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Peña-Casanova J, Sánchez-Benavides G, Sigg-Alonso J. Updating functional brain units: Insights far beyond Luria. Cortex 2024; 174:19-69. [PMID: 38492440 DOI: 10.1016/j.cortex.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/15/2024] [Accepted: 02/15/2024] [Indexed: 03/18/2024]
Abstract
This paper reviews Luria's model of the three functional units of the brain. To meet this objective, several issues were reviewed: the theory of functional systems and the contributions of phylogenesis and embryogenesis to the brain's functional organization. This review revealed several facts. In the first place, the relationship/integration of basic homeostatic needs with complex forms of behavior. Secondly, the multi-scale hierarchical and distributed organization of the brain and interactions between cells and systems. Thirdly, the phylogenetic role of exaptation, especially in basal ganglia and cerebellum expansion. Finally, the tripartite embryogenetic organization of the brain: rhinic, limbic/paralimbic, and supralimbic zones. Obviously, these principles of brain organization are in contradiction with attempts to establish separate functional brain units. The proposed new model is made up of two large integrated complexes: a primordial-limbic complex (Luria's Unit I) and a telencephalic-cortical complex (Luria's Units II and III). As a result, five functional units were delineated: Unit I. Primordial or preferential (brainstem), for life-support, behavioral modulation, and waking regulation; Unit II. Limbic and paralimbic systems, for emotions and hedonic evaluation (danger and relevance detection and contribution to reward/motivational processing) and the creation of cognitive maps (contextual memory, navigation, and generativity [imagination]); Unit III. Telencephalic-cortical, for sensorimotor and cognitive processing (gnosis, praxis, language, calculation, etc.), semantic and episodic (contextual) memory processing, and multimodal conscious agency; Unit IV. Basal ganglia systems, for behavior selection and reinforcement (reward-oriented behavior); Unit V. Cerebellar systems, for the prediction/anticipation (orthometric supervision) of the outcome of an action. The proposed brain units are nothing more than abstractions within the brain's simultaneous and distributed physiological processes. As function transcends anatomy, the model necessarily involves transition and overlap between structures. Beyond the classic approaches, this review includes information on recent systemic perspectives on functional brain organization. The limitations of this review are discussed.
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Affiliation(s)
- Jordi Peña-Casanova
- Integrative Pharmacology and Systems Neuroscience Research Group, Neuroscience Program, Hospital del Mar Medical Research Institute, Barcelona, Spain; Department of Psychiatry and Legal Medicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Test Barcelona Services, Teià, Barcelona, Spain.
| | | | - Jorge Sigg-Alonso
- Department of Behavioral and Cognitive Neurobiology, Institute of Neurobiology, National Autonomous University of México (UNAM), Queretaro, Mexico
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Malta LGF, Koerich LB, D'Ávila Pessoa GC, Araujo RN, Sant'Anna MRV, Pereira MH, Gontijo NF. Clogmia albipunctata (Williston, 1893) midgut physiology: pH control and functional relationship with Lower Diptera (nematoceran) especially with hematophagous species. Comp Biochem Physiol A Mol Integr Physiol 2024; 290:111584. [PMID: 38224901 DOI: 10.1016/j.cbpa.2024.111584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
Clogmia albipunctata (Williston, 1893) is a non-hematophagous insect belonging to the order Diptera, suborder Nematocera (Lower Diptera) and family Psychodidae. In the present work, we investigated how C. albipunctata control their midgut pH under different physiological conditions, comparing their midgut physiology with some nematoceran hematophagous species. The C. albipunctata midgut pH was measured after ingestion of sugar, protein and under the effect of the alkalinizing hormone released in the hemolymph of the hematophagous sand fly Lutzomyia longipalpis obtained just after a blood meal. The midgut pH of unfed or sugar-fed C. albipunctata is 5.5-6, and its midgut underwent alkalinization after protein ingestion or under treatment with hemolymph collected from blood fed L. longipalpis. These results suggested that in nematocerans, mechanisms for pH control seem shared between hematophagous and non-hematophagous species. This kind of pH control is convenient for successful blood digestion. The independent evolution of many hematophagous groups from the Lower Diptera suggests that characteristics involved in midgut pH control were already present in non-hematophagous species and represent a readiness for adaptation to this feeding mode.
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Affiliation(s)
- Luccas Gabriel Ferreira Malta
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Leonardo Barbosa Koerich
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Grasielle Caldas D'Ávila Pessoa
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Ricardo N Araujo
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Mauricio Roberto Viana Sant'Anna
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Marcos H Pereira
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Nelder Figueiredo Gontijo
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Minas Gerais, Brazil.
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Young MW, Wilken AT, Manafzadeh AR, Schurr AF, Bastian A, Dickinson E, Granatosky MC. The dual function of prokinesis in the feeding and locomotor systems of parrots. J Exp Biol 2023; 226:jeb246659. [PMID: 37942661 PMCID: PMC10730085 DOI: 10.1242/jeb.246659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
Prokinesis, a mode of avian cranial kinesis involving motion between the neurocranium and upper beak, has long been investigated in biomechanical analyses of avian feeding and drinking. However, the modern avian beak is also used for non-feeding functions. Here, we investigate the dual function of prokinesis in the feeding and locomotor systems of the rosy-faced lovebird (Agapornis roseicollis). Lovebirds and other parrots utilize their beak both during feeding and as a third limb during vertical climbing. Thus, we experimentally measured both force-generating potential and movement of the rosy-faced lovebird mandible and maxilla (via prokinetic flexion of the craniofacial hinge) during tripedal climbing and mandibular/maxillary adduction. We found that whereas the maxilla is primarily responsible for generating force during locomotion, the mandible is primarily responsible for generating force during forceful jaw adduction, hinting at a remarkable capacity to alter prokinetic function with differing neuromuscular control. The ability of the prokinetic apparatus to perform functions with competing optimality criteria via modulation of motor control illustrates the functional plasticity of the avian cranial kinesis and sheds new light on the adaptive significance of cranial mobility.
