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Karvalics LZ, Bujtor L. Towards the Big History of information. Approaching the origins of information behaviour. Biosystems 2023; 232:104991. [PMID: 37544407 DOI: 10.1016/j.biosystems.2023.104991] [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: 05/16/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
A palaeontological analysis of the evolutionary steps of Metazoa is tracing back the appearance and first steps of information behaviour as far as the Proterozoic Eon. Either the neural cell or the nervous system or the eyesight did not trigger the appearance of the information behaviour, but it did a novel way of diet. Carnivorous diet appeared on Earth slightly before the information behaviour as a completely new way of feeding - and what is more important: the application of light into the behavioural complexes as a radically innovative survival supporting tool. A genetic toolkit was ready for Metazoa, and the combination of the neural system, eyesight and carnivorous diet initiated the information behaviour. We provide an answer for this simple question: why did the carnivorous diet result in the first disruptive innovation in information behaviour? The junction of Big History, palaeontology and information history provides many challenging new aspects for further research.
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Affiliation(s)
| | - László Bujtor
- Institute of Geography and Environmental Sciences, Eszterházy Károly Catholic University, H-3300, Eger, Leányka str. 6-8, Hungary.
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2
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Levin M. Technological Approach to Mind Everywhere: An Experimentally-Grounded Framework for Understanding Diverse Bodies and Minds. Front Syst Neurosci 2022; 16:768201. [PMID: 35401131 PMCID: PMC8988303 DOI: 10.3389/fnsys.2022.768201] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/24/2022] [Indexed: 12/11/2022] Open
Abstract
Synthetic biology and bioengineering provide the opportunity to create novel embodied cognitive systems (otherwise known as minds) in a very wide variety of chimeric architectures combining evolved and designed material and software. These advances are disrupting familiar concepts in the philosophy of mind, and require new ways of thinking about and comparing truly diverse intelligences, whose composition and origin are not like any of the available natural model species. In this Perspective, I introduce TAME-Technological Approach to Mind Everywhere-a framework for understanding and manipulating cognition in unconventional substrates. TAME formalizes a non-binary (continuous), empirically-based approach to strongly embodied agency. TAME provides a natural way to think about animal sentience as an instance of collective intelligence of cell groups, arising from dynamics that manifest in similar ways in numerous other substrates. When applied to regenerating/developmental systems, TAME suggests a perspective on morphogenesis as an example of basal cognition. The deep symmetry between problem-solving in anatomical, physiological, transcriptional, and 3D (traditional behavioral) spaces drives specific hypotheses by which cognitive capacities can increase during evolution. An important medium exploited by evolution for joining active subunits into greater agents is developmental bioelectricity, implemented by pre-neural use of ion channels and gap junctions to scale up cell-level feedback loops into anatomical homeostasis. This architecture of multi-scale competency of biological systems has important implications for plasticity of bodies and minds, greatly potentiating evolvability. Considering classical and recent data from the perspectives of computational science, evolutionary biology, and basal cognition, reveals a rich research program with many implications for cognitive science, evolutionary biology, regenerative medicine, and artificial intelligence.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, United States
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Cambridge, MA, United States
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3
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Neuropeptide repertoire and 3D anatomy of the ctenophore nervous system. Curr Biol 2021; 31:5274-5285.e6. [PMID: 34587474 DOI: 10.1016/j.cub.2021.09.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 07/20/2021] [Accepted: 09/02/2021] [Indexed: 11/24/2022]
Abstract
Ctenophores are gelatinous marine animals famous for locomotion by ciliary combs. Due to the uncertainties of the phylogenetic placement of ctenophores and the absence of some key bilaterian neuronal genes, it has been hypothesized that their neurons evolved independently. Additionally, recent whole-body, single-cell RNA sequencing (scRNA-seq) analysis failed to identify ctenophore neurons using any of the known neuronal molecular markers. To reveal the molecular machinery of ctenophore neurons, we have characterized the neuropeptide repertoire of the ctenophore Mnemiopsis leidyi. Using the machine learning NeuroPID tool, we predicted 129 new putative neuropeptide precursors. Sixteen of them were localized to the subepithelial nerve net (SNN), sensory aboral organ (AO), and epithelial sensory cells (ESCs), providing evidence that they are neuropeptide precursors. Four of these putative neuropeptides had a behavioral effect and increased the animals' swimming speed. Intriguingly, these putative neuropeptides finally allowed us to identify neuronal cell types in single-cell transcriptomic data and reveal the molecular identity of ctenophore neurons. High-resolution electron microscopy and 3D reconstructions of the nerve net underlying the comb plates confirmed a more than 100-year-old hypothesis of anastomoses between neurites of the same cell in ctenophores and revealed that they occur through a continuous membrane. Our work demonstrates the unique ultrastructure of the peptidergic nerve net and a rich neuropeptide repertoire of ctenophores, supporting the hypothesis that the first nervous system(s) evolved as nets of peptidergic cells.
