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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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Drabeck DH, Wiese J, Gilbertson E, Arroyave J, Stiassny MLJ, Alter SE, Borowsky R, Hendrickson DA, Arcila D, McGaugh SE. Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments. Proc Biol Sci 2024; 291:20232847. [PMID: 38864338 DOI: 10.1098/rspb.2023.2847] [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: 12/15/2023] [Accepted: 05/03/2024] [Indexed: 06/13/2024] Open
Abstract
Gene loss is an important mechanism for evolution in low-light or cave environments where visual adaptations often involve a reduction or loss of eyesight. The plaat gene family encodes phospholipases essential for the degradation of organelles in the lens of the eye. These phospholipases translocate to damaged organelle membranes, inducing them to rupture. This rupture is required for lens transparency and is essential for developing a functioning eye. Plaat3 is thought to be responsible for this role in mammals, while plaat1 is thought to be responsible in other vertebrates. We used a macroevolutionary approach and comparative genomics to examine the origin, loss, synteny and selection of plaat1 across bony fishes and tetrapods. We showed that plaat1 (probably ancestral to all bony fish + tetrapods) has been lost in squamates and is significantly degraded in lineages of low-visual-acuity and blind mammals and fishes. Our findings suggest that plaat1 is important for visual acuity across bony vertebrates, and that its loss through relaxed selection and pseudogenization may have played a role in the repeated evolution of visual systems in low-light environments. Our study sheds light on the importance of gene-loss in trait evolution and provides insights into the mechanisms underlying visual acuity in low-light environments.
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Affiliation(s)
- Danielle H Drabeck
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St, Paul, MN 55108, USA
| | - Jonathan Wiese
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St, Paul, MN 55108, USA
| | - Erin Gilbertson
- Department of Epidemiology and Biostatistics, University of San Francisco, University of California, San Francisco, CA, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, NY 10024, USA
| | - S Elizabeth Alter
- Biology and Chemistry Department, California State University Monterey Bay, Chapman Academic Science Center, Seaside, CA, USA
| | - Richard Borowsky
- Department of Biology, New York University, Washington Square, New York, NY 10003, USA
| | - Dean A Hendrickson
- Biodiversity Center, Texas Natural History Collections, University of Texas at Austin, Austin, TX 78758, USA
| | - Dahiana Arcila
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St, Paul, MN 55108, USA
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Wang K, Wang J, Liang B, Chang J, Zhu Y, Chen J, Agnarsson I, Li D, Peng Y, Liu J. Eyeless cave-dwelling Leptonetela spiders still rely on light. SCIENCE ADVANCES 2023; 9:eadj0348. [PMID: 38117895 PMCID: PMC10732526 DOI: 10.1126/sciadv.adj0348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
Subterranean animals living in perpetual darkness may maintain photoresponse. However, the evolutionary processes behind the conflict between eye loss and maintenance of the photoresponse remain largely unknown. We used Leptonetela spiders to investigate the driving forces behind the maintenance of the photoresponse in cave-dwelling spiders. Our behavioral experiments showed that all eyeless/reduced-eyed cave-dwelling species retained photophobic response and that they had substantially decreased survival at cave entrances due to weak drought resistance. The transcriptomic analysis demonstrated that nearly all phototransduction pathway genes were present and that all tested phototransduction pathway genes were subjected to strong functional constraints in cave-dwelling species. Our results suggest that cave-dwelling eyeless spiders still use light and that light detection likely plays a role in avoiding the cave entrance habitat. This study confirms that some eyeless subterranean animals have retained their photosensitivity due to natural selection and provides a case of mismatch between phenotype and genotype or physiological function in a long-term evolutionary process.