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Affiliation(s)
- Melody W. Young
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY 11568, USA
| | - Alec T. Wilken
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Armita R. Manafzadeh
- Yale Institute for Biospheric Studies, Yale University, New Haven, CT 06520, USA
- Department of Earth & Planetary Sciences, Yale University, New Haven, CT 06520, USA
- Yale Peabody Museum of Natural History, New Haven, CT 06520, USA
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, CT 06520, USA
| | - Alissa F. Schurr
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY 11568, USA
| | - Aaron Bastian
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY 11568, USA
| | - Edwin Dickinson
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY 11568, USA
| | - Michael C. Granatosky
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY 11568, USA
- Center for Biomedical Innovation, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY 11568, USA
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Leca JB. Towards a three-level neo-Tinbergenian approach to object play: Structure, causes and consequences of a behavioral puzzle. Neurosci Biobehav Rev 2023; 152:105290. [PMID: 37348665 DOI: 10.1016/j.neubiorev.2023.105290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/11/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
My main goal in this paper is to propose a reformulation of foundational models in behavioral research, including Tinbergen's (1963) well-known four levels of analysis (namely, ontogenetic, mechanistic, functional, and evolutionary questions) and Mayr's (1961) dichotomy between proximate and ultimate causations. After critically evaluating these influential but problematic models, I present a three-level neo-Tinbergenian approach to behavior that considers the triadic integration of behavioral causes, structure, and consequences along a single temporal continuum. I then argue that object-directed play is a good candidate behavior to apply this new paradigm by presenting significant examples of the combined analysis of at least two of these three levels. Finally, I show how stone handling, a form of culturally-transmitted object play in macaques, is perfectly amenable to this unified three-level explanatory framework. My proposed approach fits recent theoretical and empirical advances in behavioral biology, has a heuristic value, and may provide numerous benefits to a range of behavioral scientists.
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Affiliation(s)
- Jean-Baptiste Leca
- Department of Psychology, University of Lethbridge, AB, Canada; School of Natural and Engineering Sciences National Institute of Advanced Studies, Bangalore, India.
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Rieseberg TP, Dadras A, Fürst-Jansen JMR, Dhabalia Ashok A, Darienko T, de Vries S, Irisarri I, de Vries J. Crossroads in the evolution of plant specialized metabolism. Semin Cell Dev Biol 2023; 134:37-58. [PMID: 35292191 DOI: 10.1016/j.semcdb.2022.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/17/2022] [Accepted: 03/04/2022] [Indexed: 12/25/2022]
Abstract
The monophyletic group of embryophytes (land plants) stands out among photosynthetic eukaryotes: they are the sole constituents of the macroscopic flora on land. In their entirety, embryophytes account for the majority of the biomass on land and constitute an astounding biodiversity. What allowed for the massive radiation of this particular lineage? One of the defining features of all land plants is the production of an array of specialized metabolites. The compounds that the specialized metabolic pathways of embryophytes produce have diverse functions, ranging from superabundant structural polymers and compounds that ward off abiotic and biotic challenges, to signaling molecules whose abundance is measured at the nanomolar scale. These specialized metabolites govern the growth, development, and physiology of land plants-including their response to the environment. Hence, specialized metabolites define the biology of land plants as we know it. And they were likely a foundation for their success. It is thus intriguing to find that the closest algal relatives of land plants, freshwater organisms from the grade of streptophyte algae, possess homologs for key enzymes of specialized metabolic pathways known from land plants. Indeed, some studies suggest that signature metabolites emerging from these pathways can be found in streptophyte algae. Here we synthesize the current understanding of which routes of the specialized metabolism of embryophytes can be traced to a time before plants had conquered land.
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Affiliation(s)
- Tim P Rieseberg
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Armin Dadras
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Janine M R Fürst-Jansen
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Amra Dhabalia Ashok
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtsr. 1, 37077 Goettingen, Germany.
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6
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Torday JS. Evolution, gravity, and the topology of consciousness. Prog Biophys Mol Biol 2022; 174:50-54. [PMID: 35830897 DOI: 10.1016/j.pbiomolbio.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
It has previously been hypothesized that consciousness is the aggregate of our evolutionary history, forged by ontogeny and phylogeny via cell-cell communications. In an on-going effort to identify the serial pre-adaptations that gave rise to consciousness, certain fundamental properties of the emerging cell are addressed herein. Evolution is topologic because it began as a phase transition caused by gravity attracting lipid molecules, spontaneously forming micelles submersed in the ocean that covered the primordial Earth, forming a surface boundary between the exterior Cosmos and the interior of micelles. Such protocells comply with the First Principles of Physiology-negative entropy, chemiosmosis and homeostasis-the first two principles being deterministic, the last being probabilistic, bestowing them with far more than just random chance. The mechanism of cellular evolution is based on exaptations of sequentially earlier and earlier genetic traits, working in reverse from present-day physiology all the way back to the unicellular state, which is homologous with mathematical 'knots'. Ironically, that relationship is evidence for the ontologic and epistemologic primacy of the cell, which supersedes mathematics and physics as manifestations of the Implicate Order since a conscious cell can conceive of a circle, but an unconscious circle is not able to conceive of a cell.
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Affiliation(s)
- John S Torday
- Department of Pediatrics, Obstetrics and Gynecology Evolutionary Medicine, 405 Hilgard Avenue University of California - Los Angeles, Los Angeles, CA, 90095, USA.
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James S, Liu Z, Stephens V, White GRT. Innovation in crisis: The role of 'exaptive relations' for medical device development in response to COVID-19. Technol Forecast Soc Change 2022; 182:121863. [PMID: 35855691 PMCID: PMC9276712 DOI: 10.1016/j.techfore.2022.121863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/14/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
The COVID-19 pandemic has resulted in huge disruption to the healthcare sector. In response to this, there have been collaborative efforts between many different public and private organizations to foster medical innovations. The effect of crisis upon innovation, particularly medical innovation, remains a debatable subject. In addition, the role of inter-personal relations is becoming more widely acknowledged as a critical feature of innovation. Drawing upon exaptation literature, the study aims to understand the nature of the micro-relations within medical innovations that are undertaken in response to COVID-19. The findings of this paper contribute to the limited literature that examines the performance of medical innovation in response to crisis. In addition to confirming the importance of exaptive pools, exaptive events, and exaptive forums in fostering serendipitous developments, the study makes a contribution to theory by identifying a further form of serendipitous encounter that is 'exaptive relations'.