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4
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Bennett MS. Five Breakthroughs: A First Approximation of Brain Evolution From Early Bilaterians to Humans. Front Neuroanat 2021; 15:693346. [PMID: 34489649 PMCID: PMC8418099 DOI: 10.3389/fnana.2021.693346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
Retracing the evolutionary steps by which human brains evolved can offer insights into the underlying mechanisms of human brain function as well as the phylogenetic origin of various features of human behavior. To this end, this article presents a model for interpreting the physical and behavioral modifications throughout major milestones in human brain evolution. This model introduces the concept of a "breakthrough" as a useful tool for interpreting suites of brain modifications and the various adaptive behaviors these modifications enabled. This offers a unique view into the ordered steps by which human brains evolved and suggests several unique hypotheses on the mechanisms of human brain function.
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5
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Vieira N, Rito T, Correia-Neves M, Sousa N. Sorting Out Sorting Nexins Functions in the Nervous System in Health and Disease. Mol Neurobiol 2021; 58:4070-4106. [PMID: 33931804 PMCID: PMC8280035 DOI: 10.1007/s12035-021-02388-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/05/2021] [Indexed: 12/18/2022]
Abstract
Endocytosis is a fundamental process that controls protein/lipid composition of the plasma membrane, thereby shaping cellular metabolism, sensing, adhesion, signaling, and nutrient uptake. Endocytosis is essential for the cell to adapt to its surrounding environment, and a tight regulation of the endocytic mechanisms is required to maintain cell function and survival. This is particularly significant in the central nervous system (CNS), where composition of neuronal cell surface is crucial for synaptic functioning. In fact, distinct pathologies of the CNS are tightly linked to abnormal endolysosomal function, and several genome wide association analysis (GWAS) and biochemical studies have identified intracellular trafficking regulators as genetic risk factors for such pathologies. The sorting nexins (SNXs) are a family of proteins involved in protein trafficking regulation and signaling. SNXs dysregulation occurs in patients with Alzheimer’s disease (AD), Down’s syndrome (DS), schizophrenia, ataxia and epilepsy, among others, establishing clear roles for this protein family in pathology. Interestingly, restoration of SNXs levels has been shown to trigger synaptic plasticity recovery in a DS mouse model. This review encompasses an historical and evolutionary overview of SNXs protein family, focusing on its organization, phyla conservation, and evolution throughout the development of the nervous system during speciation. We will also survey SNXs molecular interactions and highlight how defects on SNXs underlie distinct pathologies of the CNS. Ultimately, we discuss possible strategies of intervention, surveying how our knowledge about the fundamental processes regulated by SNXs can be applied to the identification of novel therapeutic avenues for SNXs-related disorders.
