
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Maria M Coelho
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Vitor C Sousa
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
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12
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Zhao Y, Chen H, Li C, Chen S, Xiao H. Comparative Transcriptomics Reveals the Molecular Genetic Basis of Cave Adaptability in Sinocyclocheilus Fish Species. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.589039] [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
Cavefish evolved a series of distinct survival mechanisms for adaptation to cave habitat. Such mechanisms include loss of eyesight and pigmentation, sensitive sensory organs, unique dietary preferences, and predation behavior. Thus, it is of great interest to understand the mechanisms underlying these adaptability traits of troglobites. The teleost genus Sinocyclocheilus (Cypriniformes: Cyprinidae) is endemic to China and has more than 70 species reported (including over 30 cavefish species). High species diversity and diverse phenotypes make the Sinocyclocheilus as an outstanding model for studying speciation and adaptive evolution. In this study, we conducted a comparative transcriptomics study on the brain tissues of two Sinocyclocheilus species (surface-dwelling species – Sinocyclocheilus malacopterus and semi-cave-dwelling species – Sinocyclocheilus rhinocerous living in the same water body. A total of 425,188,768 clean reads were generated, which contributed to 102,839 Unigenes. Bioinformatic analysis revealed a total of 3,289 differentially expressed genes (DEGs) between two species Comparing to S. malacopterus, 2,598 and 691 DEGs were found to be respectively, down-regulated and up-regulated in S. rhinocerous. Furthermore, it is also found tens of DEGs related to cave adaptability such as insulin secretion regulation (MafA, MafB, MafK, BRSK, and CDK16) and troglomorphic traits formation (CEP290, nmnat1, coasy, and pqbp1) in the cave-dwelling S. rhinocerous. Interestingly, most of the DEGs were found to be down-regulated in cavefish species and this trend of DEGs expression was confirmed through qPCR experiments. This study would provide an appropriate genetic basis for future studies on the formation of troglomorphic traits and adaptability characters of troglobites, and improve our understanding of mechanisms of cave adaptation.
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Ceinos RM, Chivite M, López-Patiño MA, Naderi F, Soengas JL, Foulkes NS, Míguez JM. Differential circadian and light-driven rhythmicity of clock gene expression and behaviour in the turbot, Scophthalmus maximus. PLoS One 2019; 14:e0219153. [PMID: 31276539 PMCID: PMC6611576 DOI: 10.1371/journal.pone.0219153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/17/2019] [Indexed: 12/19/2022] Open
Abstract
In fish, the circadian clock represents a key regulator of many aspects of biology and is controlled by combinations of abiotic and biotic factors. These environmental factors are frequently manipulated in fish farms as part of strategies designed to maximize productivity. The flatfish turbot, Scophthalmus maximus, represents one of the most important species within the aquaculture sector in Asia and Europe. Despite the strategic importance of this species, the function and regulation of the turbot circadian system remains poorly understood. Here, we have characterized the core circadian clock genes, clock1, per1, per2 and cry1 in turbot and have studied their daily expression in various tissues under a range of lighting conditions and feeding regimes. We have also explored the influence of light and feeding time on locomotor activity. Rhythmic expression of the four core clock genes was observed in all tissues studied under light dark (LD) cycle conditions. Rhythmicity of clock gene expression persisted upon transfer to artificial free running, constant conditions confirming their endogenous circadian clock control. Furthermore, turbot showed daily cycles of locomotor activity and food anticipatory activity (FAA) under LD and scheduled-feeding, with the activity phase as well as FAA coinciding with and being dependent upon exposure to light. Thus, while FAA was absent under constant dark (DD) conditions, it was still detected in constant light (LL). In contrast, general locomotor activity was arrhythmic in both constant darkness and constant light, pointing to a major contribution of light, in concert with the circadian clock, in timing locomotor activity in this species. Our data represents an important contribution to our understanding of the circadian timing system in the turbot and thereby the optimization of rearing protocols and the improvement of the well-being of turbot within fish farming environments.
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Affiliation(s)
- Rosa M. Ceinos
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
- * E-mail:
| | - Mauro Chivite
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
| | - Marcos A. López-Patiño
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
| | - Fatemeh Naderi
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
| | - José L. Soengas
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
| | - Nicholas S. Foulkes
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Jesús M. Míguez
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo (Pontevedra), Spain
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14
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Evolution Shapes the Gene Expression Response to Oxidative Stress. Int J Mol Sci 2019; 20:ijms20123040. [PMID: 31234431 PMCID: PMC6627103 DOI: 10.3390/ijms20123040] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
Reactive oxygen species (ROS) play a key role in cell physiology and function. ROS represents a potential source of damage for many macromolecules including DNA. It is thought that daily changes in oxidative stress levels were an important early factor driving evolution of the circadian clock which enables organisms to predict changes in ROS levels before they actually occur and thereby optimally coordinate survival strategies. It is clear that ROS, at relatively low levels, can serve as an important signaling molecule and also serves as a key regulator of gene expression. Therefore, the mechanisms that have evolved to survive or harness these effects of ROS are ancient evolutionary adaptations that are tightly interconnected with most aspects of cellular physiology. Our understanding of these mechanisms has been mainly based on studies using a relatively small group of genetic models. However, we know comparatively little about how these mechanisms are conserved or have adapted during evolution under different environmental conditions. In this review, we describe recent work that has revealed significant species-specific differences in the gene expression response to ROS by exploring diverse organisms. This evidence supports the notion that during evolution, rather than being highly conserved, there is inherent plasticity in the molecular mechanisms responding to oxidative stress.