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Affiliation(s)
- Steffan James
- South Wales Business School, University of South Wales, Llantwit Road, Pontypridd CF37 1DL, UK
| | - Zheng Liu
- Cardiff School of Management, Cardiff Metropolitan University, Western Ave, Cardiff CF5 2YB, UK
| | - Victoria Stephens
- South Wales Business School, University of South Wales, Llantwit Road, Pontypridd CF37 1DL, UK
| | - Gareth R T White
- Cranfield University, College Road, Cranfield, Bedford MK43 0AL, UK
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Frenkel-Pinter M, Petrov AS, Matange K, Travisano M, Glass JB, Williams LD. Adaptation and Exaptation: From Small Molecules to Feathers. J Mol Evol 2022; 90:166-175. [PMID: 35246710 PMCID: PMC8975760 DOI: 10.1007/s00239-022-10049-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
Evolution works by adaptation and exaptation. At an organismal level, exaptation and adaptation are seen in the formation of organelles and the advent of multicellularity. At the sub-organismal level, molecular systems such as proteins and RNAs readily undergo adaptation and exaptation. Here we suggest that the concepts of adaptation and exaptation are universal, synergistic, and recursive and apply to small molecules such as metabolites, cofactors, and the building blocks of extant polymers. For example, adenosine has been extensively adapted and exapted throughout biological evolution. Chemical variants of adenosine that are products of adaptation include 2' deoxyadenosine in DNA and a wide array of modified forms in mRNAs, tRNAs, rRNAs, and viral RNAs. Adenosine and its variants have been extensively exapted for various functions, including informational polymers (RNA, DNA), energy storage (ATP), metabolism (e.g., coenzyme A), and signaling (cyclic AMP). According to Gould, Vrba, and Darwin, exaptation imposes a general constraint on interpretation of history and origins; because of exaptation, extant function should not be used to explain evolutionary history. While this notion is accepted in evolutionary biology, it can also guide the study of the chemical origins of life. We propose that (i) evolutionary theory is broadly applicable from the dawn of life to the present time from molecules to organisms, (ii) exaptation and adaptation were important and simultaneous processes, and (iii) robust origin of life models can be constructed without conflating extant utility with historical basis of origins.
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Affiliation(s)
- Moran Frenkel-Pinter
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA.,Institute of Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Anton S Petrov
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Kavita Matange
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jennifer B Glass
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Loren Dean Williams
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA. .,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA. .,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA.
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Abstract
There is much evidence that the vertebrate lung originated from a progenitor structure which was present in bony fish. However, critical basic elements for the evolution of breathing in tetrapods, such as the central rhythm generator sensitive to CO2/pH and the pulmonary surfactant, were present in the lungless primitive vertebrate. This suggests that the evolution of air breathing in all vertebrates may have evolved through exaptations. It appears that the capability for proliferation of alveolar type 1 (AT1) cells is the "critical factor" which rendered possible the most radical subsequent innovation-the possibility of air breathing. "Epithelial remodeling," which consists in proliferation of alveolar cells-the structural basis for gas diffusion-observed in the alimentary tract of the gut-breathing fishes (GBF) has great potential for application in biomedical research. Such a process probably led to the gradual evolutionary development of lungs in terrestrial vertebrates. Research on the cellular and molecular mechanisms controlling proliferation of squamous epithelial cells in the GBF should contribute to explaining the regeneration-associated phenomena that occur in mammal lungs, and especially to the understanding of signal pathways which govern the process.
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Affiliation(s)
- Leszek Satora
- Department of Hydrobiology, Ichthyology and Biotechnology of Reproduction, West Pomeranian University of Technology in Szczecin, ul. Kazimierza Królewicza 4, 71-550, Szczecin, Poland.
| | - Tomasz Gawlikowski
- Department of Pharmacology, Clinical Pharmacology and Clinical Toxicology, Andrzej Frycz Modrzewski Krakow University, ul. G. Herlinga-Grudzińskiego 1, 30-705, Kraków, Poland
| | - Adam Tański
- Department of Hydrobiology, Ichthyology and Biotechnology of Reproduction, West Pomeranian University of Technology in Szczecin, ul. Kazimierza Królewicza 4, 71-550, Szczecin, Poland
| | - Krzysztof Formicki
- Department of Hydrobiology, Ichthyology and Biotechnology of Reproduction, West Pomeranian University of Technology in Szczecin, ul. Kazimierza Królewicza 4, 71-550, Szczecin, Poland
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Abstract
Local mate competition (LMC) favours female biased clutch sex ratios because it reduces competition between brothers and provides extra mating opportunities for sons. Fig wasps seem to fit LMC model assumptions and lay female-biased sex ratios as predicted. These female biased sex ratios increase fitness greatly. In line with predictions, their sex ratios become less female-biased as the number of mothers laying in the same fig increases. However, this variation results in comparatively small fitness benefits compared to just biased ratios and data suggest substantial mismatches with LMC theory. The mismatches are due to several factors. (1) Multiple foundresses typically lay too many daughters. (2) Single foundress sex ratios are explained by sequential oviposition and ladies-last models. (3) Mortality that typically exceeds 10% may decouple the link between primary sex ratios, the focus of model predictions, and secondary sex ratios of adult wasps that are counted by researchers. (4) Model assumptions are frequently violated: (a) clutch sizes are unequal, (b) oviposition may not be simultaneous (c) cryptic/multiple wasp species inhabit the same host, (d) foundress numbers are systematically undercounted, (e) inbreeding coefficient calculations are inaccurate, and (f) male wasps sometimes disperse. These data and calculations suggest that alternative explanations must be considered seriously. Substantial data show that wasps typically lay most of their male eggs first followed by mostly female eggs require a new approach. These "slope" strategies result in more accurate sex ratios that are automatically adjusted to foundress number, own and relative clutch sizes and to sequential clutches. This effect will alter sex ratios in all species once the egg capacity of a fig is crossed or when interference reduces clutch sizes. In addition to this passive response, the females of about half the studied species have a conditional response that reduces female bias under higher foundress numbers by laying more sons. Therefore, wasps seem to use a very simple strategy that increases their fitness. Natural selection could have optimized parameters of the slope strategy and possibly the existence of the slope strategy itself. Variation in the slope strategy that is the result of natural selection is adaptive. Research should therefore focus on quantifying variables of this slope strategy. Currently, it is unclear how much of the variation is adaptive as opposed to being coincidental by-products.