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Affiliation(s)
- Neide Vieira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal. .,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
| | - Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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6
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Abstract
The Ediacara Biota preserves the oldest fossil evidence of abundant, complex metazoans. Despite their significance, assigning individual taxa to specific phylogenetic groups has proved problematic. To better understand these forms, we identify developmentally controlled characters in representative taxa from the Ediacaran White Sea assemblage and compare them with the regulatory tools underlying similar traits in modern organisms. This analysis demonstrates that the genetic pathways for multicellularity, axial polarity, musculature, and a nervous system were likely present in some of these early animals. Equally meaningful is the absence of evidence for major differentiation of macroscopic body units, including distinct organs, localized sensory machinery or appendages. Together these traits help to better constrain the phylogenetic position of several key Ediacara taxa and inform our views of early metazoan evolution. An apparent lack of heads with concentrated sensory machinery or ventral nerve cords in such taxa supports the hypothesis that these evolved independently in disparate bilaterian clades.
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Affiliation(s)
- Scott D Evans
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| | - Mary L Droser
- Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
| | - Douglas H Erwin
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
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7
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Alves de Lima K, Rustenhoven J, Kipnis J. Meningeal Immunity and Its Function in Maintenance of the Central Nervous System in Health and Disease. Annu Rev Immunol 2020; 38:597-620. [DOI: 10.1146/annurev-immunol-102319-103410] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neuroimmunology, albeit a relatively established discipline, has recently sparked numerous exciting findings on microglia, the resident macrophages of the central nervous system (CNS). This review addresses meningeal immunity, a less-studied aspect of neuroimmune interactions. The meninges, a triple layer of membranes—the pia mater, arachnoid mater, and dura mater—surround the CNS, encompassing the cerebrospinal fluid produced by the choroid plexus epithelium. Unlike the adjacent brain parenchyma, the meninges contain a wide repertoire of immune cells. These constitute meningeal immunity, which is primarily concerned with immune surveillance of the CNS, and—according to recent evidence—also participates in postinjury CNS recovery, chronic neurodegenerative conditions, and even higher brain function. Meningeal immunity has recently come under the spotlight owing to the characterization of meningeal lymphatic vessels draining the CNS. Here, we review the current state of our understanding of meningeal immunity and its effects on healthy and diseased brains.
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Affiliation(s)
- Kalil Alves de Lima
- Center for Brain Immunology and Glia (BIG) and Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, Virginia 22908, USA;,
| | - Justin Rustenhoven
- Center for Brain Immunology and Glia (BIG) and Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, Virginia 22908, USA;,
| | - Jonathan Kipnis
- Center for Brain Immunology and Glia (BIG) and Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, Virginia 22908, USA;,
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8
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Fields C, Bischof J, Levin M. Morphological Coordination: A Common Ancestral Function Unifying Neural and Non-Neural Signaling. Physiology (Bethesda) 2020; 35:16-30. [DOI: 10.1152/physiol.00027.2019] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nervous systems are traditionally thought of as providing sensing and behavioral coordination functions at the level of the whole organism. What is the evolutionary origin of the mechanisms enabling the nervous systems’ information processing ability? Here, we review evidence from evolutionary, developmental, and regenerative biology suggesting a deeper, ancestral function of both pre-neural and neural cell-cell communication systems: the long-distance coordination of cell division and differentiation required to create and maintain body-axis symmetries. This conceptualization of the function of nervous system activity sheds new light on the evolutionary transition from the morphologically rudimentary, non-neural Porifera and Placazoa to the complex morphologies of Ctenophores, Cnidarians, and Bilaterians. It further allows a sharp formulation of the distinction between long-distance axis-symmetry coordination based on external coordinates, e.g., by whole-organism scale trophisms as employed by plants and sessile animals, and coordination based on body-centered coordinates as employed by motile animals. Thus we suggest that the systems that control animal behavior evolved from ancient mechanisms adapting preexisting ionic and neurotransmitter mechanisms to regulate individual cell behaviors during morphogenesis. An appreciation of the ancient, non-neural origins of bioelectrically mediated computation suggests new approaches to the study of embryological development, including embryological dysregulation, cancer, regenerative medicine, and synthetic bioengineering.