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Affiliation(s)
- Kai Wang
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jinhui Wang
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Bing Liang
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jian Chang
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yang Zhu
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jian Chen
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Ingi Agnarsson
- Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 102 Reykjavik, Iceland
| | - Daiqin Li
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yu Peng
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jie Liu
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
- School of Nuclear Technology and Chemistry and Biology, Hubei University of Science and Technology, Xianning, Hubei 437100, China
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Garduño-Sánchez MAA, De Jesus-Bonilla V, Perea S, Miranda-Gamboa R, Herrera-García A, De la Maza Benignos M, Ornelas-García CP. Mitochondrial phylogeography and molecular evolution of the rhodopsin visual pigment in troglobitic populations of Astyanax mexicanus (De Filippi, 1853). Zool Res 2023; 44:761-775. [PMID: 37464933 PMCID: PMC10415764 DOI: 10.24272/j.issn.2095-8137.2022.437] [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: 03/10/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
Cave-adapted animals provide a unique opportunity to study the evolutionary mechanisms underlying phenotypic, metabolic, behavioral, and genetic evolution in response to cave environments. The Mexican tetra ( Astyanax mexicanus) is considered a unique model system as it shows both surface and cave-dwelling morphs. To date, at least 33 different cave populations have been identified, with phylogenetic studies suggesting an origin from at least two independent surface lineages, thereby providing a unique opportunity to study parallel evolution. In the present study, we carried out the most exhaustive phylogeographic study of A. mexicanus to date, including cave and surface localities, using two mitochondrial markers (cytochrome b (cyt b) and cytochrome c oxidase subunit I ( COI)) and nuclear rhodopsin visual pigment ( rho). Additionally, we inferred the molecular evolution of rho within the two contrasting environments (cave and surface) and across three geographic regions (Sierra de El Abra, Sierra de Guatemala, and Micos). In total, 267 individuals were sequenced for the two mitochondrial fragments and 268 individuals were sequenced for the rho visual pigment from 22 cave and 46 surface populations. Phylogeographic results based on the mitochondrial data supported the two-lineage hypothesis, except for the Pachón and Chica caves, whose introgression has been largely documented. The Sierra de El Abra region depicted the largest genetic diversity, followed by the Sierra de Guatemala region. Regarding the phylogeographic patterns of rho, we recovered exclusive haplogroups for the Sierra de El Abra (Haplogroup I) and Sierra de Guatemala regions (Haplogroup IV). Moreover, a 544 bp deletion in the rho gene was observed in the Escondido cave population from Sierra de Guatemala, reducing the protein from seven to three intramembrane domains. This change may produce a loss-of-function (LOF) but requires further investigation. Regarding nonsynonymous ( dN) and synonymous ( dS) substitution rates (omega values ω), our results revealed the prevailing influence of purifying selection upon the rho pigment for both cave and surface populations (ω<1), but relaxation at the El Abra region. Notably, in contrast to the other two regions, we observed an increase in the number of dN mutations for Sierra de El Abra. However, given that a LOF was exclusively identified in the Sierra de Guatemala region, we cannot dismiss the possibility of a pleiotropic effect on the Rho protein.
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Affiliation(s)
- Marco A A Garduño-Sánchez
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04510, México
- Posgrado en Ciencias Biológicas, Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04510, México
| | - Vladimir De Jesus-Bonilla
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04510, México
- Licenciatura en Ciencias Forenses, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, México City, C.P. 04510, México
| | - Silvia Perea
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04510, México
| | - Ramses Miranda-Gamboa
- Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Temixco, Morelos C.P. 62580, Mexico
| | - Andrea Herrera-García
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04510, México
| | - Mauricio De la Maza Benignos
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, C.P. 66450, México
| | - Claudia Patricia Ornelas-García
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04510, México. E-mail:
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5
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Li S, Hannenhalli S, Ovcharenko I. De novo human brain enhancers created by single-nucleotide mutations. SCIENCE ADVANCES 2023; 9:eadd2911. [PMID: 36791193 PMCID: PMC9931207 DOI: 10.1126/sciadv.add2911] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 01/12/2023] [Indexed: 05/30/2023]
Abstract
Advanced human cognition is attributed to increased neocortex size and complexity, but the underlying evolutionary and regulatory mechanisms are largely unknown. Using human and macaque embryonic neocortical H3K27ac data coupled with a deep learning model of enhancers, we identified ~4000 enhancer gains in humans, which, per our model, can often be attributed to single-nucleotide essential mutations. Our analyses suggest that functional gains in embryonic brain development are associated with de novo enhancers whose putative target genes exhibit increased expression in progenitor cells and interneurons and partake in critical neural developmental processes. Essential mutations alter enhancer activity through altered binding of key transcription factors (TFs) of embryonic neocortex, including ISL1, POU3F2, PITX1/2, and several SOX TFs, and are associated with central nervous system disorders. Overall, our results suggest that essential mutations lead to gain of embryonic neocortex enhancers, which orchestrate expression of genes involved in critical developmental processes associated with human cognition.
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Affiliation(s)
- Shan Li
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
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6
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Pavlova VV, Krylov VV. Cavefishes in Chronobiological Research: A Narrative Review. Clocks Sleep 2023; 5:62-71. [PMID: 36810844 PMCID: PMC9944484 DOI: 10.3390/clockssleep5010007] [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: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Cavefish are vertebrates living in extreme subterranean environments with no light, temperature changes, and limited food. Circadian rhythms in these fish are suppressed in natural habitats. However, they can be found in artificial light-dark cycles and other zeitgebers. The molecular circadian clock has its peculiarities in cavefish. In Astyanax mexicanus, the core clock mechanism is tonically repressed in the caves due to the overactivation of the light input pathway. A lack of functional light input pathway but rather the entrainment of circadian genes' expression by scheduled feeding were revealed in more ancient Phreatichthys andruzzii. Different evolutionarily determined irregularities in the functioning of molecular circadian oscillators can be expected in other cavefish. The unique property of some species is the existence of surface and cave forms. Along with the ease of maintenance and breeding, it made cavefish a promising model for chronobiological studies. At the same time, a divergence of the circadian system between cavefish populations requires the strain of origin to be indicated in further research.