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Affiliation(s)
- Jaco M Greeff
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Finn Kjellberg
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
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11
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Brunet TDP, Doolittle WF, Bielawski JP. The role of purifying selection in the origin and maintenance of complex function. Stud Hist Philos Sci 2021; 87:125-135. [PMID: 34111815 DOI: 10.1016/j.shpsa.2021.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Fitness contribution alone should not be the criterion of 'function' in molecular biology and genomics. Disagreement over the use of 'function' in molecular biology and genomics is still with us, almost eight years after publicity surrounding the Encyclopedia of DNA Elements project claimed that 80.4% of the human genome comprises "functional elements". Recent approaches attempt to resolve or reformulate this debate by redefining genomic 'function' in terms of current fitness contribution. In its favour, this redefinition for the genomic context is in apparent conformity with predominant experimental practices, especially in biomedical research, and with ascription of function by selective maintenance. We argue against approaches of this kind, however, on the grounds that they could be seen as non-Darwinian, and fail to properly account for the diversity of non-adaptive processes involved in the origin and maintenance of genomic complexity. We examine cases of molecular and organismal complexity that arise neutrally, showing how purifying selection maintains non-adaptive genomic complexity. Rather than lumping different sorts of genomic complexity together by defining 'function' as fitness contribution, we argue that it is best to separate the heterogeneous contributions of preaptation, exaptation and adaptation to the historical processes of origin and maintenance for complex features.
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Affiliation(s)
- Tyler D P Brunet
- Department of the History and Philosophy of Science, University of Cambridge, United Kingdom.
| | - W Ford Doolittle
- Department of Biochemistry and Molecular Biology, Dalhousie University, Canada
| | - Joseph P Bielawski
- Departments of Biology and Mathematics and Statistics, Dalhousie University, Canada
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12
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Abstract
Transposable elements (TEs) are major components of all vertebrate genomes that can cause deleterious insertions and genomic instability. However, depending on the specific genomic context of their insertion site, TE sequences can sometimes get positively selected, leading to what are called "exaptation" events. TE sequence exaptation constitutes an important source of novelties for gene, genome and organism evolution, giving rise to new regulatory sequences, protein-coding exons/genes and non-coding RNAs, which can play various roles beneficial to the host. In this review, we focus on the development of vertebrates, which present many derived traits such as bones, adaptive immunity and a complex brain. We illustrate how TE-derived sequences have given rise to developmental innovations in vertebrates and how they thereby contributed to the evolutionary success of this lineage.
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Affiliation(s)
- Ema Etchegaray
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France.
| | - Magali Naville
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
| | - Zofia Haftek-Terreau
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
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13
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Abstract
Synaptic transmission is a fundamental neurobiological process by which neurons interact with each other and non-neuronal cells. It involves release of active substances from the presynaptic neuron onto receptive elements of postsynaptic cells, inducing waves of spreading electrochemical response. While much has been learned about the cellular and molecular mechanisms driving and governing transmitter release and sensing, the evolutionary origin of synaptic connections remains obscure. Herein, we review emerging evidence and concepts suggesting that key components of chemical synapse arose independently from neurons, in different functional and biological contexts, before the rise of multicellular living forms. We argue that throughout evolution, distinct synaptic constituents have been co-opted from ancestral forms for a new role in early metazoan, leading to the rise of chemical synapses and neurotransmission. Such a mosaic model of the origin of chemical synapses agrees with and supports the pluralistic hypothesis of evolutionary change.
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Affiliation(s)
- Saak V Ovsepian
- Institute for Biological and Medical Imaging, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany; International Centre for Neurotherapeutics, Dublin City University, Dublin, Ireland; Department of Experimental Neurobiology, National Institute of Mental Health, Klecany, Czech Republic; Department of Psychiatry and Medical Psychology, 3rd Faculty of Medicine of Charles University, Prague, Czech Republic.
| | - Valerie B O'Leary
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská, Czech Republic
| | - Nikolai P Vesselkin
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia; Faculty of Medicine, The State University of Saint Petersburg, St. Petersburg, Russia
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14
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Abstract
We propose that the two dominant culture institutions (individualist and collectivist) are neither learned nor cognitively represented by the people who practice them. Instead, they exist as group-level payoff structures that reflect differential distributions of child attachment patterns within a society. Individualist societies reflect an overrepresentation of insecure-avoidant attachments and collectivist societies reflect an overrepresentation of insecure-anxious attachments. Moreover, attachment patterns are embodied rather than representational-schedule-induced rather than incrementally shaped or verbally learned. If attachment patterns are schedule-induced, the prospects are poorer for effecting cultural change through economic incentives or informational campaigns (top-down). Rather, cultural practices will be responsive to changes in family practices-to the extent they affect attachment patterns (bottom-up). For example, if breastfeeding rates decline or the workforce participation of women increases, a society will become more individualist and less collectivist. That is because those practices increase avoidant as compared to anxious attachments. Moreover, because insecurely attached children are behaviorally less flexible than are securely attached children, the former have a greater impact on cultural practices than do the latter.