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Affiliation(s)
- Chris Fields
- 23 Rue des Lavandières, Caunes Minervois, France
| | - Johanna Bischof
- Allen Discovery Center at Tufts University, Medford, Massachusetts
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, Massachusetts
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9
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Martinez-Corral R, Liu J, Prindle A, Süel GM, Garcia-Ojalvo J. Metabolic basis of brain-like electrical signalling in bacterial communities. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180382. [PMID: 31006362 PMCID: PMC6553584 DOI: 10.1098/rstb.2018.0382] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2019] [Indexed: 12/20/2022] Open
Abstract
Information processing in the mammalian brain relies on a careful regulation of the membrane potential dynamics of its constituent neurons, which propagates across the neuronal tissue via electrical signalling. We recently reported the existence of electrical signalling in a much simpler organism, the bacterium Bacillus subtilis. In dense bacterial communities known as biofilms, nutrient-deprived B. subtilis cells in the interior of the colony use electrical communication to transmit stress signals to the periphery, which interfere with the growth of peripheral cells and reduce nutrient consumption, thereby relieving stress from the interior. Here, we explicitly address the interplay between metabolism and electrophysiology in bacterial biofilms, by introducing a spatially extended mathematical model that combines the metabolic and electrical components of the phenomenon in a discretized reaction-diffusion scheme. The model is experimentally validated by environmental and genetic perturbations, and confirms that metabolic stress is transmitted through the bacterial population via a potassium wave. Interestingly, this behaviour is reminiscent of cortical spreading depression in the brain, characterized by a wave of electrical activity mediated by potassium diffusion that has been linked to various neurological disorders, calling for future studies on the evolutionary link between the two phenomena. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.
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Affiliation(s)
- Rosa Martinez-Corral
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona 08003, Spain
| | - Jintao Liu
- Center for Infectious Diseases Research and Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, People's Republic of China
| | - Arthur Prindle
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Gürol M. Süel
- Division of Biological Sciences, San Diego Center for Systems Biology and Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona 08003, Spain
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10
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Spontaneous body contractions are modulated by the microbiome of Hydra. Sci Rep 2017; 7:15937. [PMID: 29162937 PMCID: PMC5698334 DOI: 10.1038/s41598-017-16191-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/08/2017] [Indexed: 02/08/2023] Open
Abstract
Spontaneous contractile activity, such as gut peristalsis, is ubiquitous in animals and is driven by pacemaker cells. In humans, disruption of the contraction pattern leads to gastrointestinal conditions, which are also associated with gut microbiota dysbiosis. Spontaneous contractile activity is also present in animals lacking gastrointestinal tract. Here we show that spontaneous body contractions in Hydra are modulated by symbiotic bacteria. Germ-free animals display strongly reduced and less regular contraction frequencies. These effects are partially restored by reconstituting the natural microbiota. Moreover, soluble molecule(s) produced by symbiotic bacteria may be involved in contraction frequency modulation. As the absence of bacteria does not impair the contractile ability itself, a microbial effect on the pacemakers seems plausible. Our findings indicate that the influence of bacteria on spontaneous contractile activity is present in the early-branching cnidarian hydra as well as in Bilateria, and thus suggest an evolutionary ancient origin of interaction between bacteria and metazoans, opening a window into investigating the roots of human motility disorders.
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11
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Abstract
The evolutionary origin of synapses and neurons is an enigmatic subject that inspires much debate. Non-bilaterian metazoans, both with and without neurons and their closest relatives already contain many components of the molecular toolkits for synapse functions. The origin of these components and their assembly into ancient synaptic signaling machineries are particularly important in light of recent findings on the phylogeny of non-bilaterian metazoans. The evolution of synapses and neurons are often discussed only from a metazoan perspective leaving a considerable gap in our understanding. By taking an integrative approach we highlight the need to consider different, but extremely relevant phyla and to include the closest unicellular relatives of metazoans, the ichthyosporeans, filastereans and choanoflagellates, to fully understand the evolutionary origin of synapses and neurons. This approach allows for a detailed understanding of when and how the first pre- and postsynaptic signaling machineries evolved.