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Affiliation(s)
- Vera V. Pavlova
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia
| | - Viacheslav V. Krylov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia
- Scientific and Technological Center of Unique Instrumentation, Russian Academy of Sciences, 117342 Moscow, Russia
- Correspondence:
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7
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Zhao Q, Shao F, Li Y, Yi SV, Peng Z. Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes. Mol Ecol 2022; 31:5831-5845. [PMID: 36125323 PMCID: PMC9828065 DOI: 10.1111/mec.16700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.
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Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Department of Laboratory Animal Science, College of Basic Medical SciencesArmy Medical University (Third Military Medical University)ChongqingChina
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Key Laboratory of Sichuan Province for Fish Conservation and Utilization in the Upper Reaches of the Yangtze RiverNeijiang Normal University College of Life SciencesNeijiangChina
| | - Soojin V. Yi
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Academy of Plateau Science and SustainabilityQinghai Normal UniversityXiningChina
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8
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Comparisons of chemosensory gene repertoires in human and non-human feeding Anopheles mosquitoes link olfactory genes to anthropophily. iScience 2022; 25:104521. [PMID: 35754720 PMCID: PMC9213756 DOI: 10.1016/j.isci.2022.104521] [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: 12/09/2021] [Revised: 05/08/2022] [Accepted: 05/30/2022] [Indexed: 11/06/2022] Open
Abstract
We investigate the genetic basis of anthropophily (human host use) in a non-model mosquito species group, the Anopheles farauti complex from the southwest Pacific. This complex has experienced multiple transitions from anthropophily to zoophily, contrasting with well-studied systems (the global species Aedes aegypti and the African Anopheles gambiae complex) that have evolved to be specialist anthropophiles. By performing tests of selection and assessing evolutionary patterns for >200 olfactory genes from nine genomes, we identify several candidate genes associated with differences in anthropophily in this complex. Based on evolutionary patterns (phylogenetic relationships, fixed amino acid differences, and structural differences) as well as results from selection analyses, we identify numerous genes that are likely to play an important role in mosquitoes’ ability to detect humans as hosts. Our findings contribute to the understanding of the evolution of insect olfactory gene families and mosquito host preference as well as having potential applied outcomes. Genomes of Anopheles mosquitoes with differing host preferences were sequenced Evolutionary comparisons were performed on >200 insect chemosensory genes These comparisons revealed candidate genes involved in human feeding Two of the main candidates identified were co-receptor Ir8a and Or75
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Chen Y, Wang D, Li N, Wang D, Liu XH, Song Y. Accelerated evolution of Vkorc1 in desert rodent species reveals genetic preadaptation to anticoagulant rodenticides. PEST MANAGEMENT SCIENCE 2022; 78:2704-2713. [PMID: 35394111 DOI: 10.1002/ps.6905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 03/23/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Some rodent species living in arid areas show elevated physiological tolerance to anti-vitamin K rodenticides (AVKs), which seems to be due to some unknown selective pressures that rodents may experience in desert habitats. Genes involved in the ϒ-carboxylation of blood coagulation, including vitamin K epoxide reductase complex, subunit 1 (Vkorc1), ϒ-glutamyl-carboxylase (Ggcx) and NAD(P)H quinone one dehydrogenase (Nqo1) are associated with anticoagulant resistance, or some levels of elevated tolerance, in rodents. To detect whether the DNA sequences of the three genes are also under natural selection in the desert rodent species, we analyzed the Vkorc1, Ggcx and Nqo1 genes of the desert rodents and compared them with other rodent species. RESULTS We found an accelerated evolutionary rate in Vkorc1 of desert rodents, especially in Mus spretus, Nannospalax galili and Psammomys obesus. By contrast, signals of positive selection were absent for Ggcx and Nqo1 in all species. Mapping the amino acid variations on the VKORC1 protein three-dimensional model suggested most interspecific amino acid variations occur on the outer surface of the VKORC1 pocket, whereas most intraspecific amino acid changes and known AVK resistance mutations occurred on the inner surface and endoplasmic reticulum luminal loop regions. Some desert-species-specific amino acid variations were found on the positions where known resistance mutations occurred, indicating these variations might be related to the elevated physical tolerance to AVKs in desert rodents. CONCLUSION The evolution of Vkorc1 has been accelerated in some desert rodent species, indicating genetic preadaptation to anticoagulant rodenticides. Positive selection and relaxed selection have been detected in Psammomys obesus and Nannospalax galili, indicating the two rodent species might also show tolerance to AVKs, which needs further verification. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Yan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dawei Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ning Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Deng Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xiao-Hui Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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10