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Affiliation(s)
- Paul S. Strand
- Department of Psychology, Washington State University, Tri-Cities, 2710 Crimson Way, Richland, WA 99354 USA
| | - Jordan J. Vossen
- Department of Psychology, Washington State University, 322 Johnson Tower, Pullman, WA 99164 USA
| | - Erinn Savage
- Department of Psychology, Washington State University, 322 Johnson Tower, Pullman, WA 99164 USA
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15
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Forsberg L, Sigurdsson S, Launer LJ, Gudnason V, Ullén F. Structural covariability hubs in old age. Neuroimage 2019; 189:307-315. [PMID: 30669008 DOI: 10.1016/j.neuroimage.2019.01.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/14/2018] [Accepted: 01/12/2019] [Indexed: 02/07/2023] Open
Abstract
Studies have shown that inter-individual differences in grey matter, as measured by voxel-based morphometry, are coordinated between voxels. This has been done by studying covariance maps based on a limited number of seed regions. Here, we used GPU-based (Graphics Processing Unit) accelerated computing to calculate, for the first time, the aggregated map of the total structural topographical organisation in the brain on voxel level in a large sample of 960 healthy individuals in the age range 68-83 years. This map describes for each voxel the number of significant correlations with all other grey matter voxels in the brain. Voxels that correlate significantly with many other voxels are called hubs. A majority of these hubs were found in the basal ganglia, the thalamus, the brainstem, and the cerebellum; subcortical regions that have been preserved through vertebrate evolution, interact with large portions of the neocortex and play fundamental roles for the control of a wide range of behaviours. No significant difference in the level of covariability could be found with increasing age or between men and women in these hubs.
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Affiliation(s)
- Lars Forsberg
- The Icelandic Heart Association, IS-201, Kopavogur, Iceland; Department of Neuroscience, Karolinska Institutet, S-17177, Stockholm, Sweden.
| | | | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute of Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vilmundur Gudnason
- The Icelandic Heart Association, IS-201, Kopavogur, Iceland; The University of Iceland, IS-101, Reykjavik, Iceland
| | - Fredrik Ullén
- Department of Neuroscience, Karolinska Institutet, S-17177, Stockholm, Sweden
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16
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Conforti S, Dietrich J, Kuhn T, Koppenhagen NV, Baur J, Rohner PT, Blanckenhorn WU, Schäfer MA. Comparative effects of the parasiticide ivermectin on survival and reproduction of adult sepsid flies. Ecotoxicol Environ Saf 2018; 163:215-222. [PMID: 30055386 DOI: 10.1016/j.ecoenv.2018.07.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 07/06/2018] [Accepted: 07/08/2018] [Indexed: 06/08/2023]
Abstract
Ivermectin is a veterinary pharmaceutical widely applied against parasites of livestock. Being effective against pests, it is also known to have lethal and sublethal effects on non-target organisms. While considerable research demonstrates the impact of ivermectin residues in livestock dung on the development and survival of dung feeding insect larvae, surprisingly little is known about its fitness effects on adults. We tested the impact of ivermectin on the survival of adult sepsid dung fly species (Diptera: Sepsidae) in the laboratory, using an ecologically relevant and realistic range of 69-1978 µg ivermectin/kg wet dung, and compared the sensitivities of larvae and adults in a phylogenetic framework. For one representative, relatively insensitive species, Sepsis punctum, we further investigated effects of ivermectin on female fecundity and male fertility. Moreover, we tested whether females can differentiate between ivermectin-spiked and non-contaminated dung in the wild. Adult sepsid flies exposed to ivermectin suffered increased mortality, whereby closely related species varied strongly in their sensitivity. Adult susceptibility to the drug correlated with larval susceptibility, showing a phylogenetic signal and demonstrating systemic variation in ivermectin sensitivity. Exposure of S. punctum females to even low concentrations of ivermectin lowered the number of eggs laid, while treatment of males reduced egg-to-adult offspring survival, presumably via impairment of sperm quality or quantity. The fitness impact was amplified when both parents were exposed. Lastly, sepsid flies did not discriminate against ivermectin-spiked dung in the field. Treatment of livestock with avermectins may thus have even more far-reaching sublethal ecological consequences than currently assumed via effects on adult dung-feeding insects.
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Affiliation(s)
- Sheena Conforti
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Jana Dietrich
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Thierry Kuhn
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Nicola van Koppenhagen
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Julian Baur
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Patrick T Rohner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Wolf U Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Martin A Schäfer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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17
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Platt RN, Vandewege MW, Ray DA. Mammalian transposable elements and their impacts on genome evolution. Chromosome Res 2018; 26:25-43. [PMID: 29392473 PMCID: PMC5857283 DOI: 10.1007/s10577-017-9570-z] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/12/2017] [Accepted: 12/28/2017] [Indexed: 12/22/2022]
Abstract
Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate themselves in a genome. Mammalian genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. As a result, TEs have had significant impacts on mammalian evolution. Here we summarize the current understanding of TE content in mammal genomes and find that, with a few exceptions, most fall within a predictable range of observations. First, one third to one half of the genome is derived from TEs. Second, most mammalian genomes are dominated by LINE and SINE retrotransposons, more limited LTR retrotransposons, and minimal DNA transposon accumulation. Third, most mammal genome contains at least one family of actively accumulating retrotransposon. Finally, horizontal transfer of TEs among lineages is rare. TE exaptation events are being recognized with increasing frequency. Despite these beneficial aspects of TE content and activity, the majority of TE insertions are neutral or deleterious. To limit the deleterious effects of TE proliferation, the genome has evolved several defense mechanisms that act at the epigenetic, transcriptional, and post-transcriptional levels. The interaction between TEs and these defense mechanisms has led to an evolutionary arms race where TEs are suppressed, evolve to escape suppression, then are suppressed again as the defense mechanisms undergo compensatory change. The result is complex and constantly evolving interactions between TEs and host genomes.