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Affiliation(s)
- Pawel Burkhardt
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Simon G Sprecher
- Institute of Cell and Developmental Biology, Department of Biology, University of Fribourg, Fribourg, Switzerland
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12
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Abstract
A complex genetic repertoire underlies the apparently simple body plan of sponges. Among the genes present in poriferans are those fundamental to the sensory and nervous systems of other animals. Sponges are dynamic and sensitive animals and it is intuitive to link these genes to behaviour. The proposal that ctenophores are the earliest diverging metazoan has led to the question of whether sponges possess a 'pre-nervous' system or have undergone nervous system loss. Both lines of thought generally assume that the last common ancestor of sponges and eumetazoans possessed the genetic modules that underlie sensory abilities. By corollary extant sponges may possess a sensory cell homologous to one present in the last common ancestor, a hypothesis that has been studied by gene expression. We have performed a meta-analysis of all gene expression studies published to date to explore whether gene expression is indicative of a feature's sensory function. In sponges we find that eumetazoan sensory-neural markers are not particularly expressed in structures with known sensory functions. Instead it is common for these genes to be expressed in cells with no known or uncharacterized sensory function. Indeed, many sensory-neural markers so far studied are expressed during development, perhaps because many are transcription factors. This suggests that the genetic signal of a sponge sensory cell is dissimilar enough to be unrecognizable when compared to a bilaterian sensory or neural cell. It is possible that sensory-neural markers have as yet unknown functions in sponge cells, such as assembling an immunological synapse in the larval globular cell. Furthermore, the expression of sensory-neural markers in non-sensory cells, such as adult and larval epithelial cells, suggest that these cells may have uncharacterized sensory functions. While this does not rule out the co-option of ancestral sensory modules in later evolving groups, a distinct genetic foundation may underlie the sponge sensory system.
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Affiliation(s)
- Jasmine L Mah
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
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13
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van Duijn M. Phylogenetic origins of biological cognition: convergent patterns in the early evolution of learning. Interface Focus 2017; 7:20160158. [PMID: 28479986 PMCID: PMC5413897 DOI: 10.1098/rsfs.2016.0158] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Various forms of elementary learning have recently been discovered in organisms lacking a nervous system, such as protists, fungi and plants. This finding has fundamental implications for how we view the role of convergent evolution in biological cognition. In this article, I first review the evidence for basic forms of learning in aneural organisms, focusing particularly on habituation and classical conditioning and considering the plausibility for convergent evolution of these capacities. Next, I examine the possible role of convergent evolution regarding these basic learning abilities during the early evolution of nervous systems. The evolution of nervous systems set the stage for at least two major events relevant to convergent evolution that are central to biological cognition: (i) nervous systems evolved, perhaps more than once, because of strong selection pressures for sustaining sensorimotor strategies in increasingly larger multicellular organisms and (ii) associative learning was a subsequent adaptation that evolved multiple times within the neuralia. Although convergent evolution of basic forms of learning among distantly related organisms such as protists, plants and neuralia is highly plausible, more research is needed to verify whether these forms of learning within the neuralia arose through convergent or parallel evolution.
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Affiliation(s)
- Marc van Duijn
- Faculty of Arts, Culture and Cognition, Rijksuniversiteit Groningen, Oude Boteringestraat 34, Groningen, The Netherlands
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14
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Abstract
The study of evolutionary patterns of cognitive convergence would be greatly helped by a clear demarcation of cognition. Cognition is often used as an equivalent of mind, making it difficult to pin down empirically or to apply it confidently beyond the human condition. Recent developments in embodied cognition and philosophy of biology now suggest an interpretation that dissociates cognition from this mental context. Instead, it anchors cognition in a broad range of biological cases of intelligence, provisionally marked by a basic cognitive toolkit. This conception of cognition as an empirically based phenomenon provides a suitable and greatly expanded domain for studies of evolutionary convergence. This paper first introduces this wide, biologically embodied interpretation of cognition. Second, it discusses examples drawn from studies on bacteria, plants and fungi that all provide cases fulfilling the criteria for this wide interpretation. Third, the field of early nervous system evolution is used to illustrate how biologically embodied cognition raises new fundamental questions for research on animal cognition. Finally, an outline is given of the implications for the evolutionary convergence of cognition.