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Langille BL, Tierney SM, Bertozzi T, Beasley-Hall PG, Bradford TM, Fagan-Jeffries EP, Hyde J, Leijs R, Richardson M, Saint KM, Stringer DN, Villastrigo A, Humphreys WF, Austin AD, Cooper SJB. Parallel decay of vision genes in subterranean water beetles. Mol Phylogenet Evol 2022; 173:107522. [PMID: 35595008 DOI: 10.1016/j.ympev.2022.107522] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022]
Abstract
In the framework of neutral theory of molecular evolution, genes specific to the development and function of eyes in subterranean animals living in permanent darkness are expected to evolve by relaxed selection, ultimately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolutionary time remains controversial. In previous studies, we characterized an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon capture, we present evidence of parallel coding sequence decay, resulting from the accumulation of frameshift mutations and premature stop codons, in eight phototransduction genes (arrestins, opsins, ninaC and transient receptor potential channel genes) in 32 subterranean species in contrast to surface species, where these genes have open reading frames. Our results provide strong evidence to support neutral evolutionary processes as a major contributing factor to the loss of phototransduction genes in subterranean animals, with the ultimate fate being the irreversible loss of a light detection system.
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Affiliation(s)
- Barbara L Langille
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia.
| | - Simon M Tierney
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Terry Bertozzi
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Perry G Beasley-Hall
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Tessa M Bradford
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Erinn P Fagan-Jeffries
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Josephine Hyde
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Western Australia Department of Biodiversity Conservation and Attractions, Kensington, WA 6151, Australia
| | - Remko Leijs
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Matthew Richardson
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Kathleen M Saint
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Danielle N Stringer
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Adrián Villastrigo
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia; Institute of Evolutionary Biology, Passeig Marítim de la Barceloneta, 37-49, 08003, Spain
| | - William F Humphreys
- Western Australian Museum, Locked Bag 40, Welshpool DC, WA 6986, Australia; School of Animal Biology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
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11
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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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12
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Regulation of ddb2 expression in blind cavefish and zebrafish reveals plasticity in the control of sunlight-induced DNA damage repair. PLoS Genet 2021; 17:e1009356. [PMID: 33544716 PMCID: PMC7891740 DOI: 10.1371/journal.pgen.1009356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/18/2021] [Accepted: 01/12/2021] [Indexed: 11/19/2022] Open
Abstract
We have gained considerable insight into the mechanisms which recognize and repair DNA damage, but how they adapt to extreme environmental challenges remains poorly understood. Cavefish have proven to be fascinating models for exploring the evolution of DNA repair in the complete absence of UV-induced DNA damage and light. We have previously revealed that the Somalian cavefish Phreatichthys andruzzii, lacks photoreactivation repair via the loss of light, UV and ROS-induced photolyase gene transcription mediated by D-box enhancer elements. Here, we explore whether other systems repairing UV-induced DNA damage have been similarly affected in this cavefish model. By performing a comparative study using P. andruzzii and the surface-dwelling zebrafish, we provide evidence for a conservation of sunlight-regulated Nucleotide Excision Repair (NER). Specifically, the expression of the ddb2 gene which encodes a key NER recognition factor is robustly induced following exposure to light, UV and oxidative stress in both species. As in the case of the photolyase genes, D-boxes in the ddb2 promoter are sufficient to induce transcription in zebrafish. Interestingly, despite the loss of D-box-regulated photolyase gene expression in P. andruzzii, the D-box is required for ddb2 induction by visible light and oxidative stress in cavefish. However, in the cavefish ddb2 gene this D-box-mediated induction requires cooperation with an adjacent, highly conserved E2F element. Furthermore, while in zebrafish UV-induced ddb2 expression results from transcriptional activation accompanied by stabilization of the ddb2 mRNA, in P. andruzzii UV induces ddb2 expression exclusively via an increase in mRNA stability. Thus, we reveal plasticity in the transcriptional and post transcriptional mechanisms regulating the repair of sunlight-induced DNA damage under long-term environmental challenges.