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Affiliation(s)
- Roy N Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
| | | | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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18
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Schartl M, Schories S, Wakamatsu Y, Nagao Y, Hashimoto H, Bertin C, Mourot B, Schmidt C, Wilhelm D, Centanin L, Guiguen Y, Herpin A. Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements. BMC Biol 2018; 16:16. [PMID: 29378592 PMCID: PMC5789577 DOI: 10.1186/s12915-018-0485-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/11/2018] [Indexed: 12/21/2022] Open
Abstract
Background Sex determination relies on a hierarchically structured network of genes, and is one of the most plastic processes in evolution. The evolution of sex-determining genes within a network, by neo- or sub-functionalization, also requires the regulatory landscape to be rewired to accommodate these novel gene functions. We previously showed that in medaka fish, the regulatory landscape of the master male-determining gene dmrt1bY underwent a profound rearrangement, concomitantly with acquiring a dominant position within the sex-determining network. This rewiring was brought about by the exaptation of a transposable element (TE) called Izanagi, which is co-opted to act as a silencer to turn off the dmrt1bY gene after it performed its function in sex determination. Results We now show that a second TE, Rex1, has been incorporated into Izanagi. The insertion of Rex1 brought in a preformed regulatory element for the transcription factor Sox5, which here functions in establishing the temporal and cell-type-specific expression pattern of dmrt1bY. Mutant analysis demonstrates the importance of Sox5 in the gonadal development of medaka, and possibly in mice, in a dmrt1bY-independent manner. Moreover, Sox5 medaka mutants have complete female-to-male sex reversal. Conclusions Our work reveals an unexpected complexity in TE-mediated transcriptional rewiring, with the exaptation of a second TE into a network already rewired by a TE. We also show a dual role for Sox5 during sex determination: first, as an evolutionarily conserved regulator of germ-cell number in medaka, and second, by de novo regulation of dmrt1 transcriptional activity during primary sex determination due to exaptation of the Rex1 transposable element. Electronic supplementary material The online version of this article (10.1186/s12915-018-0485-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manfred Schartl
- Physiological Chemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Hospital, 97080, Würzburg, Germany.,Texas Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Susanne Schories
- Physiological Chemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Yuko Wakamatsu
- Physiological Chemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Yusuke Nagao
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Hisashi Hashimoto
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Chloé Bertin
- INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France
| | - Brigitte Mourot
- INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France
| | - Cornelia Schmidt
- Physiological Chemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Dagmar Wilhelm
- Department of Anatomy & Neuroscience, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Lazaro Centanin
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Yann Guiguen
- INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France
| | - Amaury Herpin
- Physiological Chemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany. .,INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France.
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19
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Pérez-Moreno JL, Balázs G, Wilkins B, Herczeg G, Bracken-Grissom HD. The role of isolation on contrasting phylogeographic patterns in two cave crustaceans. BMC Evol Biol 2017; 17:247. [PMID: 29216829 PMCID: PMC5721366 DOI: 10.1186/s12862-017-1094-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/24/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The underlying mechanisms and processes that prompt the colonisation of extreme environments, such as caves, constitute major research themes of evolutionary biology and biospeleology. The special adaptations required to survive in subterranean environments (low food availability, hypoxic waters, permanent darkness), and the geographical isolation of caves, nominate cave biodiversity as ideal subjects to answer long-standing questions concerning the interplay amongst adaptation, biogeography, and evolution. The present project aims to examine the phylogeographic patterns exhibited by two sympatric species of surface and cave-dwelling peracarid crustaceans (Asellus aquaticus and Niphargus hrabei), and in doing so elucidate the possible roles of isolation and exaptation in the colonisation and successful adaptation to the cave environment. RESULTS Specimens of both species were sampled from freshwater hypogean (cave) and epigean (surface) habitats in Hungary, and additional data from neighbouring countries were sourced from Genbank. Sequencing of mitochondrial and nuclear loci revealed, through haplotype network reconstruction (TCS) and phylogenetic inference, the genetic structure, phylogeographic patterns, and divergence-time estimates of A. aquaticus and N. hrabei surface and cave populations. Contrasting phylogeographic patterns were found between species, with A. aquaticus showing strong genetic differentiation between cave and surface populations and N. hrabei lacking any evidence of genetic structure mediated by the cave environment. Furthermore, N. hrabei populations show very low levels of genetic differentiation throughout their range, which suggests the possibility of recent expansion events over the last few thousand years. CONCLUSIONS Isolation by cave environment, rather than distance, is likely to drive the genetic structuring observed between immediately adjacent cave and surface populations of A. aquaticus, a predominantly surface species with only moderate exaptations to subterranean life. For N. hrabei, in which populations exhibit a fully 'cave-adapted' (troglomorphic) phenotype, the lack of genetic structure suggests that subterranean environments do not pose a dispersal barrier for this surface-cave species.
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Affiliation(s)
- Jorge L. Pérez-Moreno
- Department of Biological Sciences, Florida International University - Biscayne Bay Campus, 3000 NE 151 St., North Miami, FL 33181 USA
| | - Gergely Balázs
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, H-1117 Hungary
| | - Blake Wilkins
- Department of Biological Sciences, Florida International University - Biscayne Bay Campus, 3000 NE 151 St., North Miami, FL 33181 USA
| | - Gábor Herczeg
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, H-1117 Hungary
| | - Heather D. Bracken-Grissom
- Department of Biological Sciences, Florida International University - Biscayne Bay Campus, 3000 NE 151 St., North Miami, FL 33181 USA
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20
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Abstract
Cancer arises from a series of genetic and epigenetic changes, which result in abnormal expression or mutational activation of oncogenes, as well as suppression/inactivation of tumor suppressor genes. Aberrant expression of coding genes or long non-coding RNAs (lncRNAs) with oncogenic properties can be caused by translocations, gene amplifications, point mutations or other less characterized mechanisms. One such mechanism is the inappropriate usage of normally dormant, tissue-restricted or cryptic enhancers or promoters that serve to drive oncogenic gene expression. Dispersed across the human genome, endogenous retroviruses (ERVs) provide an enormous reservoir of autonomous gene regulatory modules, some of which have been co-opted by the host during evolution to play important roles in normal regulation of genes and gene networks. This review focuses on the “dark side” of such ERV regulatory capacity. Specifically, we discuss a growing number of examples of normally dormant or epigenetically repressed ERVs that have been harnessed to drive oncogenes in human cancer, a process we term onco-exaptation, and we propose potential mechanisms that may underlie this phenomenon.