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Circadian Clocks in Fish-What Have We Learned so far? BIOLOGY 2019; 8:biology8010017. [PMID: 30893815 PMCID: PMC6466151 DOI: 10.3390/biology8010017] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/07/2019] [Accepted: 03/09/2019] [Indexed: 12/24/2022]
Abstract
Zebrafish represent the one alternative vertebrate, genetic model system to mice that can be easily manipulated in a laboratory setting. With the teleost Medaka (Oryzias latipes), which now has a significant following, and over 30,000 other fish species worldwide, there is great potential to study the biology of environmental adaptation using teleosts. Zebrafish are primarily used for research on developmental biology, for obvious reasons. However, fish in general have also contributed to our understanding of circadian clock biology in the broadest sense. In this review, we will discuss selected areas where this contribution seems most unique. This will include a discussion of the issue of central versus peripheral clocks, in which zebrafish played an early role; the global nature of light sensitivity; and the critical role played by light in regulating cell biology. In addition, we also discuss the importance of the clock in controlling the timing of fundamental aspects of cell biology, such as the temporal control of the cell cycle. Many of these findings are applicable to the majority of vertebrate species. However, some reflect the unique manner in which “fish” can solve biological problems, in an evolutionary context. Genome duplication events simply mean that many fish species have more gene copies to “throw at a problem”, and evolution seems to have taken advantage of this “gene abundance”. How this relates to their poor cousins, the mammals, remains to be seen.
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Gómez-Boronat M, Sáiz N, Delgado MJ, de Pedro N, Isorna E. Time-Lag in Feeding Schedule Acts as a Stressor That Alters Circadian Oscillators in Goldfish. Front Physiol 2018; 9:1749. [PMID: 30568601 PMCID: PMC6290069 DOI: 10.3389/fphys.2018.01749] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022] Open
Abstract
The circadian system controls temporal homeostasis in all vertebrates. The light-dark (LD) cycle is the most important zeitgeber (“time giver”) of circadian system, but feeding time also acts as a potent synchronizer in the functional organization of the teleost circadian system. In mammals is well known that food intake during the rest phase promotes circadian desynchrony which has been associated with metabolic diseases. However, the impact of a misalignment of LD and feeding cycles in the entrainment of fish circadian oscillators is largely unknown. The objective of this work was to investigate how a time-lag feeding alters temporal homeostasis and if this could be considered a stressor. To this aim, goldfish maintained under a 12 h light-12 h darkness were fed at mid-photophase (SF6) or mid-scotophase (SF18). Daily rhythms of locomotor activity, clock genes expression in hypothalamus, liver, and head kidney, and circulating cortisol were studied. Results showed that SF6 fish showed daily rhythms of bmal1a and clock1a in all studied tissues, being in antiphase with rhythms of per1 genes, as expected for proper functioning clocks. The 12 h shift in scheduled feeding induced a short phase advance (4–5-h) of the clock genes daily rhythms in the hypothalamus, while in the liver the shift for clock genes expression rhythms was the same that the feeding time shift (∼12 h). In head kidney, acrophases of per genes underwent a 12-h shift in SF18 animals, but only 6 h shift for clock1a. Plasma cortisol levels showed a significant daily rhythm in animals fed at SF6, but not in SF18 fish fed, which displayed higher cortisol values throughout the 24-h. Altogether, results indicate that hypothalamus, liver, and head kidney oscillate in phase in SF6 fish, but these clocks are desynchronized in SF18 fish, which could explain cortisol alterations. These data reinforce the hypothesis that the misalignment of external cues (daily photocycle and feeding time) alters fish temporal homeostasis and it might be considered a stressor for the animals.
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Affiliation(s)
- Miguel Gómez-Boronat
- Departamento de Genética, Fisiología y Microbiología, Unidad Docente de Fisiología Animal, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Nuria Sáiz
- Departamento de Genética, Fisiología y Microbiología, Unidad Docente de Fisiología Animal, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - María J Delgado
- Departamento de Genética, Fisiología y Microbiología, Unidad Docente de Fisiología Animal, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Nuria de Pedro
- Departamento de Genética, Fisiología y Microbiología, Unidad Docente de Fisiología Animal, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Esther Isorna
- Departamento de Genética, Fisiología y Microbiología, Unidad Docente de Fisiología Animal, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
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