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13
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Kirchner S, Sattmann H, Haring E, Victor R, Kruckenhauser L. Hidden diversity—Delimitation of cryptic species and phylogeography of the cyprinid
Garra
species complex in Northern Oman. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Sandra Kirchner
- Department of Evolutionary Biology University of Vienna Vienna Austria
- Central Research Laboratories Natural History Museum Vienna Vienna Austria
| | - Helmut Sattmann
- Third Zoological Department Natural History Museum Vienna Vienna Austria
| | - Elisabeth Haring
- Department of Evolutionary Biology University of Vienna Vienna Austria
- Central Research Laboratories Natural History Museum Vienna Vienna Austria
| | | | - Luise Kruckenhauser
- Department of Evolutionary Biology University of Vienna Vienna Austria
- Central Research Laboratories Natural History Museum Vienna Vienna Austria
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14
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Termignoni-Garcia F, Louder MIM, Balakrishnan CN, O’Connell L, Edwards SV. Prospects for sociogenomics in avian cooperative breeding and parental care. Curr Zool 2020; 66:293-306. [PMID: 32440290 PMCID: PMC7233861 DOI: 10.1093/cz/zoz057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/20/2019] [Indexed: 01/08/2023] Open
Abstract
For the last 40 years, the study of cooperative breeding (CB) in birds has proceeded primarily in the context of discovering the ecological, geographical, and behavioral drivers of helping. The advent of molecular tools in the early 1990s assisted in clarifying the relatedness of helpers to those helped, in some cases, confirming predictions of kin selection theory. Methods for genome-wide analysis of sequence variation, gene expression, and epigenetics promise to add new dimensions to our understanding of avian CB, primarily in the area of molecular and developmental correlates of delayed breeding and dispersal, as well as the ontogeny of achieving parental status in nature. Here, we outline key ways in which modern -omics approaches, in particular genome sequencing, transcriptomics, and epigenetic profiling such as ATAC-seq, can be used to add a new level of analysis of avian CB. Building on recent and ongoing studies of avian social behavior and sociogenomics, we review how high-throughput sequencing of a focal species or clade can provide a robust foundation for downstream, context-dependent destructive and non-destructive sampling of specific tissues or physiological states in the field for analysis of gene expression and epigenetics. -Omics approaches have the potential to inform not only studies of the diversification of CB over evolutionary time, but real-time analyses of behavioral interactions in the field or lab. Sociogenomics of birds represents a new branch in the network of methods used to study CB, and can help clarify ways in which the different levels of analysis of CB ultimately interact in novel and unexpected ways.
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Affiliation(s)
- Flavia Termignoni-Garcia
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Matthew I M Louder
- International Research Center for Neurointelligence, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Lauren O’Connell
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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15
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Schneider K, Adams CE, Elmer KR. Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids. BMC Genomics 2019; 20:1010. [PMID: 31870285 PMCID: PMC6929470 DOI: 10.1186/s12864-019-6361-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/01/2019] [Indexed: 12/11/2022] Open
Abstract
Background Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup. Results All selection analyses are based on Coregonus and Salvelinus compared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such as ap1m2, involved in immunity and development, and slc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genes syn3, with a role in neural processes, and ctsk, involved in bone remodelling. Conclusions Our approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.
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Affiliation(s)
- Kevin Schneider
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, G63 0AW, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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16
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Simon N, Fujita S, Porter M, Yoshizawa M. Expression of extraocular opsin genes and light-dependent basal activity of blind cavefish. PeerJ 2019; 7:e8148. [PMID: 31871836 PMCID: PMC6924323 DOI: 10.7717/peerj.8148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/03/2019] [Indexed: 12/26/2022] Open
Abstract
Background Animals living in well-lit environments utilize optical stimuli for detecting visual information, regulating the homeostatic pacemaker, and controlling patterns of body pigmentation. In contrast, many subterranean animal species without optical stimuli have evolved regressed binocular eyes and body pigmentation. Interestingly, some fossorial and cave-dwelling animals with regressed eyes still respond to light. These light-dependent responses may be simply evolutionary residuals or they may be adaptive, where negative phototaxis provides avoidance of predator-rich surface environments. However, the relationship between these non-ocular light responses and the underlying light-sensing Opsin proteins has not been fully elucidated. Methods To highlight the potential functions of opsins in a blind subterranean animal, we used the Mexican cave tetra to investigate opsin gene expression in the eyes and several brain regions of both surface and cave-dwelling adults. We performed database surveys, expression analyses by quantitative reverse transcription PCR (RT-qPCR), and light-dependent locomotor activity analysis using pinealectomized fish, one of the high-opsin expressing organs of cavefish. Results Based on conservative criteria, we identified 33 opsin genes in the cavefish genome. Surveys of available RNAseq data found 26 of these expressed in the surface fish eye as compared to 24 expressed in cavefish extraocular tissues, 20 of which were expressed in the brain. RT-qPCR of 26 opsins in surface and cavefish eye and brain tissues showed the highest opsin-expressing tissue in cavefish was the pineal organ, which expressed exo-rhodopsin at 72.7% of the expression levels in surface fish pineal. However, a pinealectomy resulted in no change to the light-dependent locomotor activity in juvenile cavefish and surface fish. Therefore, we conclude that, after 20,000 or more years of evolution in darkness, cavefish light-dependent basal activity is regulated by a non-pineal extraocular organ.