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Affiliation(s)
- Artem Babaian
- Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada ; Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Dixie L Mager
- Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada ; Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
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21
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Hosseini SR, Wagner A. The potential for non-adaptive origins of evolutionary innovations in central carbon metabolism. BMC Syst Biol 2016; 10:97. [PMID: 27769243 PMCID: PMC5073748 DOI: 10.1186/s12918-016-0343-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/12/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Biological systems are rife with examples of pre-adaptations or exaptations. They range from the molecular scale - lens crystallins, which originated from metabolic enzymes - to the macroscopic scale, such as feathers used in flying, which originally served thermal insulation or waterproofing. An important class of exaptations are novel and useful traits with non-adaptive origins. Whether such origins could be frequent cannot be answered with individual examples, because it is a question about a biological system's potential for exaptation. We here take a step towards answering this question by analyzing central carbon metabolism, and novel traits that allow an organism to survive on novel sources of carbon and energy. We have previously applied flux balance analysis to this system and predicted the viability of 1015 metabolic genotypes on each of ten different carbon sources. RESULTS We here use this exhaustive genotype-phenotype map to ask whether a central carbon metabolism that is viable on a given, focal carbon source C - the equivalent of an adaptation in our framework - is usually or rarely viable on one or more other carbon sources C new - a potential exaptation. We show that most metabolic genotypes harbor potential exaptations, that is, they are viable on one or more carbon sources C new . The nature and number of these carbon sources depends on the focal carbon source C itself, and on the biochemical similarity between C and C new . Moreover, metabolisms that show a higher biomass yield on C, and that are more complex, i.e., they harbor more metabolic reactions, are viable on a greater number of carbon sources C new . CONCLUSIONS A high potential for exaptation results from correlations between the phenotypes of different genotypes, and such correlations are frequent in central carbon metabolism. If they are similarly abundant in other metabolic or biological systems, innovations may frequently have non-adaptive ("exaptive") origins.
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Affiliation(s)
- Sayed-Rzgar Hosseini
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Bldg. Y27, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.,The Swiss Institute of Bioinformatics, Bioinformatics, Quartier Sorge, Batiment Genopode, 1015, Lausanne, Switzerland
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Bldg. Y27, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland. .,The Swiss Institute of Bioinformatics, Bioinformatics, Quartier Sorge, Batiment Genopode, 1015, Lausanne, Switzerland. .,The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
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22
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Markopoulos G, Noutsopoulos D, Mantziou S, Gerogiannis D, Thrasyvoulou S, Vartholomatos G, Kolettas E, Tzavaras T. Genomic analysis of mouse VL30 retrotransposons. Mob DNA 2016; 7:10. [PMID: 27158269 PMCID: PMC4859993 DOI: 10.1186/s13100-016-0066-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/25/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Retrotransposons are mobile elements that have a high impact on shaping the mammalian genomes. Since the availability of whole genomes, genomic analyses have provided novel insights into retrotransposon biology. However, many retrotransposon families and their possible genomic impact have not yet been analysed. RESULTS Here, we analysed the structural features, the genomic distribution and the evolutionary history of mouse VL30 LTR-retrotransposons. In total, we identified 372 VL30 sequences categorized as 86 full-length and 49 truncated copies as well as 237 solo LTRs, with non-random chromosomal distribution. Full-length VL30s were highly conserved elements with intact retroviral replication signals, but with no protein-coding capacity. Analysis of LTRs revealed a high number of common transcription factor binding sites, possibly explaining the known inducible and tissue-specific expression of individual elements. The overwhelming majority of full-length and truncated elements (82/86 and 40/49, respectively) contained one or two specific motifs required for binding of the VL30 RNA to the poly-pyrimidine tract-binding protein-associated splicing factor (PSF). Phylogenetic analysis revealed three VL30 groups with the oldest emerging ~17.5 Myrs ago, while the other two were characterized mostly by new genomic integrations. Most VL30 sequences were found integrated either near, adjacent or inside transcription start sites, or into introns or at the 3' end of genes. In addition, a significant number of VL30s were found near Krueppel-associated box (KRAB) genes functioning as potent transcriptional repressors. CONCLUSION Collectively, our study provides data on VL30s related to their: (a) number and structural features involved in their transcription that play a role in steroidogenesis and oncogenesis; (b) evolutionary history and potential for retrotransposition; and (c) unique genomic distribution and impact on gene expression.
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Affiliation(s)
- Georgios Markopoulos
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece ; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (IMBB-FORTH), University Campus, Ioannina, 45110 Greece
| | - Dimitrios Noutsopoulos
- Laboratory of Molecular Biology and Genetics, Department of Biological Applications and Technology, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece
| | - Stefania Mantziou
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece
| | - Demetrios Gerogiannis
- Department of Computer Science, School of Sciences, University of Ioannina, Ioannina, 45110 Greece
| | - Soteroula Thrasyvoulou
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece
| | - Georgios Vartholomatos
- Hematology Laboratory, Unit of Molecular Biology, University Hospital of Ioannina, Ioannina, 45110 Greece
| | - Evangelos Kolettas
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece ; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (IMBB-FORTH), University Campus, Ioannina, 45110 Greece
| | - Theodore Tzavaras
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece
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23
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Naville M, Warren IA, Haftek-Terreau Z, Chalopin D, Brunet F, Levin P, Galiana D, Volff JN. Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates. Clin Microbiol Infect 2016; 22:312-323. [PMID: 26899828 DOI: 10.1016/j.cmi.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 12/24/2022]
Abstract
Viruses and transposable elements, once considered as purely junk and selfish sequences, have repeatedly been used as a source of novel protein-coding genes during the evolution of most eukaryotic lineages, a phenomenon called 'molecular domestication'. This is exemplified perfectly in mammals and other vertebrates, where many genes derived from long terminal repeat (LTR) retroelements (retroviruses and LTR retrotransposons) have been identified through comparative genomics and functional analyses. In particular, genes derived from gag structural protein and envelope (env) genes, as well as from the integrase-coding and protease-coding sequences, have been identified in humans and other vertebrates. Retroelement-derived genes are involved in many important biological processes including placenta formation, cognitive functions in the brain and immunity against retroelements, as well as in cell proliferation, apoptosis and cancer. These observations support an important role of retroelement-derived genes in the evolution and diversification of the vertebrate lineage.
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Affiliation(s)
- M Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - I A Warren
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - Z Haftek-Terreau
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - D Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France; Department of Genetics, University of Georgia, Athens, GA, USA
| | - F Brunet
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - P Levin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - D Galiana
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - J-N Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France.