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Affiliation(s)
- Fred A Keijzer
- Department of Theoretical Philosophy, University of Groningen, Groningen, The Netherlands
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15
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An optimised phylogenetic method sheds more light on the main branching events of rhodopsin-like superfamily. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 20:85-94. [PMID: 27614546 DOI: 10.1016/j.cbd.2016.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 08/11/2016] [Accepted: 08/11/2016] [Indexed: 11/21/2022]
Abstract
The comparative genomics between different rhodopsin-like family groups (α, β, γ and δ) is not well studied. We used a combination of phylogenetic analysis and statistical genomic methods to compare rhodopsin-like family proteins in species likely symbolic of this family's evolutionary progression. For intra-cluster relationships, we applied mathematical optimisation to enhance the tree search produced by the neighbour joining method (NJ) and compared it with maximum likelihood (ML) method. To infer inter-clusters relationships, we used Needleman-Wunsch analysis (NW), HHsearch, ancestral sequence reconstruction and phylogenetic network analysis. Using this workflow, we were able to identify key evolutionary events in the rhodopsin-like family receptors. We found that α rhodopsin-like group gave rise to the β group, while the γ rhodopsin-like group diverged from the β group. We tracked the diversification of every cluster, revealing that fungal opsin is the most ancient member of the α group, while adenosine receptors could be the first member to diverge in the MECA (melanocortin, endothelial differentiation sphingolipid, cannabinoid, and adenosine receptors) subfamily and that histamine receptors could be the parent of the amines receptors, while hypocretin receptors might be the most ancient member of the β group. SOG (somatostatin, opioid, galanin) receptors formed the most ancient members of the γ group. Our analysis indicated that basal receptors might be playing a role in early evolution of the nervous system. This is evident in Trichoplax adhaerens genome, where we located histamine receptors and adenosine receptors.
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16
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Ryan JF, Chiodin M. Where is my mind? How sponges and placozoans may have lost neural cell types. Philos Trans R Soc Lond B Biol Sci 2015; 370:20150059. [PMID: 26554046 PMCID: PMC4650130 DOI: 10.1098/rstb.2015.0059] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2015] [Indexed: 01/01/2023] Open
Abstract
Recent phylogenomic evidence suggests that ctenophores may be the sister group to the rest of animals. This phylogenetic arrangement opens the possibility that sponges and placozoans could have lost neural cell types or that the ctenophore nervous system evolved independently. We critically review evidence to date that has been put forth in support of independent evolution of neural cell types in ctenophores. We observe a reluctance in the literature to consider a lost nervous system in sponges and placozoans and suggest that this may be due to historical bias and the commonly misconstrued concept of animal complexity. In support of the idea of loss (or modification beyond recognition), we provide hypothetical scenarios to show how sponges and placozoans may have benefitted from the loss and/or modification of their neural cell types.
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Affiliation(s)
- Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St Augustine, FL 32080, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Marta Chiodin
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St Augustine, FL 32080, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
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17
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Pisani D, Pett W, Dohrmann M, Feuda R, Rota-Stabelli O, Philippe H, Lartillot N, Wörheide G. Genomic data do not support comb jellies as the sister group to all other animals. Proc Natl Acad Sci U S A 2015; 112:15402-7. [PMID: 26621703 PMCID: PMC4687580 DOI: 10.1073/pnas.1518127112] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the "Ctenophora-sister" hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.
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Affiliation(s)
- Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom; School of Biological Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom;
| | - Walker Pett
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France
| | - Martin Dohrmann
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany
| | - Roberto Feuda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige 38010, Italy
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d'Ecologie Expérimentale du CNRS, Moulis 09200, France; Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montreal, QC, Canada H3C 3J7
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France
| | - Gert Wörheide
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany; Bayerische Staatssammlung für Paläontologie und Geologie, Munich 80333, Germany
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