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Affiliation(s)
- Noah Simon
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America.,Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States of America
| | - Suguru Fujita
- Department of Biological Sciences, University of Tokyo, Tokyo, Japan
| | - Megan Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Masato Yoshizawa
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
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17
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Fuselli S. Beyond drugs: the evolution of genes involved in human response to medications. Proc Biol Sci 2019; 286:20191716. [PMID: 31640517 DOI: 10.1098/rspb.2019.1716] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The genetic variation of our species reflects human demographic history and adaptation to diverse local environments. Part of this genetic variation affects individual responses to exogenous substances, such as food, pollutants and drugs, and plays an important role in drug efficacy and safety. This review provides a synthesis of the evolution of loci implicated in human pharmacological response and metabolism, interpreted within the theoretical framework of population genetics and molecular evolution. In particular, I review and discuss key evolutionary aspects of different pharmacogenes in humans and other species, such as the relationship between the type of substrates and rate of evolution; the selective pressure exerted by landscape variables or dietary habits; expected and observed patterns of rare genetic variation. Finally, I discuss how this knowledge can be translated directly or after the implementation of specific studies, into practical guidelines.
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Affiliation(s)
- Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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18
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Sovrano VA, Potrich D, Foà A, Bertolucci C. Extra-Visual Systems in the Spatial Reorientation of Cavefish. Sci Rep 2018; 8:17698. [PMID: 30523284 PMCID: PMC6283829 DOI: 10.1038/s41598-018-36167-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 11/11/2018] [Indexed: 01/23/2023] Open
Abstract
Disoriented humans and animals are able to reorient themselves using environmental geometry ("metric properties" and "sense") and local features, also relating geometric to non-geometric information. Here we investigated the presence of these reorientation spatial skills in two species of blind cavefish (Astyanax mexicanus and Phreatichthys andruzzii), in order to understand the possible role of extra-visual senses in similar spatial tasks. In a rectangular apparatus, with all homogeneous walls (geometric condition) or in presence of a tactilely different wall (feature condition), cavefish were required to reorient themselves after passive disorientation. We provided the first evidence that blind cavefish, using extra-visual systems, were able i) to use geometric cues, provided by the shape of the tank, in order to recognize two geometric equivalent corners on the diagonal, and ii) to integrate the geometric information with the salient cue (wall with a different surface structure), in order to recover a specific corner. These findings suggest the ecological salience of the environmental geometry for spatial orientation in animals and, despite the different niches of adaptation, a potential shared background for spatial navigation. The geometric spatial encoding seems to constitute a common cognitive tool needed when the environment poses similar requirements to living organisms.
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Affiliation(s)
- Valeria Anna Sovrano
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy.
- Department of Psychology and Cognitive Science, University of Trento, Rovereto, Italy.
| | - Davide Potrich
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | - Augusto Foà
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Cristiano Bertolucci
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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19
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Zhao H, Di Mauro G, Lungu-Mitea S, Negrini P, Guarino AM, Frigato E, Braunbeck T, Ma H, Lamparter T, Vallone D, Bertolucci C, Foulkes NS. Modulation of DNA Repair Systems in Blind Cavefish during Evolution in Constant Darkness. Curr Biol 2018; 28:3229-3243.e4. [PMID: 30318355 DOI: 10.1016/j.cub.2018.08.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/19/2018] [Accepted: 08/16/2018] [Indexed: 11/18/2022]
Abstract
How the environment shapes the function and evolution of DNA repair systems is poorly understood. In a comparative study using zebrafish and the Somalian blind cavefish, Phreatichthys andruzzii, we reveal that during evolution for millions of years in continuous darkness, photoreactivation DNA repair function has been lost in P. andruzzii. We demonstrate that this loss results in part from loss-of-function mutations in pivotal DNA-repair genes. Specifically, C-terminal truncations in P. andruzzii DASH and 6-4 photolyase render these proteins predominantly cytoplasmic, with consequent loss in their functionality. In addition, we reveal a general absence of light-, UV-, and ROS-induced expression of P. andruzzii DNA-repair genes. This results from a loss of function of the D-box enhancer element, which coordinates and enhances DNA repair in response to sunlight. Our results point to P. andruzzii being the only species described, apart from placental mammals, that lacks the highly evolutionary conserved photoreactivation function. We predict that in the DNA repair systems of P. andruzzii, we may be witnessing the first stages in a process that previously occurred in the ancestors of placental mammals during the Mesozoic era.