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Hoffman M, Taylor BE, Harris MB. Evolution of lung breathing from a lungless primitive vertebrate. Respir Physiol Neurobiol 2015; 224:11-6. [PMID: 26476056 DOI: 10.1016/j.resp.2015.09.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 11/25/2022]
Abstract
Air breathing was critical to the terrestrial radiation and evolution of tetrapods and arose in fish. The vertebrate lung originated from a progenitor structure present in primitive boney fish. The origin of the neural substrates, which are sensitive to metabolically produced CO2 and which rhythmically activate respiratory muscles to match lung ventilation to metabolic demand, is enigmatic. We have found that a distinct periodic centrally generated rhythm, described as "cough" and occurring in lamprey in vivo and in vitro, is modulated by central sensitivity to CO2. This suggests that elements critical for the evolution of breathing in tetrapods, were present in the most basal vertebrate ancestors prior to the evolution of the lung. We propose that the evolution of breathing in all vertebrates occurred through exaptations derived from these critical basal elements.
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Affiliation(s)
- M Hoffman
- Department of Veterinary Medicine, University of Alaska Fairbanks, United States
| | - B E Taylor
- Institute of Arctic Biology, University of Alaska Fairbanks, United States; Department of Biology and Wildlife, University of Alaska Fairbanks, United States
| | - M B Harris
- Department of Veterinary Medicine, University of Alaska Fairbanks, United States; Institute of Arctic Biology, University of Alaska Fairbanks, United States; Department of Biology and Wildlife, University of Alaska Fairbanks, United States.
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25
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Caminiti R, Innocenti GM, Battaglia-Mayer A. Organization and evolution of parieto-frontal processing streams in macaque monkeys and humans. Neurosci Biobehav Rev 2015; 56:73-96. [PMID: 26112130 DOI: 10.1016/j.neubiorev.2015.06.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 05/08/2015] [Accepted: 06/09/2015] [Indexed: 01/01/2023]
Abstract
The functional organization of the parieto-frontal system is crucial for understanding cognitive-motor behavior and provides the basis for interpreting the consequences of parietal lesions in humans from a neurobiological perspective. The parieto-frontal connectivity defines some main information streams that, rather than being devoted to restricted functions, underlie a rich behavioral repertoire. Surprisingly, from macaque to humans, evolution has added only a few, new functional streams, increasing however their complexity and encoding power. In fact, the characterization of the conduction times of parietal and frontal areas to different target structures has recently opened a new window on cortical dynamics, suggesting that evolution has amplified the probability of dynamic interactions between the nodes of the network, thanks to communication patterns based on temporally-dispersed conduction delays. This might allow the representation of sensory-motor signals within multiple neural assemblies and reference frames, as to optimize sensory-motor remapping within an action space characterized by different and more complex demands across evolution.
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Affiliation(s)
- Roberto Caminiti
- Department of Physiology and Pharmacology, University of Rome SAPIENZA, P.le Aldo Moro 5, 00185 Rome, Italy.
| | - Giorgio M Innocenti
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden; Brain and Mind Institute, Federal Institute of Technology, EPFL, Lausanne, Switzerland
| | - Alexandra Battaglia-Mayer
- Department of Physiology and Pharmacology, University of Rome SAPIENZA, P.le Aldo Moro 5, 00185 Rome, Italy
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26
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Abstract
The phenomenon of preadaptation, or exaptation (wherein a trait that originally evolved to solve one problem is co-opted to solve a new problem) presents a formidable challenge to efforts to describe biological phenomena using a classical (Kolmogorovian) mathematical framework. We develop a quantum framework for exaptation with examples from both biological and cultural evolution. The state of a trait is written as a linear superposition of a set of basis states, or possible forms the trait could evolve into, in a complex Hilbert space. These basis states are represented by mutually orthogonal unit vectors, each weighted by an amplitude term. The choice of possible forms (basis states) depends on the adaptive function of interest (e.g., ability to metabolize lactose or thermoregulate), which plays the role of the observable. Observables are represented by self-adjoint operators on the Hilbert space. The possible forms (basis states) corresponding to this adaptive function (observable) are called eigenstates. The framework incorporates key features of exaptation: potentiality, contextuality, nonseparability, and emergence of new features. However, since it requires that one enumerate all possible contexts, its predictive value is limited, consistent with the assertion that there exists no biological equivalent to "laws of motion" by which we can predict the evolution of the biosphere.
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Affiliation(s)
- Liane Gabora
- Department of Psychology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, British Columbia V1V 1V7, Canada.
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Brożek J, Bourgoin T. Morphology and distribution of the external labial sensilla in Fulgoromorpha (Insecta: Hemiptera). ZOOMORPHOLOGY 2013; 132:33-65. [PMID: 23420415 PMCID: PMC3570763 DOI: 10.1007/s00435-012-0174-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 08/24/2012] [Accepted: 08/30/2012] [Indexed: 11/30/2022]
Abstract
The present paper describes the sensory structures on the apical segment of the labium in fifteen fulgoromorphan families (Hemiptera: Fulgoromorpha), using the scanning electron microscope. Thirteen morphologically distinct types of sensilla are identified: five types of multiporous sensilla, four types of uniporous sensilla and four types of nonporous sensilla. Three subapical sensory organ types are also recognized, formed from one to several sensilla, each characteristic of a family group. Sensilla chaetica (mechanoreceptive sensilla) fall into three categories dependent on length and are numerous and evenly distributed on the surface of the labium except where they occur on specialized sensory fields. The planthopper morphological ground plan is represented by two apical pair of sensory fields (dorsal and ventral) on which 11 dorsal pairs of sensilla (10 peg-like pairs + 1 specialized pair dome or cupola-like) and 2 ventral pairs of sensilla basiconica occur. Two main patterns (cixiid and issid) together with more specialized ones (derbid, lophopid, flatid and fulgorid) are reported. Disparity and diversity of the sensory structures are analyzed from a taxonomic and functional perspective. A gustatory function is provided for several chemoreceptive labial sensilla, as in the antennal flagellum sensilla in some other Hemiptera. This represents a more recently evolved function for the planthopper labium. Finally, further lines of study are suggested for future work on the phylogeny of the group based on the studied characters.
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Affiliation(s)
- Jolanta Brożek
- Department of Zoology, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
| | - Thierry Bourgoin
- Département Systématique and Evolution, Museum National d’Histoire Naturelle, UMR 7205, MNHN-CNRS, 45 rue Buffon, 75005 Paris, France
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