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Affiliation(s)
- Haiyu Zhao
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Giuseppe Di Mauro
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Sebastian Lungu-Mitea
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld, 69120 Heidelberg, Germany; Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Pietro Negrini
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Andrea Maria Guarino
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Biology, University of Naples "Federico II," 80126 Naples, Italy
| | - Elena Frigato
- Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Thomas Braunbeck
- Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Hongju Ma
- Botanical Institute, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Daniela Vallone
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Cristiano Bertolucci
- Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Nicholas S Foulkes
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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20
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Mutations in blind cavefish target the light-regulated circadian clock gene, period 2. Sci Rep 2018; 8:8754. [PMID: 29884790 PMCID: PMC5993827 DOI: 10.1038/s41598-018-27080-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/21/2018] [Indexed: 01/09/2023] Open
Abstract
Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.
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21
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Bourguignon T, Tang Q, Ho SYW, Juna F, Wang Z, Arab DA, Cameron SL, Walker J, Rentz D, Evans TA, Lo N. Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics. Mol Biol Evol 2018; 35:970-983. [DOI: 10.1093/molbev/msy013] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Thomas Bourguignon
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Frantisek Juna
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | | | - James Walker
- Department of Agriculture and Water Resources, Cairns, QLD, Australia
| | - David Rentz
- School of Marine and Tropical Biology, James Cook University, Townsville, QLD, Australia
| | - Theodore A Evans
- School of Animal Biology, University of Western Australia, Perth, WA, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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22
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Eberlein C, Nielly-Thibault L, Maaroufi H, Dubé AK, Leducq JB, Charron G, Landry CR. The Rapid Evolution of an Ohnolog Contributes to the Ecological Specialization of Incipient Yeast Species. Mol Biol Evol 2017; 34:2173-2186. [PMID: 28482005 DOI: 10.1093/molbev/msx153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Identifying the molecular changes that lead to ecological specialization during speciation is one of the major goals of molecular evolution. One question that remains to be thoroughly investigated is whether ecological specialization derives strictly from adaptive changes and their associated trade-offs, or from conditionally neutral mutations that accumulate under relaxed selection. We used whole-genome sequencing, genome annotation and computational analyses to identify genes that have rapidly diverged between two incipient species of Saccharomyces paradoxus that occupy different climatic regions along a south-west to north-east gradient. As candidate loci for ecological specialization, we identified genes that show signatures of adaptation and accelerated rates of amino acid substitutions, causing asymmetric evolution between lineages. This set of genes includes a glycyl-tRNA-synthetase, GRS2, which is known to be transcriptionally induced under heat stress in the model and sister species S. cerevisiae. Molecular modelling, expression analysis and fitness assays suggest that the accelerated evolution of this gene in the Northern lineage may be caused by relaxed selection. GRS2 arose during the whole-genome duplication (WGD) that occurred 100 million years ago in the yeast lineage. While its ohnolog GRS1 has been preserved in all post-WGD species, GRS2 has frequently been lost and is evolving rapidly, suggesting that the fate of this ohnolog is still to be resolved. Our results suggest that the asymmetric evolution of GRS2 between the two incipient S. paradoxus species contributes to their restricted climatic distributions and thus that ecological specialization derives at least partly from relaxed selection rather than a molecular trade-off resulting from adaptive evolution.
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Affiliation(s)
- Chris Eberlein
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
| | - Lou Nielly-Thibault
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada.,Big Data Research Center (CRDM), Université Laval, Québec, QC, Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
| | - Jean-Baptiste Leducq
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Guillaume Charron
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
| | - Christian R Landry
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada.,Big Data Research Center (CRDM), Université Laval, Québec, QC, Canada
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23
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Investigating gene flow between the blind cavefish Garra barreimiae and its conspecific surface populations. Sci Rep 2017; 7:5130. [PMID: 28698621 PMCID: PMC5506003 DOI: 10.1038/s41598-017-05194-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/25/2017] [Indexed: 11/08/2022] Open
Abstract
Cave-dwelling taxa often share the same phenotypic modifications like absence of eyes and pigmentation. These “troglomorphic characters” are expressed in the populations of Garra barreimiae from the Al Hoota Cave and nearby Hoti Pit in Northern Oman. Surface morphotypes of this cyprinid species are common throughout the distribution area. Very rarely individuals with intermediate phenotypes can be found. In the present study, potential gene flow between cave and surface populations was tested and population structure within five sampling sites was assessed. Overall, 213 individuals were genotyped at 18 microsatellite loci. We found that the cave populations have lower genetic diversity and are clearly isolated from the surface populations, which seem to be sporadically in contact with each other. The results indicate a recent genetic bottleneck in the cave populations. Thus, it can be assumed that during climatic changes the connection between cave and surface water bodies was disjoined, leaving a subpopulation trapped inside. Nevertheless, occasional gene flow between the morphotypes is detectable, but hybridisation seems only possible in cave habitat with permanent connection to surface water. Individuals from surface sites bearing intermediate phenotypes but cave genotypes imply that phenotypic plasticity might play a role in the development of the phenotype.
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24
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Raible F, Takekata H, Tessmar-Raible K. An Overview of Monthly Rhythms and Clocks. Front Neurol 2017; 8:189. [PMID: 28553258 PMCID: PMC5428424 DOI: 10.3389/fneur.2017.00189] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/20/2017] [Indexed: 12/18/2022] Open
Abstract
Organisms have evolved to cope with geophysical cycles of different period lengths. In this review, we focus on the adaptations of animals to the lunar cycle, specifically, on the occurrence of biological rhythms with monthly (circalunar) or semi-monthly (circasemilunar) period lengths. Systematic experimental investigation, starting in the early twentieth century, has allowed scientists to distinguish between mythological belief and scientific facts concerning the influence of the lunar cycle on animals. These studies revealed that marine animals of various taxa exhibit circalunar or circasemilunar reproductive rhythms. Some of these rely on endogenous oscillators (circalunar or circasemilunar clocks), whereas others are directly driven by external cues, such as the changes in nocturnal illuminance. We review current insight in the molecular and cellular mechanisms involved in circalunar rhythms, focusing on recent work in corals, annelid worms, midges, and fishes. In several of these model systems, the transcript levels of some core circadian clock genes are affected by both light and endogenous circalunar oscillations. How these and other molecular changes relate to the changes in physiology or behavior over the lunar cycle remains to be determined. We further review the possible relevance of circalunar rhythms for terrestrial species, with a particular focus on mammalian reproduction. Studies on circalunar rhythms of conception or birth rates extend to humans, where the lunar cycle was suggested to also affect sleep and mental health. While these reports remain controversial, factors like the increase in "light pollution" by artificial light might contribute to discrepancies between studies. We finally discuss the existence of circalunar oscillations in mammalian physiology. We speculate that these oscillations could be the remnant of ancient circalunar oscillators that were secondarily uncoupled from a natural entrainment mechanism, but still maintained relevance for structuring the timing of reproduction or physiology. The analysis and comparison of circalunar rhythms and clocks are currently challenging due to the heterogeneity of samples concerning species diversity, environmental conditions, and chronobiological conditions. We suggest that future research will benefit from the development of standardized experimental paradigms, and common principles for recording and reporting environmental conditions, especially light spectra and intensities.
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Affiliation(s)
- Florian Raible
- Max Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Hiroki Takekata
- Max Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna Biocenter, Vienna, Austria
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25
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Foulkes NS, Whitmore D, Vallone D, Bertolucci C. Studying the Evolution of the Vertebrate Circadian Clock: The Power of Fish as Comparative Models. ADVANCES IN GENETICS 2016; 95:1-30. [PMID: 27503352 DOI: 10.1016/bs.adgen.2016.05.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The utility of any model species cannot be judged solely in terms of the tools and approaches it provides for genetic analysis. A fundamental consideration is also how its biology has been shaped by the environment and the ecological niche which it occupies. By comparing different species occupying very different habitats we can learn how molecular and cellular mechanisms change during evolution in order to optimally adapt to their environment. Such knowledge is as important as understanding how these mechanisms work. This is illustrated by the use of fish models for studying the function and evolution of the circadian clock. In this review we outline our current understanding of how fish clocks sense and respond to light and explain how this differs fundamentally from the situation with mammalian clocks. In addition, we present results from comparative studies involving two species of blind cavefish, Astyanax mexicanus and Phreatichthys andruzzii. This work reveals the consequences of evolution in perpetual darkness for the circadian clock and its regulation by light as well as for other mechanisms such as DNA repair, sleep, and metabolism which directly or indirectly are affected by regular exposure to sunlight. Major differences in the cave habitats inhabited by these two cavefish species have a clear impact on shaping the molecular and cellular adaptations to life in complete darkness.
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Affiliation(s)
- N S Foulkes
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany; Centre for Organismal Studies, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | | | - D Vallone
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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